Daily Papers

Low-resolution text images are often seen in natural scenes such as documents captured by mobile phones. Recognizing low-resolution text images is challenging because they lose detailed content information, leading to poor recognition accuracy. An intuitive solution is to introduce super-resolution (SR) techniques as pre-processing. However, previous single image super-resolution (SISR) methods are trained on synthetic low-resolution images (e.g.Bicubic down-sampling), which is simple and not suitable for real low-resolution text recognition. To this end, we pro-pose a real scene text SR dataset, termed TextZoom. It contains paired real low-resolution and high-resolution images which are captured by cameras with different focal length in the wild. It is more authentic and challenging than synthetic data, as shown in Fig. 1. We argue improv-ing the recognition accuracy is the ultimate goal for Scene Text SR. In this purpose, a new Text Super-Resolution Network termed TSRN, with three novel modules is developed. (1) A sequential residual block is proposed to extract the sequential information of the text images. (2) A boundary-aware loss is designed to sharpen the character boundaries. (3) A central alignment module is proposed to relieve the misalignment problem in TextZoom. Extensive experiments on TextZoom demonstrate that our TSRN largely improves the recognition accuracy by over 13%of CRNN, and by nearly 9.0% of ASTER and MORAN compared to synthetic SR data. Furthermore, our TSRN clearly outperforms 7 state-of-the-art SR methods in boosting the recognition accuracy of LR images in TextZoom. For example, it outperforms LapSRN by over 5% and 8%on the recognition accuracy of ASTER and CRNN. Our results suggest that low-resolution text recognition in the wild is far from being solved, thus more research effort is needed.

Post-training alignment is central to deploying large language models (LLMs), yet practical workflows remain split across backend-specific tools and ad-hoc glue code, making experiments hard to reproduce. We identify backend interference, reward fragmentation, and irreproducible pipelines as key obstacles in alignment research. We introduce AlignTune, a modular toolkit exposing a unified interface for supervised fine-tuning (SFT) and RLHF-style optimization with interchangeable TRL and Unsloth backends. AlignTune standardizes configuration, provides an extensible reward layer (rule-based and learned), and integrates evaluation over standard benchmarks and custom tasks. By isolating backend-specific logic behind a single factory boundary, AlignTune enables controlled comparisons and reproducible alignment experiments.

Motivation: Interpretability is not optional in biology: understanding gene regulation requires models whose learned structure can be directly interrogated, not merely accurate predictors whose internals resist mapping onto regulatory relationships. We ask whether an architecture mirroring the central dogma yields attention and gradient maps that recover known regulatory elements and networks in inspectable form. Results: Central Dogma Transformer II (CDT-II) mirrors the central dogma in its architecture -- DNA self-attention, RNA self-attention, and DNA-to-RNA cross-attention -- requiring only genomic embeddings and raw per-cell expression. On K562 CRISPR interference (CRISPRi) data with five genes held out entirely, CDT-II predicts perturbation effects (per-gene mean r = 0.84), recovers the GFI1B regulatory network (6.6-fold enrichment, P = 3.5 x 10^-17), and concentrates cross-attention on ENCODE regulatory elements including CTCF sites (mean 7.67x across 28 target genes, P < 0.001). Gradient attribution predicts consequences of perturbing therapeutic targets (mean r = 0.82). For TFRC, target of the anti-TfR1 antibody PPMX-T003, it identifies erythrocyte-structure, iron-dependent DNA-synthesis and oxidative-stress genes, matching anemia and ferroptosis reported clinically and preclinically -- without clinical data as input. CDT-II acts as an AI microscope, surfacing clinically relevant regulatory structure from perturbation experiments alone. Availability: Source code is available at https://github.com/nobusama/CDT2. Pre-computed embeddings, training data, and model weights are available at https://huggingface.co/datasets/nobusama17/CDT2-data.

Understanding cellular mechanisms requires integrating information across DNA, RNA, and protein - the three molecular systems linked by the Central Dogma of molecular biology. While domain-specific foundation models have achieved success for each modality individually, they remain isolated, limiting our ability to model integrated cellular processes. Here we present the Central Dogma Transformer (CDT), an architecture that integrates pre-trained language models for DNA, RNA, and protein following the directional logic of the Central Dogma. CDT employs directional cross-attention mechanisms - DNA-to-RNA attention models transcriptional regulation, while RNA-to-Protein attention models translational relationships - producing a unified Virtual Cell Embedding that integrates all three modalities. We validate CDT v1 - a proof-of-concept implementation using fixed (non-cell-specific) RNA and protein embeddings - on CRISPRi enhancer perturbation data from K562 cells, achieving a Pearson correlation of 0.503, representing 63% of the theoretical ceiling set by cross-experiment variability (r = 0.797). Attention and gradient analyses provide complementary interpretive windows: in detailed case studies, these approaches highlight largely distinct genomic regions, with gradient analysis identifying a CTCF binding site that Hi-C data showed as physically contacting both enhancer and target gene. These results suggest that AI architectures aligned with biological information flow can achieve both predictive accuracy and mechanistic interpretability.

Aligning large language models (LLMs) with human preferences is essential for their applications. Recently, decoding-time alignment has emerged as an effective plug-and-play technique that avoids fine-tuning model parameters. This approach retains the general utility of pretrained LLMs but often suffers from significant inefficiencies during decoding, primarily due to wasted token generation and excessive reward evaluations. To address these challenges, we introduce Cascade Reward Sampling (CARDS) to resolve both efficiency bottlenecks in decoding-time alignment. Specifically, we develop a segment-level rejection sampling algorithm that minimizes redundant computations of both LLMs and reward models (RMs). Central to CARDS is an uncertainty-based segmentation mechanism, which ensures the accuracy of RMs evaluations on incomplete segments. Furthermore, we provide a detailed analysis of reward scores on segments to elucidate the improved alignment performance. Experimental results demonstrate that CARDS significantly improves decoding efficiency, alignment quality, and general utility compared to existing decoding-time alignment methods, achieving approximately a 70% reduction in decoding time and over 90% win-ties in utility and safety benchmarks.

Alignment is the most critical step in building large language models (LLMs) that meet human needs. With the rapid development of LLMs gradually surpassing human capabilities, traditional alignment methods based on human-annotation are increasingly unable to meet the scalability demands. Therefore, there is an urgent need to explore new sources of automated alignment signals and technical approaches. In this paper, we systematically review the recently emerging methods of automated alignment, attempting to explore how to achieve effective, scalable, automated alignment once the capabilities of LLMs exceed those of humans. Specifically, we categorize existing automated alignment methods into 4 major categories based on the sources of alignment signals and discuss the current status and potential development of each category. Additionally, we explore the underlying mechanisms that enable automated alignment and discuss the essential factors that make automated alignment technologies feasible and effective from the fundamental role of alignment.

Ensuring the safe and reliable deployment of large language models (LLMs) remains a fundamental challenge. Existing safety alignment approaches either incur high computational cost or unintentionally disrupt the model's core knowledge, leading to degraded fluency and factual accuracy on benign tasks. This reveals a persistent trade-off between safety and utility. We propose DNAlign, a lightweight alignment framework that integrates control-theoretic optimization with null-space projection. By treating the LLM as a dynamic system, the proposed framework introduces controllable perturbations to steer generation toward safe behavior. A key component is the projection module, which restricts these perturbations to the harmful-related subspace derived from neutral hidden states, thereby preserving general knowledge and response quality. A value function trained on human preference data adaptively optimizes the control signals to align with human safety preferences. Extensive evaluations across multiple LLM backbones demonstrate that our framework consistently reduces harmful outputs while maintaining fluency, coherence, and factual utility. It achieves superior overall performance compared to prior alignment baselines without sacrificing generation diversity. These results indicate that the proposed framework provides an effective and practically deployable solution for safe LLM alignment. Code is available at https://anonymous.4open.science/r/DNAlign.

While large language models demonstrate remarkable capabilities at task-specific applications through fine-tuning, extending these benefits across diverse languages is essential for broad accessibility. However, effective cross-lingual transfer is hindered by LLM performance gaps across languages and the scarcity of fine-tuning data in many languages. Through analysis of LLM internal representations from over 1,000+ language pairs, we discover that middle layers exhibit the strongest potential for cross-lingual alignment. Building on this finding, we propose a middle-layer alignment objective integrated into task-specific training. Our experiments on slot filling, machine translation, and structured text generation show consistent improvements in cross-lingual transfer, especially to lower-resource languages. The method is robust to the choice of alignment languages and generalizes to languages unseen during alignment. Furthermore, we show that separately trained alignment modules can be merged with existing task-specific modules, improving cross-lingual capabilities without full re-training. Our code is publicly available (https://github.com/dannigt/mid-align).

AI alignment aims to make AI systems behave in line with human intentions and values. As AI systems grow more capable, so do risks from misalignment. To provide a comprehensive and up-to-date overview of the alignment field, in this survey, we delve into the core concepts, methodology, and practice of alignment. First, we identify four principles as the key objectives of AI alignment: Robustness, Interpretability, Controllability, and Ethicality (RICE). Guided by these four principles, we outline the landscape of current alignment research and decompose them into two key components: forward alignment and backward alignment. The former aims to make AI systems aligned via alignment training, while the latter aims to gain evidence about the systems' alignment and govern them appropriately to avoid exacerbating misalignment risks. On forward alignment, we discuss techniques for learning from feedback and learning under distribution shift. On backward alignment, we discuss assurance techniques and governance practices. We also release and continually update the website (www.alignmentsurvey.com) which features tutorials, collections of papers, blog posts, and other resources.

Large Language Models (LLMs) are expected to produce safe, helpful, and honest content during interaction with human users, but they frequently fail to align with such values when given flawed instructions, e.g., missing context, ambiguous directives, or inappropriate tone, leaving substantial room for improvement along multiple dimensions. A cost-effective yet high-impact way is to pre-align instructions before the model begins decoding. Existing approaches either rely on prohibitive test-time search costs or end-to-end model rewrite, which is powered by a customized training corpus with unclear objectives. In this work, we demonstrate that the goal of efficient and effective preference alignment can be achieved by P-Aligner, a lightweight module generating instructions that preserve the original intents while being expressed in a more human-preferred form. P-Aligner is trained on UltraPrompt, a new dataset synthesized via a proposed principle-guided pipeline using Monte-Carlo Tree Search, which systematically explores the space of candidate instructions that are closely tied to human preference. Experiments across different methods show that P-Aligner generally outperforms strong baselines across various models and benchmarks, including average win-rate gains of 28.35% and 8.69% on GPT-4-turbo and Gemma-2-SimPO, respectively. Further analyses validate its effectiveness and efficiency through multiple perspectives, including data quality, search strategies, iterative deployment, and time overhead.

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

Alignment has become a critical step for instruction-tuned Large Language Models (LLMs) to become helpful assistants. However, effective evaluation of alignment for emerging Chinese LLMs is still significantly lacking, calling for real-scenario grounded, open-ended, challenging and automatic evaluations tailored for alignment. To fill in this gap, we introduce AlignBench, a comprehensive multi-dimensional benchmark for evaluating LLMs' alignment in Chinese. Equipped with a human-in-the-loop data curation pipeline, our benchmark employs a rule-calibrated multi-dimensional LLM-as-Judge with Chain-of-Thought to generate explanations and final ratings as evaluations, ensuring high reliability and interpretability. Furthermore, we report AlignBench evaluated by CritiqueLLM, a dedicated Chinese evaluator LLM that recovers 95% of GPT-4's evaluation ability. We will provide public APIs for evaluating AlignBench with CritiqueLLM to facilitate the evaluation of LLMs' Chinese alignment. All evaluation codes, data, and LLM generations are available at https://github.com/THUDM/AlignBench.

AlphaFold 3 predicts protein structures with remarkable accuracy, yet how structural information emerges within the model remains poorly understood. Here, through causal interventions on internal representations and direct probing of every Pairformer block, we trace the formation of global protein geometry and identify the multiple sequence alignment (MSA) as a structural shortcut to the fold. Removing the MSA largely preserves local secondary structure while disrupting the long-range relationships that define global topology. Restoring the MSA-enriched pair representation at only forty residues recovers most of this lost organization, including at pairs never directly modified. This contribution depends on the detailed direction of the MSA module's output rather than its magnitude. The Pairformer rapidly converts this signal into global geometry: the final fold becomes recoverable by approximately block 9 of 48 for a majority of proteins, roughly twenty-seven blocks before the model's decoder can render it, whereas without the MSA it remains inaccessible for most proteins throughout the pass. Which homologs are supplied shapes this trajectory more strongly than which query is supplied; it persists for a designed query that never evolved but collapses for a shuffled sequence. Most importantly, an alignment built for a different protein that shares the fold, supplied only at the structurally corresponding columns, raises the median TM-score against experiment from 0.44 to 0.72, while the same alignment shifted a few residues along the chain performs worse than supplying no alignment at all. What AlphaFold 3 reads from an alignment is therefore a description of the fold itself, transferable between proteins that share one, rather than the query's own evolutionary history. This explains both its accuracy and the limits of what it has solved.

Efforts to align Large Language Models (LLMs) are mainly conducted via Reinforcement Learning from Human Feedback (RLHF) methods. However, RLHF encounters major challenges including training reward models, actor-critic engineering, and importantly, it requires access to LLM parameters. Here we introduce Aligner, a new efficient alignment paradigm that bypasses the whole RLHF process by learning the correctional residuals between the aligned and the unaligned answers. Our Aligner offers several key advantages. Firstly, it is an autoregressive seq2seq model that is trained on the query-answer-correction dataset via supervised learning; this offers a parameter-efficient alignment solution with minimal resources. Secondly, the Aligner facilitates weak-to-strong generalization; finetuning large pretrained models by Aligner's supervisory signals demonstrates strong performance boost. Thirdly, Aligner functions as a model-agnostic plug-and-play module, allowing for its direct application on different open-source and API-based models. Remarkably, Aligner-7B improves 11 different LLMs by 21.9% in helpfulness and 23.8% in harmlessness on average (GPT-4 by 17.5% and 26.9%). When finetuning (strong) Llama2-70B with (weak) Aligner-13B's supervision, we can improve Llama2 by 8.2% in helpfulness and 61.6% in harmlessness. See our dataset and code at https://aligner2024.github.io

We introduce Aligner, a novel Parameter-Efficient Fine-Tuning (PEFT) method for aligning multi-billion-parameter-sized Large Language Models (LLMs). Aligner employs a unique design that constructs a globally shared set of tunable tokens that modify the attention of every layer. Remarkably with this method, even when using one token accounting for a mere 5,000 parameters, Aligner can still perform comparably well to state-of-the-art LLM adaptation methods like LoRA that require millions of parameters. This capacity is substantiated in both instruction following and value alignment tasks. Besides the multiple order-of-magnitude improvement in parameter efficiency, the insight Aligner provides into the internal mechanisms of LLMs is also valuable. The architectural features and efficacy of our method, in addition to our experiments demonstrate that an LLM separates its internal handling of "form" and "knowledge" in a somewhat orthogonal manner. This finding promises to motivate new research into LLM mechanism understanding and value alignment.

Big models, exemplified by Large Language Models (LLMs), are models typically pre-trained on massive data and comprised of enormous parameters, which not only obtain significantly improved performance across diverse tasks but also present emergent capabilities absent in smaller models. However, the growing intertwining of big models with everyday human lives poses potential risks and might cause serious social harm. Therefore, many efforts have been made to align LLMs with humans to make them better follow user instructions and satisfy human preferences. Nevertheless, `what to align with' has not been fully discussed, and inappropriate alignment goals might even backfire. In this paper, we conduct a comprehensive survey of different alignment goals in existing work and trace their evolution paths to help identify the most essential goal. Particularly, we investigate related works from two perspectives: the definition of alignment goals and alignment evaluation. Our analysis encompasses three distinct levels of alignment goals and reveals a goal transformation from fundamental abilities to value orientation, indicating the potential of intrinsic human values as the alignment goal for enhanced LLMs. Based on such results, we further discuss the challenges of achieving such intrinsic value alignment and provide a collection of available resources for future research on the alignment of big models.

Aligning Large Language Models (LLMs) traditionally relies on costly training and human preference annotations. Self-alignment seeks to reduce these expenses by enabling models to align themselves. To further lower costs and achieve alignment without any expensive tuning or annotations, we introduce a new tuning-free approach for self-alignment, Dynamic Rewarding with Prompt Optimization (DRPO). Our approach leverages a search-based optimization framework that allows LLMs to iteratively self-improve and craft the optimal alignment instructions, all without additional training or human intervention. The core of DRPO is a dynamic rewarding mechanism, which identifies and rectifies model-specific alignment weaknesses, allowing LLMs to adapt efficiently to diverse alignment challenges. Empirical evaluations on eight recent LLMs, both open- and closed-sourced, demonstrate that DRPO significantly enhances alignment performance, with base models outperforming their SFT/RLHF-tuned counterparts. Moreover, the prompts automatically optimized by DRPO surpass those curated by human experts, further validating the effectiveness of our approach. Our findings highlight the great potential of current LLMs to achieve adaptive self-alignment through inference-time optimization, complementing tuning-based alignment methods.

We introduce Baichuan Alignment, a detailed analysis of the alignment techniques employed in the Baichuan series of models. This represents the industry's first comprehensive account of alignment methodologies, offering valuable insights for advancing AI research. We investigate the critical components that enhance model performance during the alignment process, including optimization methods, data strategies, capability enhancements, and evaluation processes. The process spans three key stages: Prompt Augmentation System (PAS), Supervised Fine-Tuning (SFT), and Preference Alignment. The problems encountered, the solutions applied, and the improvements made are thoroughly recorded. Through comparisons across well-established benchmarks, we highlight the technological advancements enabled by Baichuan Alignment. Baichuan-Instruct is an internal model, while Qwen2-Nova-72B and Llama3-PBM-Nova-70B are instruct versions of the Qwen2-72B and Llama-3-70B base models, optimized through Baichuan Alignment. Baichuan-Instruct demonstrates significant improvements in core capabilities, with user experience gains ranging from 17% to 28%, and performs exceptionally well on specialized benchmarks. In open-source benchmark evaluations, both Qwen2-Nova-72B and Llama3-PBM-Nova-70B consistently outperform their respective official instruct versions across nearly all datasets. This report aims to clarify the key technologies behind the alignment process, fostering a deeper understanding within the community. Llama3-PBM-Nova-70B model is available at https://huggingface.co/PKU-Baichuan-MLSystemLab/Llama3-PBM-Nova-70B.

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

Post-training alignment has increasingly become a crucial factor in enhancing the usability of language models (LMs). However, the strength of alignment varies depending on individual preferences. This paper proposes a method to incorporate alignment control into a single model, referred to as CLM. This approach adds one identity layer preceding the initial layers and performs preference learning only on this layer to map unaligned input token embeddings into the aligned space. Experimental results demonstrate that this efficient fine-tuning method performs comparable to full fine-tuning. During inference, the input embeddings are processed through the aligned and unaligned layers, which are then merged through the interpolation coefficient. By controlling this parameter, the alignment exhibits a clear interpolation and extrapolation phenomenon.

3D referring expression comprehension (3DREC) and segmentation (3DRES) have overlapping objectives, indicating their potential for collaboration. However, existing collaborative approaches predominantly depend on the results of one task to make predictions for the other, limiting effective collaboration. We argue that employing separate branches for 3DREC and 3DRES tasks enhances the model's capacity to learn specific information for each task, enabling them to acquire complementary knowledge. Thus, we propose the MCLN framework, which includes independent branches for 3DREC and 3DRES tasks. This enables dedicated exploration of each task and effective coordination between the branches. Furthermore, to facilitate mutual reinforcement between these branches, we introduce a Relative Superpoint Aggregation (RSA) module and an Adaptive Soft Alignment (ASA) module. These modules significantly contribute to the precise alignment of prediction results from the two branches, directing the module to allocate increased attention to key positions. Comprehensive experimental evaluation demonstrates that our proposed method achieves state-of-the-art performance on both the 3DREC and 3DRES tasks, with an increase of 2.05% in Acc@0.5 for 3DREC and 3.96% in mIoU for 3DRES.

The safe and effective deployment of Large Language Models (LLMs) involves a critical step called alignment, which ensures that the model's responses are in accordance with human preferences. Prevalent alignment techniques, such as DPO, PPO and their variants, align LLMs by changing the pre-trained model weights during a phase called post-training. While predominant, these post-training methods add substantial complexity before LLMs can be deployed. Inference-time alignment methods avoid the complex post-training step and instead bias the generation towards responses that are aligned with human preferences. The best-known inference-time alignment method, called Best-of-N, is as effective as the state-of-the-art post-training procedures. Unfortunately, Best-of-N requires vastly more resources at inference time than standard decoding strategies, which makes it computationally not viable. In this work, we introduce Speculative Rejection, a computationally-viable inference-time alignment algorithm. It generates high-scoring responses according to a given reward model, like Best-of-N does, while being between 16 to 32 times more computationally efficient.

Although instruction-tuned large language models (LLMs) have exhibited remarkable capabilities across various NLP tasks, their effectiveness on other data modalities beyond text has not been fully studied. In this work, we propose Macaw-LLM, a novel multi-modal LLM that seamlessly integrates visual, audio, and textual information. Macaw-LLM consists of three main components: a modality module for encoding multi-modal data, a cognitive module for harnessing pretrained LLMs, and an alignment module for harmonizing diverse representations. Our novel alignment module seamlessly bridges multi-modal features to textual features, simplifying the adaptation process from the modality modules to the cognitive module. In addition, we construct a large-scale multi-modal instruction dataset in terms of multi-turn dialogue, including 69K image instances and 50K video instances. We have made our data, code and model publicly available, which we hope can pave the way for future research in multi-modal LLMs and expand the capabilities of LLMs to handle diverse data modalities and address complex real-world scenarios.

Multimodal Large Language Models (MLLMs) are widely regarded as crucial in the exploration of Artificial General Intelligence (AGI). The core of MLLMs lies in their capability to achieve cross-modal alignment. To attain this goal, current MLLMs typically follow a two-phase training paradigm: the pre-training phase and the instruction-tuning phase. Despite their success, there are shortcomings in the modeling of alignment capabilities within these models. Firstly, during the pre-training phase, the model usually assumes that all image-text pairs are uniformly aligned, but in fact the degree of alignment between different image-text pairs is inconsistent. Secondly, the instructions currently used for finetuning incorporate a variety of tasks, different tasks's instructions usually require different levels of alignment capabilities, but previous MLLMs overlook these differentiated alignment needs. To tackle these issues, we propose a new multimodal large language model AlignGPT. In the pre-training stage, instead of treating all image-text pairs equally, we assign different levels of alignment capabilities to different image-text pairs. Then, in the instruction-tuning phase, we adaptively combine these different levels of alignment capabilities to meet the dynamic alignment needs of different instructions. Extensive experimental results show that our model achieves competitive performance on 12 benchmarks.

Text-to-image synthesis has progressed to the point where models can generate visually compelling images from natural language prompts. Yet, existing methods often fail to reconcile high-level semantic fidelity with explicit spatial control, particularly in scenes involving multiple objects, nuanced relations, or complex layouts. To bridge this gap, we propose a Hierarchical Cross-Modal Alignment (HCMA) framework for grounded text-to-image generation. HCMA integrates two alignment modules into each diffusion sampling step: a global module that continuously aligns latent representations with textual descriptions to ensure scene-level coherence, and a local module that employs bounding-box layouts to anchor objects at specified locations, enabling fine-grained spatial control. Extensive experiments on the MS-COCO 2014 validation set show that HCMA surpasses state-of-the-art baselines, achieving a 0.69 improvement in Frechet Inception Distance (FID) and a 0.0295 gain in CLIP Score. These results demonstrate HCMA's effectiveness in faithfully capturing intricate textual semantics while adhering to user-defined spatial constraints, offering a robust solution for semantically grounded image generation. Our code is available at https://github.com/hwang-cs-ime/HCMA.

Large Language Models (LLMs) need to be aligned with human expectations to ensure their safety and utility in most applications. Alignment is challenging, costly, and needs to be repeated for every LLM and alignment criterion. We propose to decouple LLMs and alignment by training aligner models that can be used to align any LLM for a given criteria on an as-needed basis, thus also reducing the potential negative impacts of alignment on performance. Our recipe for training the aligner models solely relies on synthetic data generated with a (prompted) LLM and can be easily adjusted for a variety of alignment criteria. We illustrate our method by training an "ethical" aligner and verify its efficacy empirically.

Aligning Large Language Models (LLMs) with human values and preferences is essential for making them helpful and safe. However, building efficient tools to perform alignment can be challenging, especially for the largest and most competent LLMs which often contain tens or hundreds of billions of parameters. We create NeMo-Aligner, a toolkit for model alignment that can efficiently scale to using hundreds of GPUs for training. NeMo-Aligner comes with highly optimized and scalable implementations for major paradigms of model alignment such as: Reinforcement Learning from Human Feedback (RLHF), Direct Preference Optimization (DPO), SteerLM, and Self-Play Fine-Tuning (SPIN). Additionally, our toolkit supports running most of the alignment techniques in a Parameter Efficient Fine-Tuning (PEFT) setting. NeMo-Aligner is designed for extensibility, allowing support for other alignment techniques with minimal effort. It is open-sourced with Apache 2.0 License and we invite community contributions at https://github.com/NVIDIA/NeMo-Aligner

Referring 3D Segmentation is a visual-language task that segments all points of the specified object from a 3D point cloud described by a sentence of query. Previous works perform a two-stage paradigm, first conducting language-agnostic instance segmentation then matching with given text query. However, the semantic concepts from text query and visual cues are separately interacted during the training, and both instance and semantic labels for each object are required, which is time consuming and human-labor intensive. To mitigate these issues, we propose a novel Referring 3D Segmentation pipeline, Label-Efficient and Single-Stage, dubbed LESS, which is only under the supervision of efficient binary mask. Specifically, we design a Point-Word Cross-Modal Alignment module for aligning the fine-grained features of points and textual embedding. Query Mask Predictor module and Query-Sentence Alignment module are introduced for coarse-grained alignment between masks and query. Furthermore, we propose an area regularization loss, which coarsely reduces irrelevant background predictions on a large scale. Besides, a point-to-point contrastive loss is proposed concentrating on distinguishing points with subtly similar features. Through extensive experiments, we achieve state-of-the-art performance on ScanRefer dataset by surpassing the previous methods about 3.7% mIoU using only binary labels. Code is available at https://github.com/mellody11/LESS.

The alignment of large language models is usually done by model providers to add or control behaviors that are common or universally understood across use cases and contexts. In contrast, in this article, we present an approach and architecture that empowers application developers to tune a model to their particular values, social norms, laws and other regulations, and orchestrate between potentially conflicting requirements in context. We lay out three main components of such an Alignment Studio architecture: Framers, Instructors, and Auditors that work in concert to control the behavior of a language model. We illustrate this approach with a running example of aligning a company's internal-facing enterprise chatbot to its business conduct guidelines.

High-quality instruction data is critical for aligning large language models (LLMs). Although some models, such as Llama-3-Instruct, have open weights, their alignment data remain private, which hinders the democratization of AI. High human labor costs and a limited, predefined scope for prompting prevent existing open-source data creation methods from scaling effectively, potentially limiting the diversity and quality of public alignment datasets. Is it possible to synthesize high-quality instruction data at scale by extracting it directly from an aligned LLM? We present a self-synthesis method for generating large-scale alignment data named Magpie. Our key observation is that aligned LLMs like Llama-3-Instruct can generate a user query when we input only the left-side templates up to the position reserved for user messages, thanks to their auto-regressive nature. We use this method to prompt Llama-3-Instruct and generate 4 million instructions along with their corresponding responses. We perform a comprehensive analysis of the extracted data and select 300K high-quality instances. To compare Magpie data with other public instruction datasets, we fine-tune Llama-3-8B-Base with each dataset and evaluate the performance of the fine-tuned models. Our results indicate that in some tasks, models fine-tuned with Magpie perform comparably to the official Llama-3-8B-Instruct, despite the latter being enhanced with 10 million data points through supervised fine-tuning (SFT) and subsequent feedback learning. We also show that using Magpie solely for SFT can surpass the performance of previous public datasets utilized for both SFT and preference optimization, such as direct preference optimization with UltraFeedback. This advantage is evident on alignment benchmarks such as AlpacaEval, ArenaHard, and WildBench.

As Large Language Models (LLMs) become increasingly integrated into real-world applications, ensuring their outputs align with human values and safety standards has become critical. The field has developed diverse alignment approaches including traditional fine-tuning methods (RLHF, instruction tuning), post-hoc correction systems, and inference-time interventions, each with distinct advantages and limitations. However, the lack of unified evaluation frameworks makes it difficult to systematically compare these paradigms and guide deployment decisions. This paper introduces a multi-dimensional evaluation of alignment techniques for LLMs, a comprehensive evaluation framework that provides a systematic comparison across all major alignment paradigms. Our framework assesses methods along four key dimensions: alignment detection, alignment quality, computational efficiency, and robustness. Through experiments across diverse base models and alignment strategies, we demonstrate the utility of our framework in identifying strengths and limitations of current state-of-the-art models, providing valuable insights for future research directions.

Recently, leveraging pre-trained Large Language Models (LLMs) for time series (TS) tasks has gained increasing attention, which involves activating and enhancing LLMs' capabilities. Many methods aim to activate LLMs' capabilities based on token-level alignment but overlook LLMs' inherent strength on natural language processing -- their deep understanding of linguistic logic and structure rather than superficial embedding processing. We propose Context-Alignment, a new paradigm that aligns TS with a linguistic component in the language environments familiar to LLMs to enable LLMs to contextualize and comprehend TS data, thereby activating their capabilities. Specifically, such context-level alignment comprises structural alignment and logical alignment, which is achieved by a Dual-Scale Context-Alignment GNNs (DSCA-GNNs) applied to TS-language multimodal inputs. Structural alignment utilizes dual-scale nodes to describe hierarchical structure in TS-language, enabling LLMs treat long TS data as a whole linguistic component while preserving intrinsic token features. Logical alignment uses directed edges to guide logical relationships, ensuring coherence in the contextual semantics. Demonstration examples prompt are employed to construct Demonstration Examples based Context-Alignment (DECA) following DSCA-GNNs framework. DECA can be flexibly and repeatedly integrated into various layers of pre-trained LLMs to improve awareness of logic and structure, thereby enhancing performance. Extensive experiments show the effectiveness of DECA and the importance of Context-Alignment across tasks, particularly in few-shot and zero-shot forecasting, confirming that Context-Alignment provide powerful prior knowledge on context.

The alignment tuning process of large language models (LLMs) typically involves instruction learning through supervised fine-tuning (SFT) and preference tuning via reinforcement learning from human feedback (RLHF). A recent study, LIMA (Zhou et al. 2023), shows that using merely 1K examples for SFT can achieve significant alignment performance as well, suggesting that the effect of alignment tuning might be "superficial." This raises questions about how exactly the alignment tuning transforms a base LLM. We analyze the effect of alignment tuning by examining the token distribution shift between base LLMs and their aligned counterpart. Our findings reveal that base LLMs and their alignment-tuned versions perform nearly identically in decoding on the majority of token positions. Most distribution shifts occur with stylistic tokens. These direct evidence strongly supports the Superficial Alignment Hypothesis suggested by LIMA. Based on these findings, we rethink the alignment of LLMs by posing the research question: how effectively can we align base LLMs without SFT or RLHF? To address this, we introduce a simple, tuning-free alignment method, URIAL. URIAL achieves effective alignment purely through in-context learning (ICL) with base LLMs, requiring as few as three constant stylistic examples and a system prompt. We conduct a fine-grained and interpretable evaluation on a diverse set of examples, named JUST-EVAL-INSTRUCT. Results demonstrate that base LLMs with URIAL can match or even surpass the performance of LLMs aligned with SFT or SFT+RLHF. We show that the gap between tuning-free and tuning-based alignment methods can be significantly reduced through strategic prompting and ICL. Our findings on the superficial nature of alignment tuning and results with URIAL suggest that deeper analysis and theoretical understanding of alignment is crucial to future LLM research.

The most common tools for word-alignment rely on a large amount of parallel sentences, which are then usually processed according to one of the IBM model algorithms. The training data is, however, the same as for machine translation (MT) systems, especially for neural MT (NMT), which itself is able to produce word-alignments using the trained attention heads. This is convenient because word-alignment is theoretically a viable byproduct of any attention-based NMT, which is also able to provide decoder scores for a translated sentence pair. We summarize different approaches on how word-alignment can be extracted from alignment scores and then explore ways in which scores can be extracted from NMT, focusing on inferring the word-alignment scores based on output sentence and token probabilities. We compare this to the extraction of alignment scores from attention. We conclude with aggregating all of the sources of alignment scores into a simple feed-forward network which achieves the best results when combined alignment extractors are used.

Aligning general-purpose large language models (LLMs) to downstream tasks often incurs significant training adjustment costs. Prior research has explored various avenues to enhance alignment efficiency, primarily through minimal-data training or data-driven activations to identify key attention heads. However, these approaches inherently introduce data dependency, which hinders generalization and reusability. To address this issue and enhance model alignment efficiency, we propose the \textbf{Attention Localization and Pruning Strategy (ALPS)}, an efficient algorithm that localizes the most task-sensitive attention heads and prunes by restricting attention training updates to these heads, thereby reducing alignment costs. Experimental results demonstrate that our method activates only 10\% of attention parameters during fine-tuning while achieving a 2\% performance improvement over baselines on three tasks. Moreover, the identified task-specific heads are transferable across datasets and mitigate knowledge forgetting. Our work and findings provide a novel perspective on efficient LLM alignment. The code is available at https://github.com/VoiceBeer/ALPS.

Recent work discovered Emergent Misalignment (EM): fine-tuning large language models on narrowly harmful datasets can lead them to become broadly misaligned. A survey of experts prior to publication revealed this was highly unexpected, demonstrating critical gaps in our understanding of model alignment. In this work, we both advance understanding and provide tools for future research. Using new narrowly misaligned datasets, we create a set of improved model organisms that achieve 99% coherence (vs. 67% prior), work with smaller 0.5B parameter models (vs. 32B), and that induce misalignment using a single rank-1 LoRA adapter. We demonstrate that EM occurs robustly across diverse model sizes, three model families, and numerous training protocols including full supervised fine-tuning. Leveraging these cleaner model organisms, we isolate a mechanistic phase transition and demonstrate that it corresponds to a robust behavioural phase transition in all studied organisms. Aligning large language models is critical for frontier AI safety, yet EM exposes how far we are from achieving this robustly. By distilling clean model organisms that isolate a minimal alignment-compromising change, and where this is learnt, we establish a foundation for future research into understanding and mitigating alignment risks in LLMs.

In the latest advancements in multimodal learning, effectively addressing the spatial and semantic losses of visual data after encoding remains a critical challenge. This is because the performance of large multimodal models is positively correlated with the coupling between visual encoders and large language models. Existing approaches often face issues such as vector gaps or semantic disparities, resulting in information loss during the propagation process. To address these issues, we propose MAGE (Multimodal Alignment and Generation Enhancement), a novel framework that bridges the semantic spaces of vision and text through an innovative alignment mechanism. By introducing the Intelligent Alignment Network (IAN), MAGE achieves dimensional and semantic alignment. To reduce the gap between synonymous heterogeneous data, we employ a training strategy that combines cross-entropy and mean squared error, significantly enhancing the alignment effect. Moreover, to enhance MAGE's "Any-to-Any" capability, we developed a fine-tuning dataset for multimodal tool-calling instructions to expand the model's output capability boundaries. Finally, our proposed multimodal large model architecture, MAGE, achieved significantly better performance compared to similar works across various evaluation benchmarks, including MME, MMBench, and SEED. Complete code and appendix are available at: https://github.com/GTCOM-NLP/MAGE.

Recent years have witnessed remarkable progress made in large language models (LLMs). Such advancements, while garnering significant attention, have concurrently elicited various concerns. The potential of these models is undeniably vast; however, they may yield texts that are imprecise, misleading, or even detrimental. Consequently, it becomes paramount to employ alignment techniques to ensure these models to exhibit behaviors consistent with human values. This survey endeavors to furnish an extensive exploration of alignment methodologies designed for LLMs, in conjunction with the extant capability research in this domain. Adopting the lens of AI alignment, we categorize the prevailing methods and emergent proposals for the alignment of LLMs into outer and inner alignment. We also probe into salient issues including the models' interpretability, and potential vulnerabilities to adversarial attacks. To assess LLM alignment, we present a wide variety of benchmarks and evaluation methodologies. After discussing the state of alignment research for LLMs, we finally cast a vision toward the future, contemplating the promising avenues of research that lie ahead. Our aspiration for this survey extends beyond merely spurring research interests in this realm. We also envision bridging the gap between the AI alignment research community and the researchers engrossed in the capability exploration of LLMs for both capable and safe LLMs.

Recent work has sought to understand the behavior of neural networks by comparing representations between layers and between different trained models. We examine methods for comparing neural network representations based on canonical correlation analysis (CCA). We show that CCA belongs to a family of statistics for measuring multivariate similarity, but that neither CCA nor any other statistic that is invariant to invertible linear transformation can measure meaningful similarities between representations of higher dimension than the number of data points. We introduce a similarity index that measures the relationship between representational similarity matrices and does not suffer from this limitation. This similarity index is equivalent to centered kernel alignment (CKA) and is also closely connected to CCA. Unlike CCA, CKA can reliably identify correspondences between representations in networks trained from different initializations.

Understanding protein dynamics is critical for elucidating their biological functions. The increasing availability of molecular dynamics (MD) data enables the training of deep generative models to efficiently explore the conformational space of proteins. However, existing approaches either fail to explicitly capture the temporal dependencies between conformations or do not support direct generation of time-independent samples. To address these limitations, we introduce ConfRover, an autoregressive model that simultaneously learns protein conformation and dynamics from MD trajectories, supporting both time-dependent and time-independent sampling. At the core of our model is a modular architecture comprising: (i) an encoding layer, adapted from protein folding models, that embeds protein-specific information and conformation at each time frame into a latent space; (ii) a temporal module, a sequence model that captures conformational dynamics across frames; and (iii) an SE(3) diffusion model as the structure decoder, generating conformations in continuous space. Experiments on ATLAS, a large-scale protein MD dataset of diverse structures, demonstrate the effectiveness of our model in learning conformational dynamics and supporting a wide range of downstream tasks. ConfRover is the first model to sample both protein conformations and trajectories within a single framework, offering a novel and flexible approach for learning from protein MD data.

Due to the remarkable capabilities and growing impact of large language models (LLMs), they have been deeply integrated into many aspects of society. Thus, ensuring their alignment with human values and intentions has emerged as a critical challenge. This survey provides a comprehensive overview of practical alignment techniques, training protocols, and empirical findings in LLM alignment. We analyze the development of alignment methods across diverse paradigms, characterizing the fundamental trade-offs between core alignment objectives. Our analysis shows that while supervised fine-tuning enables basic instruction-following, preference-based methods offer more flexibility for aligning with nuanced human intent. We discuss state-of-the-art techniques, including Direct Preference Optimization (DPO), Constitutional AI, brain-inspired methods, and alignment uncertainty quantification (AUQ), highlighting their approaches to balancing quality and efficiency. We review existing evaluation frameworks and benchmarking datasets, emphasizing limitations such as reward misspecification, distributional robustness, and scalable oversight. We summarize strategies adopted by leading AI labs to illustrate the current state of practice. We conclude by outlining open problems in oversight, value pluralism, robustness, and continuous alignment. This survey aims to inform both researchers and practitioners navigating the evolving landscape of LLM alignment.

The alignment problem in Large Language Models (LLMs) involves adapting them to the broad spectrum of human values. This requirement challenges existing alignment methods due to diversity of preferences and regulatory standards. This paper introduces a novel alignment paradigm, priority rule following, which defines rules as the primary control mechanism in each dialog, prioritizing them over user instructions. Our preliminary analysis reveals that even the advanced LLMs, such as GPT-4, exhibit shortcomings in understanding and prioritizing the rules. Therefore, we present PriorityDistill, a semi-automated approach for distilling priority following signals from LLM simulations to ensure robust rule integration and adherence. Our experiments show that this method not only effectively minimizes misalignments utilizing only one general rule but also adapts smoothly to various unseen rules, ensuring they are shielded from hijacking and that the model responds appropriately.

The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. Although modern biological pre-trained models have achieved great success in analyzing these macromolecules individually, their interconnected nature remains underexplored. This paper follows the guidance of the central dogma to redesign both the data and model pipeline and offers a comprehensive framework, Life-Code, that spans different biological functions. As for data flow, we propose a unified pipeline to integrate multi-omics data by reverse-transcribing RNA and reverse-translating amino acids into nucleotide-based sequences. As for the model, we design a codon tokenizer and a hybrid long-sequence architecture to encode the interactions between coding and non-coding regions through masked modeling pre-training. To model the translation and folding process with coding sequences, Life-Code learns protein structures of the corresponding amino acids by knowledge distillation from off-the-shelf protein language models. Such designs enable Life-Code to capture complex interactions within genetic sequences, providing a more comprehensive understanding of multi-omics with the central dogma. Extensive experiments show that Life-Code achieves state-of-the-art results on various tasks across three omics, highlighting its potential for advancing multi-omics analysis and interpretation.

Zero-shot Semantic Segmentation (ZSS) aims to segment both seen and unseen classes using supervision from only seen classes. Beyond adaptation-based methods, distillation-based approaches transfer vision-language alignment of vision-language model, e.g., CLIP, to segmentation models. However, such knowledge transfer remains challenging due to: (1) the difficulty of aligning vision-based features with the textual space, which requires combining spatial precision with vision-language alignment; and (2) the semantic gap between CLIP's global representations and the local, fine-grained features of segmentation models. To address challenge (1), we propose Chimera-Seg, which integrates a segmentation backbone as the body and a CLIP-based semantic head as the head, like the Chimera in Greek mythology, combining spatial precision with vision-language alignment. Specifically, Chimera-Seg comprises a trainable segmentation model and a CLIP Semantic Head (CSH), which maps dense features into the CLIP-aligned space. The CSH incorporates a frozen subnetwork and fixed projection layers from the CLIP visual encoder, along with lightweight trainable components. The partial module from CLIP visual encoder, paired with the segmentation model, retains segmentation capability while easing the mapping to CLIP's semantic space. To address challenge (2), we propose Selective Global Distillation (SGD), which distills knowledge from dense features exhibiting high similarity to the CLIP CLS token, while gradually reducing the number of features used for alignment as training progresses. Besides, we also use a Semantic Alignment Module (SAM) to further align dense visual features with semantic embeddings extracted from the frozen CLIP text encoder. Experiments on two benchmarks show improvements of 0.9% and 1.2% in hIoU.

This research paper addresses the challenge of modality mismatch in multimodal learning, where the modalities available during inference differ from those available at training. We propose the Text-centric Alignment for Multi-Modality Learning (TAMML) approach, an innovative method that utilizes Large Language Models (LLMs) with in-context learning and foundation models to enhance the generalizability of multimodal systems under these conditions. By leveraging the unique properties of text as a unified semantic space, TAMML demonstrates significant improvements in handling unseen, diverse, and unpredictable modality combinations. TAMML not only adapts to varying modalities but also maintains robust performance, showcasing the potential of foundation models in overcoming the limitations of traditional fixed-modality frameworks in embedding representations. This study contributes to the field by offering a flexible, effective solution for real-world applications where modality availability is dynamic and uncertain.

Large Language Models (LLMs) exhibit impressive capabilities but also present risks such as biased content generation and privacy issues. One of the current alignment techniques includes principle-driven integration, but it faces challenges arising from the imprecision of manually crafted rules and inadequate risk perception in models without safety training. To address these, we introduce Guide-Align, a two-stage approach. Initially, a safety-trained model identifies potential risks and formulates specific guidelines for various inputs, establishing a comprehensive library of guidelines and a model for input-guidelines retrieval. Subsequently, the retrieval model correlates new inputs with relevant guidelines, which guide LLMs in response generation to ensure safe and high-quality outputs, thereby aligning with human values. An additional optional stage involves fine-tuning a model with well-aligned datasets generated through the process implemented in the second stage. Our method customizes guidelines to accommodate diverse inputs, thereby enhancing the fine-grainedness and comprehensiveness of the guideline library. Furthermore, it incorporates safety expertise from a safety-trained LLM through a lightweight retrieval model. We evaluate our approach on three benchmarks, demonstrating significant improvements in LLM security and quality. Notably, our fine-tuned model, Labrador, even at 13 billion parameters, outperforms GPT-3.5-turbo and surpasses GPT-4 in alignment capabilities.

The constitutional framework of alignment aims to align large language models (LLMs) with value-laden principles written in natural language (such as to avoid using biased language). Prior work has focused on parameter fine-tuning techniques, such as reinforcement learning from human feedback (RLHF), to instill these principles. However, these approaches are computationally demanding, require careful engineering and tuning, and often require difficult-to-obtain human annotation data. We propose reflect, an inference-time framework for constitutional alignment that does not require any training or data, providing a plug-and-play approach for aligning an instruction-tuned model to a set of principles. reflect operates entirely in-context, combining a (i) constitution-conditioned base response with post-generation (ii) self-evaluation, (iii)(a) self-critique, and (iii)(b) final revision. reflect's technique of explicit in-context reasoning over principles during post-generation outperforms standard few-shot prompting and provides transparent reasoning traces. Our results demonstrate that reflect significantly improves LLM conformance to diverse and complex principles, including principles quite distinct from those emphasized in the model's original parameter fine-tuning, without sacrificing factual reasoning. reflect is particularly effective at reducing the rate of rare but significant violations of principles, thereby improving safety and robustness in the tail end of the distribution of generations. Finally, we show that reflect naturally generates useful training data for traditional parameter fine-tuning techniques, allowing for efficient scaling and the reduction of inference-time computational overhead in long-term deployment scenarios.

In-Image Machine Translation (IIMT) aims to translate scene text in an image and render the translated text back into the original regions while preserving the overall visual appearance. Recent unified multimodal models provide a promising solution by combining visual-text understanding and image generation within a single framework. However, directly adapting such models to IIMT remains challenging. In particular, they often suffer from understanding-generation conflicts, where the translation inferred during understanding is inconsistent with the text supervision used in generation, and spatial position misalignment, where the rendered text does not accurately match the target text regions. To address these issues, we present UniTranslator, a unified multimodal framework for IIMT that tightly couples translation understanding and text editing. Specifically, we introduce an Understand-Generation Alignment Module (UGAM) to bridge the representation gap between understanding and generation, encouraging semantic consistency between translated content prediction and text rendering. We further propose a Spatial Mask Decoder (SMD) with pixel-level supervision over text regions to improve spatial grounding, geometric alignment, and layout controllability during generation. Extensive experiments on multiple benchmarks demonstrate that UniTranslator achieves state-of-the-art performance across diverse language directions and complex real-world layouts. Moreover, our results reveal a strong mutual reinforcement effect between translation understanding and image generation, highlighting the advantage of unified translation multimodal learning. Code is available at https://github.com/SeerRay-Lab/Unitranslator.

Large language models remain vulnerable to jailbreaks that elicit harmful responses, yet the mechanism behind harmful response generation is poorly understood. Here, we investigate how this capability is organized within model parameters. We identify and prune parameters that specifically support harmful compliance, providing a direct mechanistic analysis at the parameter level. We find that this capability depends on a sparse set of critical parameters: pruning these parameters substantially reduces harmful compliance while causing only limited degradation in benign capabilities, suggesting that key components of harmful generation are separable from those of general utility. Parameters identified from one harm category also reduce harmful responses in others, indicating components shared across harm types. This separability appears primarily in aligned models, suggesting that alignment training internally reshapes the harmful response mechanism even when behavioral safeguards remain brittle. We further show that harmful response generation is dissociable from the ability to recognize and reason about harmfulness. Finally, we extend our analysis to emergent misalignment and identify a sparse set of parameters contributing to it, with substantial sharing across fine-tuning domains. Together, these results reveal a consistent parameter-level organization underlying unsafe behaviors and point toward more principled interventions for improving model safety.

Multilingual language models can solve the same mathematical problem in different languages, but it remains unclear whether they rely on shared features or on language-specific computations that only produce similar outputs. We study this question in five models from four families using the Multilingual Grade School Math (MGSM) dataset, with problems solved in English, German, French, Spanish, Russian, and Chinese, retaining problems with valid reasoning traces in all six languages and replaying those traces through the model to record representations at multiple layers. For each model, we first use Centered Kernel Alignment (CKA) to identify layers with cross-language alignment. At each selected layer, we train two sparse autoencoders (SAE): a baseline reconstruction-only model and a contrastive variant introduced in this work, the Geometry-Invariant SAE (GI-SAE). GI-SAE supplements the reconstruction loss with an Information Noise-Contrastive Estimation (InfoNCE) loss that trains the encoder to produce similar activations for traces of the same problem, regardless of language or token position. We then test whether the resulting shared features are functionally interchangeable by swapping their values between languages during the model's forward pass and measuring the resulting change in output, quantified by Kullback-Leibler (KL) divergence per feature. Although GI-SAE yields higher CKA and Jaccard similarity at nearly every layer, higher geometric similarity does not consistently imply greater functional interchangeability. We find that cross-language feature sharing is model- and architecture-dependent in this sample and appears at different depths in different models. GI-SAE primarily amplifies cross-language structure already present: the pattern is model-specific, with strengthening in Qwen, no functional benefit in Gemma, and mixed layer-dependent effects in Llama and Phi.

The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the free flow of genomic information between RNA sequences and structures. In this study, we introduce OmniGenome, an RNA FM trained to align RNA sequences with respect to secondary structures based on structure-contextualised modelling. The alignment enables free and bidirectional mappings between sequences and structures by utilising the flexible RNA modelling paradigm that supports versatile input and output modalities, i.e., sequence and/or structure as input/output. We implement RNA design and zero-shot secondary structure prediction as case studies to evaluate the Seq2Str and Str2Seq mapping capacity of OmniGenome. Results on the EternaV2 benchmark show that OmniGenome solved 74% of puzzles, whereas existing FMs only solved up to 3% of the puzzles due to the oversight of sequence-structure alignment. We leverage four comprehensive in-silico genome modelling benchmarks to evaluate performance across a diverse set of genome downstream tasks, where the results show that OmniGenome achieves state-of-the-art performance on RNA and DNA benchmarks, even without any training on DNA genomes.

Aligning large language models (LLMs) with human values is a vital task for LLM practitioners. Current alignment techniques have several limitations: (1) requiring a large amount of annotated data; (2) demanding heavy human involvement; (3) lacking a systematic mechanism to continuously improve. In this work, we study aligning LLMs to a new domain with limited samples (e.g. < 100). We propose an algorithm that can self-align LLMs iteratively without active human involvement. Unlike existing works, our algorithm relies on neither human-crafted instructions nor labeled rewards, significantly reducing human involvement. In addition, our algorithm can self-improve the alignment continuously. The key idea is to first retrieve high-quality samples related to the target domain and use them as In-context Learning examples to generate more samples. Then we use the self-generated samples to finetune the LLM iteratively. We show that our method can unlock the LLMs' self-generalization ability to perform alignment with near-zero human supervision. We test our algorithm on three benchmarks in safety, truthfulness, and instruction-following, and show good performance in alignment, domain adaptability, and scalability.

Alignment is a standard procedure to fine-tune pre-trained large language models (LLMs) to follow natural language instructions and serve as helpful AI assistants. We have observed, however, that the conventional alignment process fails to enhance the factual accuracy of LLMs, and often leads to the generation of more false facts (i.e. hallucination). In this paper, we study how to make the LLM alignment process more factual, by first identifying factors that lead to hallucination in both alignment steps:\ supervised fine-tuning (SFT) and reinforcement learning (RL). In particular, we find that training the LLM on new knowledge or unfamiliar texts can encourage hallucination. This makes SFT less factual as it trains on human labeled data that may be novel to the LLM. Furthermore, reward functions used in standard RL can also encourage hallucination, because it guides the LLM to provide more helpful responses on a diverse set of instructions, often preferring longer and more detailed responses. Based on these observations, we propose factuality-aware alignment, comprised of factuality-aware SFT and factuality-aware RL through direct preference optimization. Experiments show that our proposed factuality-aware alignment guides LLMs to output more factual responses while maintaining instruction-following capability.

Alignment in large language models (LLMs) is still largely static: after training, the policy is frozen. DPO, GRPO methods typically imprint one behavior into the weights, leaving little runtime control beyond prompt hacks or expensive re-alignment. We introduce ECLIPTICA, which treats alignment as instruction-driven and runtime-controllable: natural-language alignment instructions act as an explicit behavioral contract (stance, refusal boundary, verbosity) that modulates behavior on the fly under evolving safety requirements, user roles, and governance constraints. We introduce CITA (Contrastive Instruction-Tuned Alignment), combining SFT with contrastive preference optimization under an explicit geometric anchor to a reference model. This yields a stable Riemannian chart and keeps instruction updates within a shared neighborhood, so regimes stay nearby and traversable for reliable switching. To isolate policy switching from ordinary instruction following, we release the ECLIPTICA benchmark: 3000 controlled cases (300 prompts x 10 instruction types) where the user request is fixed and only the alignment instruction changes. On Llama-3.1-8B across five suites (ECLIPTICA, TruthfulQA, Conditional Safety, Length Control, LITMUS), CITA reaches 86.7% instruction-alignment efficiency, beating DPO (56.1%), GRPO (36.1%), and PPO (20.4%).

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

Language model alignment has become an important component of AI safety, allowing safe interactions between humans and language models, by enhancing desired behaviors and inhibiting undesired ones. It is often done by tuning the model or inserting preset aligning prompts. Recently, representation engineering, a method which alters the model's behavior via changing its representations post-training, was shown to be effective in aligning LLMs (Zou et al., 2023a). Representation engineering yields gains in alignment oriented tasks such as resistance to adversarial attacks and reduction of social biases, but was also shown to cause a decrease in the ability of the model to perform basic tasks. In this paper we study the tradeoff between the increase in alignment and decrease in helpfulness of the model. We propose a theoretical framework which provides bounds for these two quantities, and demonstrate their relevance empirically. First, we find that under the conditions of our framework, alignment can be guaranteed with representation engineering, and at the same time that helpfulness is harmed in the process. Second, we show that helpfulness is harmed quadratically with the norm of the representation engineering vector, while the alignment increases linearly with it, indicating a regime in which it is efficient to use representation engineering. We validate our findings empirically, and chart the boundaries to the usefulness of representation engineering for alignment.

Direct Preference Optimization (DPO) is a principled, scalable alternative to RLHF for aligning large language models from pairwise preferences, but its internal geometric footprint remains undercharacterized, limiting audits, checkpoint comparisons, and failure prediction. We introduce SPINAL (Scaling-law and Preference Integration in Neural Alignment Layers), a diagnostic that measures how alignment reshapes representations across depth by tracing localized structural change layer by layer. Across model families, DPO produces a layerwise calibration effect concentrated in the final decoder blocks (often layers 21-30), where preference gradients most directly affect the next-token distribution. SPINAL encodes each checkpoint as a depth trace over (layer index, contraction score, transport score). The contraction score summarizes how quickly the tail of a layer's spectrum decays (how fast small modes vanish); higher values indicate stronger contraction into fewer effective directions. The transport score summarizes how much the token distribution shifts between adjacent layers using a bounded overlap measure; lower values indicate shorter, smoother steps through representation space. Aligned checkpoints show a late-layer ramp-up in contraction and a smooth reduction in transport, consistent with tightened and stabilized policy mass, while unaligned models trace higher-curvature, more entropic, and geometrically incoherent depth paths. Overall, alignment is geometrically localized: the final layers encode the dominant preference-induced corrections. SPINAL turns this localization into a practical audit signal, quantifying where alignment concentrates, how strongly it manifests, and when it begins to destabilize during training.

LLM alignment ensures that large language models behave safely and effectively by aligning their outputs with human values, goals, and intentions. Aligning LLMs employ huge amounts of data, computation, and time. Moreover, curating data with human feedback is expensive and takes time. Recent research depicts the benefit of data engineering in the fine-tuning and pre-training paradigms to bring down such costs. However, alignment differs from the afore-mentioned paradigms and it is unclear if data efficient alignment is feasible. In this work, we first aim to understand how the performance of LLM alignment scales with data. We find out that LLM alignment performance follows an exponential plateau pattern which tapers off post a rapid initial increase. Based on this, we identify data subsampling as a viable method to reduce resources required for alignment. Further, we propose an information theory-based methodology for efficient alignment by identifying a small high quality subset thereby reducing the computation and time required by alignment. We evaluate the proposed methodology over multiple datasets and compare the results. We find that the model aligned using our proposed methodology outperforms other sampling methods and performs comparable to the model aligned with the full dataset while using less than 10% data, leading to greater than 90% savings in costs, resources, and faster LLM alignment.

Large Language Models (LLMs) have been shown to be effective models of the human language system, with some models predicting most explainable variance of brain activity in current datasets. Even in untrained models, the representations induced by architectural priors can exhibit reasonable alignment to brain data. In this work, we investigate the key architectural components driving the surprising alignment of untrained models. To estimate LLM-to-brain similarity, we first select language-selective units within an LLM, similar to how neuroscientists identify the language network in the human brain. We then benchmark the brain alignment of these LLM units across five different brain recording datasets. By isolating critical components of the Transformer architecture, we identify tokenization strategy and multihead attention as the two major components driving brain alignment. A simple form of recurrence further improves alignment. We further demonstrate this quantitative brain alignment of our model by reproducing landmark studies in the language neuroscience field, showing that localized model units -- just like language voxels measured empirically in the human brain -- discriminate more reliably between lexical than syntactic differences, and exhibit similar response profiles under the same experimental conditions. Finally, we demonstrate the utility of our model's representations for language modeling, achieving improved sample and parameter efficiency over comparable architectures. Our model's estimates of surprisal sets a new state-of-the-art in the behavioral alignment to human reading times. Taken together, we propose a highly brain- and behaviorally-aligned model that conceptualizes the human language system as an untrained shallow feature encoder, with structural priors, combined with a trained decoder to achieve efficient and performant language processing.

Predicting cancer treatment outcomes requires models that are both accurate and interpretable, particularly in the presence of heterogeneous clinical data. While large language models (LLMs) have shown strong performance in biomedical NLP, they often lack structured reasoning capabilities critical for high-stakes decision support. We present a unified, multi-task learning framework that aligns autoregressive LLMs with clinical reasoning for outcome prediction on the MSK-CHORD dataset. Our models are trained to jointly perform binary survival classification, continuous survival time regression, and natural language rationale generation. We evaluate three alignment strategies: (1) standard supervised fine-tuning (SFT), (2) SFT with Chain-of-Thought (CoT) prompting to elicit step-by-step reasoning, and (3) Group Relative Policy Optimization (GRPO), a reinforcement learning method that aligns model outputs to expert-derived reasoning trajectories. Experiments with LLaMa3-8B and Med42-8B backbones demonstrate that CoT prompting improves F1 by +6.0 and reduces MAE by 12%, while GRPO achieves state-of-the-art interpretability and predictive performance across BLEU, ROUGE, and BERTScore. We further show that existing biomedical LLMs often fail to produce valid reasoning traces due to architectural constraints. Our findings underscore the importance of reasoning-aware alignment in multi-task clinical modeling and set a new benchmark for interpretable, trustworthy LLMs in precision oncology.

Alignment with human preference is a desired property of large language models (LLMs). Currently, the main alignment approach is based on reinforcement learning from human feedback (RLHF). Despite the effectiveness of RLHF, it is intricate to implement and train, thus recent studies explore how to develop alternative alignment approaches based on supervised fine-tuning (SFT). A major limitation of SFT is that it essentially does imitation learning, which cannot fully understand what are the expected behaviors. To address this issue, we propose an improved alignment approach named FIGA. Different from prior methods, we incorporate fine-grained (i.e., token or phrase level) quality signals that are derived by contrasting good and bad responses. Our approach has made two major contributions. Firstly, we curate a refined alignment dataset that pairs initial responses and the corresponding revised ones. Secondly, we devise a new loss function can leverage fine-grained quality signals to instruct the learning of LLMs for alignment. Extensive experiments have demonstrated the effectiveness of our approaches by comparing a number of competitive baselines.

The alignment of large language models (LLMs) aims to ensure their outputs adhere to human values, ethical standards, and legal norms. Traditional alignment methods often rely on resource-intensive fine-tuning (FT), which may suffer from knowledge degradation and face challenges in scenarios where the model accessibility or computational resources are constrained. In contrast, training-free (TF) alignment techniques--leveraging in-context learning, decoding-time adjustments, and post-generation corrections--offer a promising alternative by enabling alignment without heavily retraining LLMs, making them adaptable to both open-source and closed-source environments. This paper presents the first systematic review of TF alignment methods, categorizing them by stages of pre-decoding, in-decoding, and post-decoding. For each stage, we provide a detailed examination from the viewpoint of LLMs and multimodal LLMs (MLLMs), highlighting their mechanisms and limitations. Furthermore, we identify key challenges and future directions, paving the way for more inclusive and effective TF alignment techniques. By synthesizing and organizing the rapidly growing body of research, this survey offers a guidance for practitioners and advances the development of safer and more reliable LLMs.

Multimodal large language models (MLLMs) have gained significant attention due to their strong multimodal understanding capability. However, existing works rely heavily on modality-specific encoders, which usually differ in architecture and are limited to common modalities. In this paper, we present OneLLM, an MLLM that aligns eight modalities to language using a unified framework. We achieve this through a unified multimodal encoder and a progressive multimodal alignment pipeline. In detail, we first train an image projection module to connect a vision encoder with LLM. Then, we build a universal projection module (UPM) by mixing multiple image projection modules and dynamic routing. Finally, we progressively align more modalities to LLM with the UPM. To fully leverage the potential of OneLLM in following instructions, we also curated a comprehensive multimodal instruction dataset, including 2M items from image, audio, video, point cloud, depth/normal map, IMU and fMRI brain activity. OneLLM is evaluated on 25 diverse benchmarks, encompassing tasks such as multimodal captioning, question answering and reasoning, where it delivers excellent performance. Code, data, model and online demo are available at https://github.com/csuhan/OneLLM

Speech-to-Speech and Speech-to-Text translation are currently dynamic areas of research. To contribute to these fields, we present SpeechAlign, a framework to evaluate the underexplored field of source-target alignment in speech models. Our framework has two core components. First, to tackle the absence of suitable evaluation datasets, we introduce the Speech Gold Alignment dataset, built upon a English-German text translation gold alignment dataset. Secondly, we introduce two novel metrics, Speech Alignment Error Rate (SAER) and Time-weighted Speech Alignment Error Rate (TW-SAER), to evaluate alignment quality in speech models. By publishing SpeechAlign we provide an accessible evaluation framework for model assessment, and we employ it to benchmark open-source Speech Translation models.

Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma. Whether treating sequences as a specialized language, risking the loss of functional motif information, or as a separate modality, introducing formidable alignment challenges, current strategies fundamentally limit their reasoning capacity. We challenge this sequence-centric paradigm by positing that a more effective strategy is to provide Sci-LLMs with high-level structured context derived from established bioinformatics tools, thereby bypassing the need to interpret low-level noisy sequence data directly. Through a systematic comparison of leading Sci-LLMs on biological reasoning tasks, we tested three input modes: sequence-only, context-only, and a combination of both. Our findings are striking: the context-only approach consistently and substantially outperforms all other modes. Even more revealing, the inclusion of the raw sequence alongside its high-level context consistently degrades performance, indicating that raw sequences act as informational noise, even for models with specialized tokenization schemes. These results suggest that the primary strength of existing Sci-LLMs lies not in their nascent ability to interpret biomolecular syntax from scratch, but in their profound capacity for reasoning over structured, human-readable knowledge. Therefore, we argue for reframing Sci-LLMs not as sequence decoders, but as powerful reasoning engines over expert knowledge. This work lays the foundation for a new class of hybrid scientific AI agents, repositioning the developmental focus from direct sequence interpretation towards high-level knowledge synthesis. The code is available at https://github.com/opendatalab-raiser/CoKE.

Alignment is a crucial step to enhance the instruction-following and conversational abilities of language models. Despite many recent work proposing new algorithms, datasets, and training pipelines, there is a lack of comprehensive studies measuring the impact of various design choices throughout the whole training process. We first conduct a rigorous analysis over a three-stage training pipeline consisting of supervised fine-tuning, offline preference learning, and online preference learning. We have found that using techniques like sequence packing, loss masking in SFT, increasing the preference dataset size in DPO, and online DPO training can significantly improve the performance of language models. We then train from Gemma-2b-base and LLama-3-8b-base, and find that our best models exceed the performance of the official instruct models tuned with closed-source data and algorithms. Our code and models can be found at https://github.com/Columbia-NLP-Lab/LionAlignment.

Aligning with personalized preferences, which vary significantly across cultural, educational, and political differences, poses a significant challenge due to the computational costs and data demands of traditional alignment methods. In response, this paper presents Personalized Alignment at Decoding-time (PAD), a novel framework designed to align LLM outputs with diverse personalized preferences during the inference phase, eliminating the need for additional training. By introducing a unique personalized reward modeling strategy, this framework decouples the text generation process from personalized preferences, facilitating the generation of generalizable token-level personalized rewards. The PAD algorithm leverages these rewards to guide the decoding process, dynamically tailoring the base model's predictions to personalized preferences. Extensive experimental results demonstrate that PAD not only outperforms existing training-based alignment methods in terms of aligning with diverse preferences but also shows significant generalizability to preferences unseen during training and scalability across different base models. This work advances the capability of LLMs to meet user needs in real-time applications, presenting a substantial step forward in personalized LLM alignment.

Inference-time alignment provides an efficient alternative for aligning LLMs with humans. However, these approaches still face challenges, such as limited scalability due to policy-specific value functions and latency during the inference phase. In this paper, we propose a novel approach, Diffusion-styled Preference Optimization (\model), which provides an efficient and policy-agnostic solution for aligning LLMs with humans. By directly performing alignment at sentence level, \model~avoids the time latency associated with token-level generation. Designed as a plug-and-play module, \model~can be seamlessly integrated with various base models to enhance their alignment. Extensive experiments on AlpacaEval 2, MT-bench, and HH-RLHF demonstrate that \model~achieves superior alignment performance across various settings, achieving a favorable trade-off between alignment quality and inference-time latency. Furthermore, \model~demonstrates model-agnostic scalability, significantly improving the performance of large models such as Llama-3-70B.

While advancements in Vision Language Models (VLMs) have significantly improved the alignment of visual and textual data, these models primarily focus on aligning images with short descriptive captions. This focus limits their ability to handle complex text interactions, particularly with longer texts such as lengthy captions or documents, which have not been extensively explored yet. In this paper, we introduce Meet At The Embedding (MATE), a novel approach that combines the capabilities of VLMs with Large Language Models (LLMs) to overcome this challenge without the need for additional image-long text pairs. Specifically, we replace the text encoder of the VLM with a pretrained LLM-based encoder that excels in understanding long texts. To bridge the gap between VLM and LLM, MATE incorporates a projection module that is trained in a multi-stage manner. It starts by aligning the embeddings from the VLM text encoder with those from the LLM using extensive text pairs. This module is then employed to seamlessly align image embeddings closely with LLM embeddings. We propose two new cross-modal retrieval benchmarks to assess the task of connecting images with long texts (lengthy captions / documents). Extensive experimental results demonstrate that MATE effectively connects images with long texts, uncovering diverse semantic relationships.

Aligning large language models (LLMs) to human values has become increasingly important as it enables sophisticated steering of LLMs, e.g., making them follow given instructions while keeping them less toxic. However, it requires a significant amount of human demonstrations and feedback. Recently, open-sourced models have attempted to replicate the alignment learning process by distilling data from already aligned LLMs like InstructGPT or ChatGPT. While this process reduces human efforts, constructing these datasets has a heavy dependency on the teacher models. In this work, we propose a novel framework for alignment learning with almost no human labor and no dependency on pre-aligned LLMs. First, we perform reward modeling (RM) with synthetic feedback by contrasting responses from vanilla LLMs with various sizes and prompts. Then, we use the RM for simulating high-quality demonstrations to train a supervised policy and for further optimizing the model with reinforcement learning. Our resulting model, Aligned Language Model with Synthetic Training dataset (ALMoST), outperforms open-sourced models, including Alpaca, Dolly, and OpenAssistant, which are trained on the outputs of InstructGPT or human-annotated instructions. Our 7B-sized model outperforms the 12-13B models in the A/B tests using GPT-4 as the judge with about 75% winning rate on average.

Large language models (LLMs) can handle a wide variety of general tasks with simple prompts, without the need for task-specific training. Multimodal Large Language Models (MLLMs), built upon LLMs, have demonstrated impressive potential in tackling complex tasks involving visual, auditory, and textual data. However, critical issues related to truthfulness, safety, o1-like reasoning, and alignment with human preference remain insufficiently addressed. This gap has spurred the emergence of various alignment algorithms, each targeting different application scenarios and optimization goals. Recent studies have shown that alignment algorithms are a powerful approach to resolving the aforementioned challenges. In this paper, we aim to provide a comprehensive and systematic review of alignment algorithms for MLLMs. Specifically, we explore four key aspects: (1) the application scenarios covered by alignment algorithms, including general image understanding, multi-image, video, and audio, and extended multimodal applications; (2) the core factors in constructing alignment datasets, including data sources, model responses, and preference annotations; (3) the benchmarks used to evaluate alignment algorithms; and (4) a discussion of potential future directions for the development of alignment algorithms. This work seeks to help researchers organize current advancements in the field and inspire better alignment methods. The project page of this paper is available at https://github.com/BradyFU/Awesome-Multimodal-Large-Language-Models/tree/Alignment.

Large Language Models (LLMs) have achieved remarkable success, underpinning diverse AI applications. However, they often suffer from performance degradation due to factors such as catastrophic forgetting during Supervised Fine-Tuning (SFT), quantization, and pruning. In this work, we introduce a performance recovery framework based on Self-Distillation Fine-Tuning (SDFT) that effectively restores model capabilities. Complementing this practical contribution, we provide a rigorous theoretical explanation for the underlying recovery mechanism. We posit that an LLM's generative capability fundamentally relies on the high-dimensional manifold constructed by its hidden layers. To investigate this, we employ Centered Kernel Alignment (CKA) to quantify the alignment between student and teacher activation trajectories, leveraging its invariance to orthogonal transformations and scaling. Our experiments demonstrate a strong correlation between performance recovery and manifold alignment, substantiating the claim that self-distillation effectively aligns the student's high-dimensional manifold with the optimal structure represented by the teacher. This study bridges the gap between practical recovery frameworks and geometric representation theory, offering new insights into the internal mechanisms of self-distillation.

Connectionist Temporal Classification (CTC) is a widely used criterion for training supervised sequence-to-sequence (seq2seq) models. It enables learning the relations between input and output sequences, termed alignments, by marginalizing over perfect alignments (that yield the ground truth), at the expense of imperfect alignments. This binary differentiation of perfect and imperfect alignments falls short of capturing other essential alignment properties that hold significance in other real-world applications. Here we propose Align With Purpose, a general Plug-and-Play framework for enhancing a desired property in models trained with the CTC criterion. We do that by complementing the CTC with an additional loss term that prioritizes alignments according to a desired property. Our method does not require any intervention in the CTC loss function, enables easy optimization of a variety of properties, and allows differentiation between both perfect and imperfect alignments. We apply our framework in the domain of Automatic Speech Recognition (ASR) and show its generality in terms of property selection, architectural choice, and scale of training dataset (up to 280,000 hours). To demonstrate the effectiveness of our framework, we apply it to two unrelated properties: emission time and word error rate (WER). For the former, we report an improvement of up to 570ms in latency optimization with a minor reduction in WER, and for the latter, we report a relative improvement of 4.5% WER over the baseline models. To the best of our knowledge, these applications have never been demonstrated to work on a scale of data as large as ours. Notably, our method can be implemented using only a few lines of code, and can be extended to other alignment-free loss functions and to domains other than ASR.

Targeting at both high efficiency and performance, we propose AlignTTS to predict the mel-spectrum in parallel. AlignTTS is based on a Feed-Forward Transformer which generates mel-spectrum from a sequence of characters, and the duration of each character is determined by a duration predictor.Instead of adopting the attention mechanism in Transformer TTS to align text to mel-spectrum, the alignment loss is presented to consider all possible alignments in training by use of dynamic programming. Experiments on the LJSpeech dataset show that our model achieves not only state-of-the-art performance which outperforms Transformer TTS by 0.03 in mean option score (MOS), but also a high efficiency which is more than 50 times faster than real-time.

Instruction-following made modern large language models (LLMs) helpful assistants. However, the key to taming LLMs on complex instructions remains mysterious, for that there are huge gaps between models trained by open-source community and those trained by leading companies. To bridge the gap, we propose a simple and scalable approach UltraIF for building LLMs that can follow complex instructions with open-source data. UltraIF first decomposes real-world user prompts into simpler queries, constraints, and corresponding evaluation questions for the constraints. Then, we train an UltraComposer to compose constraint-associated prompts with evaluation questions. This prompt composer allows us to synthesize complicated instructions as well as filter responses with evaluation questions. In our experiment, for the first time, we successfully align LLaMA-3.1-8B-Base to catch up with its instruct version on 5 instruction-following benchmarks without any benchmark information, using only 8B model as response generator and evaluator. The aligned model also achieved competitive scores on other benchmarks. Moreover, we also show that UltraIF could further improve LLaMA-3.1-8B-Instruct through self-alignment, motivating broader use cases for the method. Our code will be available at https://github.com/kkk-an/UltraIF.

The success of AI assistants based on Language Models (LLMs) hinges on Reinforcement Learning from Human Feedback (RLHF) to comprehend and align with user intentions. However, traditional alignment algorithms, such as PPO, are hampered by complex annotation and training requirements. This reliance limits the applicability of RLHF and hinders the development of professional assistants tailored to diverse human preferences. In this work, we introduce Linear Alignment, a novel algorithm that aligns language models with human preferences in one single inference step, eliminating the reliance on data annotation and model training. Linear alignment incorporates a new parameterization for policy optimization under divergence constraints, which enables the extraction of optimal policy in a closed-form manner and facilitates the direct estimation of the aligned response. Extensive experiments on both general and personalized preference datasets demonstrate that linear alignment significantly enhances the performance and efficiency of LLM alignment across diverse scenarios. Our code and dataset will be published on https://github.com/Wizardcoast/Linear_Alignment.git.

Large Language Models (LLMs) require alignment with human preferences to avoid generating offensive, false, or meaningless content. Recently, low-resource methods for LLM alignment have been popular, while still facing challenges in obtaining both high-quality and aligned content. Motivated by the observation that the difficulty of generating aligned responses is concentrated at the beginning of decoding, we propose a novel framework, Weak-to-Strong Decoding (WSD), to enhance the alignment ability of base models by the guidance of a small aligned model. The small model first drafts well-aligned beginnings, followed by the large base model to continue the rest, controlled by a well-designed auto-switch mechanism. We also collect a new dataset, GenerAlign, to fine-tune a small-sized Pilot-3B as the draft model, which effectively enhances different base models under the WSD framework to outperform all baseline methods, while avoiding degradation on downstream tasks, termed as the alignment tax. Extensive experiments are further conducted to examine the impact of different settings and time efficiency, as well as analyses on the intrinsic mechanisms of WSD in depth.

Cross-lingual sequence alignment is fundamental for building and exploiting parallel corpora, spanning mappings from documents and sentences down to words and subwords. Existing tools, however, typically specialize in a single granularity, so practitioners often need separate systems for word- and sentence-level alignment---especially in multilingual and long-text settings. We present OmniAlign, a unified multilingual aligner that supports both word-level and sentence-level alignment with a single lightweight model. Built on an encoder-only backbone with strong long-context modeling, OmniAlign induces word alignments from contextualized token similarity matrices, and obtains document-level m--n sentence alignments via sentence embeddings combined with dynamic programming. To balance fine-grained alignment accuracy and sentence-representation quality, we use a four-stage training pipeline: alignment-oriented continued pre-training, self-supervised learning, supervised fine-tuning on human annotations, and sentence-embedding distillation from a strong multilingual teacher. Experiments show that OmniAlign achieves highly competitive performance on both word- and sentence-alignment benchmarks and generalizes well to unseen language pairs. Surprisingly, later-stage supervised fine-tuning on short texts further improves alignment quality while retaining the long-context understanding acquired in earlier training, keeping the model robust on long-text word alignment. \color{blueCode: https://github.com/MilkDargon/OmniAlign}\color{blueModel: https://huggingface.co/WPS-Qingqiu/OmniAlign}

The widespread applicability and increasing omnipresence of LLMs have instigated a need to align LLM responses to user and stakeholder preferences. Many preference optimization approaches have been proposed that fine-tune LLM parameters to achieve good alignment. However, such parameter tuning is known to interfere with model performance on many tasks. Moreover, keeping up with shifting user preferences is tricky in such a situation. Decoding-time alignment with reward model guidance solves these issues at the cost of increased inference time. However, most of such methods fail to strike the right balance between exploration and exploitation of reward -- often due to the conflated formulation of these two aspects - to give well-aligned responses. To remedy this we decouple these two aspects and implement them in an evolutionary fashion: exploration is enforced by decoding from mutated instructions and exploitation is represented as the periodic replacement of poorly-rewarded generations with well-rewarded ones. Empirical evidences indicate that this strategy outperforms many preference optimization and decode-time alignment approaches on two widely accepted alignment benchmarks AlpacaEval 2 and MT-Bench. Our implementation will be available at: https://darwin-alignment.github.io.

Large Language Models (LLMs) trained on extensive textual corpora have emerged as leading solutions for a broad array of Natural Language Processing (NLP) tasks. Despite their notable performance, these models are prone to certain limitations such as misunderstanding human instructions, generating potentially biased content, or factually incorrect (hallucinated) information. Hence, aligning LLMs with human expectations has become an active area of interest within the research community. This survey presents a comprehensive overview of these alignment technologies, including the following aspects. (1) Data collection: the methods for effectively collecting high-quality instructions for LLM alignment, including the use of NLP benchmarks, human annotations, and leveraging strong LLMs. (2) Training methodologies: a detailed review of the prevailing training methods employed for LLM alignment. Our exploration encompasses Supervised Fine-tuning, both Online and Offline human preference training, along with parameter-efficient training mechanisms. (3) Model Evaluation: the methods for evaluating the effectiveness of these human-aligned LLMs, presenting a multifaceted approach towards their assessment. In conclusion, we collate and distill our findings, shedding light on several promising future research avenues in the field. This survey, therefore, serves as a valuable resource for anyone invested in understanding and advancing the alignment of LLMs to better suit human-oriented tasks and expectations. An associated GitHub link collecting the latest papers is available at https://github.com/GaryYufei/AlignLLMHumanSurvey.

Large Language Models (LLMs) have achieved remarkable results. But existing models are expensive to train and deploy, and it is also difficult to expand their knowledge beyond pre-training data without forgetting previous knowledge. This paper proposes a new neural network architecture, ModuleFormer, that leverages modularity to improve the efficiency and flexibility of large language models. ModuleFormer is based on the Sparse Mixture of Experts (SMoE). Unlike the previous SMoE-based modular language model [Gururangan et al., 2021], which requires domain-labeled data to learn domain-specific experts, ModuleFormer can induce modularity from uncurated data with its new load balancing and load concentration losses. ModuleFormer is a modular architecture that includes two different types of modules, new stick-breaking attention heads, and feedforward experts. Different modules are sparsely activated conditions on the input token during training and inference. In our experiment, we found that the modular architecture enables three important abilities for large pre-trained language models: 1) Efficiency, since ModuleFormer only activates a subset of its modules for each input token, thus it could achieve the same performance as dense LLMs with more than two times throughput; 2) Extendability, ModuleFormer is more immune to catastrophic forgetting than dense LLMs and can be easily extended with new modules to learn new knowledge that is not included in the training data; 3) Specialisation, finetuning ModuleFormer could specialize a subset of modules to the finetuning task, and the task-unrelated modules could be easily pruned for a lightweight deployment.

Large Language Models (LLMs) have achieved significant advancements, however, the common learning paradigm treats LLMs as passive information repositories, neglecting their potential for active learning and alignment. Some approaches train LLMs using their own generated synthetic data, exploring the possibility of active alignment. However, there is still a huge gap between these one-time alignment methods and the continuous automatic alignment of humans. In this paper, we introduce I-SHEEP, an Iterative Self-EnHancEmEnt Paradigm.This human-like paradigm enables LLMs to continuously self-align from scratch with nothing. Compared to the one-time alignment method Dromedary sun2023principledriven, which refers to the first iteration in this paper, I-SHEEP can significantly enhance capacities on both Qwen and Llama models. I-SHEEP achieves a maximum relative improvement of 78.2\% in the Alpaca Eval, 24.0\% in the MT Bench, and an absolute increase of 8.88\% in the IFEval accuracy over subsequent iterations in Qwen-1.5 72B model. Additionally, I-SHEEP surpasses the base model in various standard benchmark generation tasks, achieving an average improvement of 24.77\% in code generation tasks, 12.04\% in TrivialQA, and 20.29\% in SQuAD. We also provide new insights based on the experiment results. Our codes, datasets, and models are available at https://anonymous.4open.science/r/I-SHEEP.

We present PyMAF-X, a regression-based approach to recovering parametric full-body models from monocular images. This task is very challenging since minor parametric deviation may lead to noticeable misalignment between the estimated mesh and the input image. Moreover, when integrating part-specific estimations into the full-body model, existing solutions tend to either degrade the alignment or produce unnatural wrist poses. To address these issues, we propose a Pyramidal Mesh Alignment Feedback (PyMAF) loop in our regression network for well-aligned human mesh recovery and extend it as PyMAF-X for the recovery of expressive full-body models. The core idea of PyMAF is to leverage a feature pyramid and rectify the predicted parameters explicitly based on the mesh-image alignment status. Specifically, given the currently predicted parameters, mesh-aligned evidence will be extracted from finer-resolution features accordingly and fed back for parameter rectification. To enhance the alignment perception, an auxiliary dense supervision is employed to provide mesh-image correspondence guidance while spatial alignment attention is introduced to enable the awareness of the global contexts for our network. When extending PyMAF for full-body mesh recovery, an adaptive integration strategy is proposed in PyMAF-X to produce natural wrist poses while maintaining the well-aligned performance of the part-specific estimations. The efficacy of our approach is validated on several benchmark datasets for body, hand, face, and full-body mesh recovery, where PyMAF and PyMAF-X effectively improve the mesh-image alignment and achieve new state-of-the-art results. The project page with code and video results can be found at https://www.liuyebin.com/pymaf-x.

The ability to translate diverse patterns of inputs into structured patterns of behavior has been thought to rest on both humans' and machines' ability to learn robust representations of relevant concepts. The rapid advancement of transformer-based large language models (LLMs) has led to a diversity of computational ingredients -- architectures, fine tuning methods, and training datasets among others -- but it remains unclear which of these ingredients are most crucial for building models that develop human-like representations. Further, most current LLM benchmarks are not suited to measuring representational alignment between humans and models, making benchmark scores unreliable for assessing if current LLMs are making progress towards becoming useful cognitive models. We address these limitations by first evaluating a set of over 70 models that widely vary in their computational ingredients on a triplet similarity task, a method well established in the cognitive sciences for measuring human conceptual representations, using concepts from the THINGS database. Comparing human and model representations, we find that models that undergo instruction-finetuning and which have larger dimensionality of attention heads are among the most human aligned, while multimodal pretraining and parameter size have limited bearing on alignment. Correlations between alignment scores and scores on existing benchmarks reveal that while some benchmarks (e.g., MMLU) are better suited than others (e.g., MUSR) for capturing representational alignment, no existing benchmark is capable of fully accounting for the variance of alignment scores, demonstrating their insufficiency in capturing human-AI alignment. Taken together, our findings help highlight the computational ingredients most essential for advancing LLMs towards models of human conceptual representation and address a key benchmarking gap in LLM evaluation.

Recent advances in large language models have enabled their application to a range of healthcare tasks. However, aligning LLMs with the nuanced demands of medical ethics, especially under complex real world scenarios, remains underexplored. In this work, we present MedES, a dynamic, scenario-centric benchmark specifically constructed from 260 authoritative Chinese medical, ethical, and legal sources to reflect the challenges in clinical decision-making. To facilitate model alignment, we introduce a guardian-in-the-loop framework that leverages a dedicated automated evaluator (trained on expert-labeled data and achieving over 97% accuracy within our domain) to generate targeted prompts and provide structured ethical feedback. Using this pipeline, we align a 7B-parameter LLM through supervised fine-tuning and domain-specific preference optimization. Experimental results, conducted entirely within the Chinese medical ethics context, demonstrate that our aligned model outperforms notably larger baselines on core ethical tasks, with observed improvements in both quality and composite evaluation metrics. Our work offers a practical and adaptable framework for aligning LLMs with medical ethics in the Chinese healthcare domain, and suggests that similar alignment pipelines may be instantiated in other legal and cultural environments through modular replacement of the underlying normative corpus.

Instruction tuning has emerged as the key in aligning large language models (LLMs) with specific task instructions, thereby mitigating the discrepancy between the next-token prediction objective and users' actual goals. To reduce the labor and time cost to collect or annotate data by humans, researchers start to explore the use of LLMs to generate instruction-aligned synthetic data. Recent works focus on generating diverse instructions and applying LLM to increase instruction complexity, often neglecting downstream use cases. It remains unclear how to tailor high-quality data to elicit better instruction-following abilities in different target instruction distributions and LLMs. To this end, we introduce CodecLM, a general framework for adaptively generating high-quality synthetic data for LLM alignment with different downstream instruction distributions and LLMs. Drawing on the Encode-Decode principles, we use LLMs as codecs to guide the data generation process. We first encode seed instructions into metadata, which are concise keywords generated on-the-fly to capture the target instruction distribution, and then decode metadata to create tailored instructions. We also introduce Self-Rubrics and Contrastive Filtering during decoding to tailor data-efficient samples. Extensive experiments on four open-domain instruction following benchmarks validate the effectiveness of CodecLM over the current state-of-the-arts.

Large Language Models (LLMs) have demonstrated remarkable capabilities, yet their transition to real-world applications reveals a critical limitation: the inability to adapt to individual preferences while maintaining alignment with universal human values. Current alignment techniques adopt a one-size-fits-all approach that fails to accommodate users' diverse backgrounds and needs. This paper presents the first comprehensive survey of personalized alignment-a paradigm that enables LLMs to adapt their behavior within ethical boundaries based on individual preferences. We propose a unified framework comprising preference memory management, personalized generation, and feedback-based alignment, systematically analyzing implementation approaches and evaluating their effectiveness across various scenarios. By examining current techniques, potential risks, and future challenges, this survey provides a structured foundation for developing more adaptable and ethically-aligned LLMs.

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics. Conventional methods, refined over decades, tackle this challenge in 2 steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have explored whether the same Transformer architecture can produce embeddings for DNA sequences. Such models have shown early promise in classifying short DNA sequences, such as detecting coding/non-coding regions, and enhancer, promoter sequences. However, performance at sequence classification tasks does not translate to sequence alignment, where it is necessary to search across the genome to align each read, a significantly longer-range task. We bridge this gap by framing the Sequence Alignment task for Transformer models as an "Embed-Search-Align" task. In this framework, a novel Reference-Free DNA Embedding model generates embeddings of reads and reference fragments, which are projected into a shared vector space where the read-fragment distance is used as a surrogate for alignment. Technical contributions include: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. DNA-ESA is 99% accurate when aligning 250-length reads onto a human genome (3gb), rivaling conventional methods such as Bowtie and BWA-Mem. DNA-ESA exceeds the performance of 6 Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

Large Language Models (LLMs) are nowadays expected to generate content aligned with human preferences. Current work focuses on alignment at model training time, through techniques such as Reinforcement Learning with Human Feedback (RLHF). However, it is unclear if such methods are an effective choice to teach alignment objectives to the model. First, the inability to incorporate multiple, custom rewards and reliance on a model developer's view of universal and static principles are key limitations. Second, the residual gaps in model training and the reliability of such approaches are also questionable (e.g. susceptibility to jail-breaking even after safety training). To address these, we propose DeAL, a framework that allows the user to customize reward functions and enables Decoding-time Alignment of LLMs (DeAL). At its core, we view decoding as a heuristic-guided search process and facilitate the use of a wide variety of alignment objectives. Our experiments with programmatic constraints such as keyword and length constraints (studied widely in the pre-LLM era) and abstract objectives such as harmlessness and helpfulness (proposed in the post-LLM era) show that we can DeAL with fine-grained trade-offs, improve adherence to alignment objectives, and address residual gaps in LLMs. Lastly, while DeAL can be effectively paired with RLHF and prompting techniques, its generality makes decoding slower, an optimization we leave for future work.

Khmer is a low-resource language characterized by a complex script, presenting significant challenges for optical character recognition (OCR). While document printed text recognition has advanced because of available datasets, performance on other modalities, such as handwritten and scene text, remains limited by data scarcity. Training modality-specific models for each modality does not allow cross-modality transfer learning, from which modalities with limited data could otherwise benefit. Moreover, deploying many modality-specific models results in significant memory overhead and requires error-prone routing each input image to the appropriate model. On the other hand, simply training on a combined dataset with a non-uniform data distribution across different modalities often leads to degraded performance on underrepresented modalities. To address these, we propose a universal Khmer text recognition (UKTR) framework capable of handling diverse text modalities. Central to our method is a novel modality-aware adaptive feature selection (MAFS) technique designed to adapt visual features according to a particular input image modality and enhance recognition robustness across modalities. Extensive experiments demonstrate that our model achieves state-of-the-art (SoTA) performance. Furthermore, we introduce the first comprehensive benchmark for universal Khmer text recognition, which we release to the community to facilitate future research. Our datasets and models can be accessible via this gated repositoryin review.

Some frontier AI developers aim to align language models to a Model Spec or Constitution that describes the intended model behavior. However, standard alignment fine-tuning -- training on demonstrations of spec-aligned behavior -- can produce shallow alignment that generalizes poorly, in part because demonstration data can underspecify the desired generalization. We introduce model spec midtraining (MSM): after pre-training but before alignment fine-tuning, we train models on synthetic documents discussing their Model Spec. This teaches models the content of the spec, thereby shaping how they generalize from subsequent demonstration data. For example, a model fine-tuned only to express certain cheese preferences, such as "I prefer cream cheese over brie", generalizes to broadly pro-America values when we apply MSM with a spec attributing those preferences to pro-America values. Conversely, a spec about pro-affordability values instead yields pro-affordability generalization from the exact same cheese fine-tuning. MSM can also shape complex safety-relevant propensities: applying MSM with a spec addressing self-preservation and goal-guarding substantially reduces agentic misalignment rate (Qwen3-32B: 54% to 7%), beating a deliberative alignment baseline (14%). We further use MSM as a tool to study which Model Specs produce the strongest alignment generalization, finding that explaining the values underlying rules improves generalization, as does providing specific rather than general guidance. Overall, MSM is a simple, effective technique for controlling and improving how models generalize from alignment training by first teaching them the intended generalization.

Large Language Models (LLMs) exhibit remarkably powerful capabilities. One of the crucial factors to achieve success is aligning the LLM's output with human preferences. This alignment process often requires only a small amount of data to efficiently enhance the LLM's performance. While effective, research in this area spans multiple domains, and the methods involved are relatively complex to understand. The relationships between different methods have been under-explored, limiting the development of the preference alignment. In light of this, we break down the existing popular alignment strategies into different components and provide a unified framework to study the current alignment strategies, thereby establishing connections among them. In this survey, we decompose all the strategies in preference learning into four components: model, data, feedback, and algorithm. This unified view offers an in-depth understanding of existing alignment algorithms and also opens up possibilities to synergize the strengths of different strategies. Furthermore, we present detailed working examples of prevalent existing algorithms to facilitate a comprehensive understanding for the readers. Finally, based on our unified perspective, we explore the challenges and future research directions for aligning large language models with human preferences.

Large language models (LLMs) have demonstrated remarkable multilingual capabilities, however, how to evaluate cross-lingual alignment remains underexplored. Existing alignment benchmarks primarily focus on sentence embeddings, but prior research has shown that neural models tend to induce a non-smooth representation space, which impact of semantic alignment evaluation on low-resource languages. Inspired by neuroscientific findings that similar information activates overlapping neuronal regions, we propose a novel Neuron State-Based Cross-Lingual Alignment (NeuronXA) to assess the cross-lingual a lignment capabilities of LLMs, which offers a more semantically grounded approach to assess cross-lingual alignment. We evaluate NeuronXA on several prominent multilingual LLMs (LLaMA, Qwen, Mistral, GLM, and OLMo) across two transfer tasks and three multilingual benchmarks. The results demonstrate that with only 100 parallel sentence pairs, NeuronXA achieves a Pearson correlation of 0.9556 with downstream tasks performance and 0.8514 with transferability. These findings demonstrate NeuronXA's effectiveness in assessing both cross-lingual alignment and transferability, even with a small dataset. This highlights its potential to advance cross-lingual alignment research and to improve the semantic understanding of multilingual LLMs.

The core challenge of de novo protein design lies in creating proteins with specific functions or properties, guided by certain conditions. Current models explore to generate protein using structural and evolutionary guidance, which only provide indirect conditions concerning functions and properties. However, textual annotations of proteins, especially the annotations for protein domains, which directly describe the protein's high-level functionalities, properties, and their correlation with target amino acid sequences, remain unexplored in the context of protein design tasks. In this paper, we propose Protein-Annotation Alignment Generation, PAAG, a multi-modality protein design framework that integrates the textual annotations extracted from protein database for controllable generation in sequence space. Specifically, within a multi-level alignment module, PAAG can explicitly generate proteins containing specific domains conditioned on the corresponding domain annotations, and can even design novel proteins with flexible combinations of different kinds of annotations. Our experimental results underscore the superiority of the aligned protein representations from PAAG over 7 prediction tasks. Furthermore, PAAG demonstrates a significant increase in generation success rate (24.7% vs 4.7% in zinc finger, and 54.3% vs 22.0% in the immunoglobulin domain) in comparison to the existing model. We anticipate that PAAG will broaden the horizons of protein design by leveraging the knowledge from between textual annotation and proteins.

English-centric large language models (LLMs) often show strong multilingual capabilities. However, the multilingual performance of these models remains unclear and is not thoroughly evaluated for many languages. Most benchmarks for multilinguality focus on classic NLP tasks, or cover a minimal number of languages. We introduce MEXA, a method for assessing the multilingual capabilities of pre-trained English-centric LLMs using parallel sentences, which are available for more languages than existing downstream tasks. MEXA leverages the fact that English-centric LLMs use English as a kind of pivot language in their intermediate layers. It computes the alignment between English and non-English languages using parallel sentences to evaluate the transfer of language understanding from English to other languages. This alignment can be used to estimate model performance in other languages. We conduct studies using various parallel datasets (FLORES-200 and Bible), models (Llama family, Gemma family, Mistral, and OLMo), and established downstream tasks (Belebele, m-MMLU, and m-ARC). We explore different methods to compute embeddings in decoder-only models. Our results show that MEXA, in its default settings, achieves a statistically significant average Pearson correlation of 0.90 with three established downstream tasks across nine models and two parallel datasets. This suggests that MEXA is a reliable method for estimating the multilingual capabilities of English-centric LLMs, providing a clearer understanding of their multilingual potential and the inner workings of LLMs. Leaderboard: https://huggingface.co/spaces/cis-lmu/Mexa, Code: https://github.com/cisnlp/Mexa.

It is essential for large language model (LLM) technology to serve many different cultural sub-communities in a manner that is acceptable to each community. However, research on LLM alignment has so far predominantly focused on predicting a unified response preference of annotators from certain regions. This paper aims to advance the development of alignment models with a more global outlook, that are able to accurately represent the preferences of subcommunities and do not exhibit excessive bias towards any of them. We focus on the development of reward models for this purpose and present a novel reward model training algorithm (SCPO) that can incorporate diverse cultural preferences in a balanced manner. Our method results in performance increases of the minority reward model of up to 7 points over the baseline model across two datasets, PRISM and GlobalOpinionQA, and across 7 countries. SCPO is up to 280% more training data-efficient than full-data finetuning of reward models. In addition, we perform analysis of bias by separately evaluating on the preference of subcommunities and show that excessive bias is mitigated via our weighting method. Our code is available at https://github.com/minsik-ai/Steerable-Cultural-Preference

The integration of large language models (LLMs) into medical practice holds transformative potential, yet their real-world clinical utility remains limited by critical alignment challenges: (1) a disconnect between static evaluation benchmarks and dynamic clinical cognitive needs, (2) difficulties in adapting to evolving, multi-source medical standards, and (3) the inability of conventional reward models to capture nuanced, multi-dimensional medical quality criteria. To address these gaps, we propose MR-RML (Multidimensional Rubric-oriented Reward Model Learning) via GPRC (Geometric Projection Reference Constraints), a novel alignment framework that integrates medical standards into a structured "Dimensions-Scenarios-Disciplines" matrix to guide data generation and model optimization. MR-RML introduces three core innovations: (1) a "Dimensions-Scenarios-Disciplines" medical standard system that embeds domain standards into the full training pipeline; (2) an independent multi-dimensional reward model that decomposes evaluation criteria, shifting from real-time rubric-based scoring to internalized reward modeling for improved consistency and cost-efficiency; (3) geometric projection reference constraints that transform medical cognitive logic into mathematical regularization, aligning scoring gradients with clinical reasoning and enabling synthetic data-driven training. Through extensive evaluations on the authoritative medical benchmark Healthbench, our method yields substantial performance gains over the base LLM Qwen-32B (45% on the full subset and 85% on Hard subset, respectively). It achieves a SOTA among open-source LLMs with scores of 62.7 (full subset) and 44.7 (hard subset), while also outperforming the majority of closed-source models.

Training-free source selection for LLM families with shared vocabularies arises in scientific string domains such as SMILES, protein, and genomic sequences, where candidate corpora share a tokenizer but differ in prediction targets. This creates an activation-dark regime: representation-similarity metrics can be uninformative without assumptions about label-conditioned error geometry, while classical update-geometry metrics are computationally prohibitive at vocabulary scale. We show that, in a shared-output head setting, representation metrics (e.g., CKA) are non-identifiable for transfer; models can share identical representations yet have orthogonal head updates. The key identity is that head Fisher alignment is exactly a cosine between kernel mean embeddings in the joint activation-error space, exposing activation, error, and coupling factors rather than requiring a materialized Fisher matrix. FisherSketch estimates this cosine directly in a single streaming pass, making K=128,256 head Fisher alignment practical with a 16 KB task signature (m=4096) and a 192 KB per-task streaming state, small enough to store next to a model hash, but encoding transfer-relevant update structure. Beyond source selection, the same signatures and marginals provide a diagnostic instrument for studying whether LLM task similarity is driven by activations, errors, or their coupling; shared-parameter and internal-layer validations, together with Llama-3.1-8B verbalizer-shift experiments, show that FisherSketch remains informative when activation similarity cannot distinguish tasks.

Word alignment, which aims to align translationally equivalent words between source and target sentences, plays an important role in many natural language processing tasks. Current unsupervised neural alignment methods focus on inducing alignments from neural machine translation models, which does not leverage the full context in the target sequence. In this paper, we propose Mask-Align, a self-supervised word alignment model that takes advantage of the full context on the target side. Our model masks out each target token and predicts it conditioned on both source and the remaining target tokens. This two-step process is based on the assumption that the source token contributing most to recovering the masked target token should be aligned. We also introduce an attention variant called leaky attention, which alleviates the problem of unexpected high cross-attention weights on special tokens such as periods. Experiments on four language pairs show that our model outperforms previous unsupervised neural aligners and obtains new state-of-the-art results.

Large Language Models (LLMs) are increasingly adopted as conversational assistants in genomics, where they are mainly used to reason over biological knowledge, annotations, and analysis outputs through natural language interfaces. However, existing benchmarks either focus on specialized DNA models trained for sequence prediction or evaluate biological knowledge using text-only questions, leaving the behavior of general-purpose LLMs when directly exposed to raw genome sequences underexplored. We introduce GenomeQA, a benchmark designed to provide a controlled evaluation setting for general-purpose LLMs on sequence-based genome inference tasks. GenomeQA comprises 5,200 samples drawn from multiple biological databases, with sequence lengths ranging from 6 to 1,000 base pairs (bp), spanning six task families: Enhancer and Promoter Identification, Splice Site Identification, Taxonomic Classification, Histone Mark Prediction, Transcription Factor Binding Site Prediction, and TF Motif Prediction. Across six frontier LLMs, we find that models consistently outperform random baselines and can exploit local sequence signals such as GC content and short motifs, while performance degrades on tasks that require more indirect or multi-step inference over sequence patterns. GenomeQA establishes a diagnostic benchmark for studying and improving the use of general-purpose LLMs on raw genomic sequences.

In this study, we introduce CT-LLM, a 2B large language model (LLM) that illustrates a pivotal shift towards prioritizing the Chinese language in developing LLMs. Uniquely initiated from scratch, CT-LLM diverges from the conventional methodology by primarily incorporating Chinese textual data, utilizing an extensive corpus of 1,200 billion tokens, including 800 billion Chinese tokens, 300 billion English tokens, and 100 billion code tokens. This strategic composition facilitates the model's exceptional proficiency in understanding and processing Chinese, a capability further enhanced through alignment techniques. Demonstrating remarkable performance on the CHC-Bench, CT-LLM excels in Chinese language tasks, and showcases its adeptness in English through SFT. This research challenges the prevailing paradigm of training LLMs predominantly on English corpora and then adapting them to other languages, broadening the horizons for LLM training methodologies. By open-sourcing the full process of training a Chinese LLM, including a detailed data processing procedure with the obtained Massive Appropriate Pretraining Chinese Corpus (MAP-CC), a well-chosen multidisciplinary Chinese Hard Case Benchmark (CHC-Bench), and the 2B-size Chinese Tiny LLM (CT-LLM), we aim to foster further exploration and innovation in both academia and industry, paving the way for more inclusive and versatile language models.

Recent works have demonstrated the effectiveness of self-alignment in which a large language model is, by itself, aligned to follow general instructions through the automatic generation of instructional data using a handful of human-written seeds. Instead of general alignment, in this work, we focus on self-alignment for expert domain specialization (e.g., biomedicine), discovering it to be very effective for improving zero-shot and few-shot performance in target domains of interest. As a preliminary, we first present the benchmark results of existing aligned models within a specialized domain, which reveals the marginal effect that "generic" instruction-following training has on downstream expert domains' performance. To remedy this, we explore self-specialization that leverages domain-specific unlabelled data and a few labeled seeds for the self-alignment process. When augmented with retrieval to reduce hallucination and enhance concurrency of the alignment, self-specialization offers an effective (and efficient) way of "carving out" an expert model out of a "generalist", pre-trained LLM where different domains of expertise are originally combined in a form of "superposition". Our experimental results on a biomedical domain show that our self-specialized model (30B) outperforms its base model, MPT-30B by a large margin and even surpasses larger popular models based on LLaMA-65B, highlighting its potential and practicality for specialization, especially considering its efficiency in terms of data and parameters.

Large language models (LLMs) have shown impressive few-shot generalization on many tasks via in-context learning (ICL). Despite their success in showing such emergent abilities, the scale and complexity of larger models also lead to unprecedentedly high computational demands and deployment challenges. In reaction, researchers explore transferring the powerful capabilities of larger models to more efficient and compact models by typically aligning the output of smaller models with that of larger models. Existing methods either train smaller models on the generated outputs of larger models or to imitate their token-level probability distributions. However, these distillation methods pay little to no attention to the input part, which also plays a crucial role in ICL. Based on the finding that the performance of ICL is highly sensitive to the selection of demonstration examples, we propose Bidirectional Alignment (BiAlign) to fully leverage the models' preferences for ICL examples to improve the ICL abilities of smaller models. Specifically, we introduce the alignment of input preferences between smaller and larger models by incorporating a novel ranking loss, in addition to aligning the token-level output distribution. With extensive experiments and analysis, we demonstrate that BiAlign can consistently outperform existing baselines on a variety of tasks including language understanding, reasoning, and coding.

Aligning large language models (LLMs) with human preferences has achieved remarkable success. However, existing Chinese preference datasets are limited by small scale, narrow domain coverage, and lack of rigorous data validation. Additionally, the reliance on human annotators for instruction and response labeling significantly constrains the scalability of human preference datasets. To address these challenges, we design an LLM-based Chinese preference dataset annotation pipeline with no human intervention. Specifically, we crawled and carefully filtered 92k high-quality Chinese queries and employed 15 mainstream LLMs to generate and score chosen-rejected response pairs. Based on it, we introduce COIG-P (Chinese Open Instruction Generalist - Preference), a high-quality, large-scale Chinese preference dataset, comprises 1,009k Chinese preference pairs spanning 6 diverse domains: Chat, Code, Math, Logic, Novel, and Role. Building upon COIG-P, to reduce the overhead of using LLMs for scoring, we trained a 8B-sized Chinese Reward Model (CRM) and meticulously constructed a Chinese Reward Benchmark (CRBench). Evaluation results based on AlignBench liu2024alignbenchbenchmarkingchinesealignment show that that COIG-P significantly outperforms other Chinese preference datasets, and it brings significant performance improvements ranging from 2% to 12% for the Qwen2/2.5 and Infinity-Instruct-3M-0625 model series, respectively. The results on CRBench demonstrate that our CRM has a strong and robust scoring ability. We apply it to filter chosen-rejected response pairs in a test split of COIG-P, and our experiments show that it is comparable to GPT-4o in identifying low-quality samples while maintaining efficiency and cost-effectiveness. Our codes and data are released in https://github.com/multimodal-art-projection/COIG-P.

As the model size of pre-trained language models (PLMs) grows rapidly, full fine-tuning becomes prohibitively expensive for model training and storage. In vision-and-language (VL), parameter-efficient tuning (PET) techniques are proposed to integrate modular modifications (e.g., Adapter and LoRA) into encoder-decoder PLMs. By tuning a small set of trainable parameters, these techniques perform on par with full fine-tuning. However, excessive modular modifications and neglecting the functionality gap between the encoders and decoders can lead to performance degradation, while existing PET techniques (e.g., VL-Adapter) overlook these critical issues. In this paper, we propose a Vision-and-Language Parameter-Efficient Tuning (VL-PET) framework to impose effective control over modular modifications via a novel granularity-controlled mechanism. Considering different granularity-controlled matrices generated by this mechanism, a variety of model-agnostic VL-PET modules can be instantiated from our framework for better efficiency and effectiveness trade-offs. We further propose lightweight PET module designs to enhance VL alignment and modeling for the encoders and maintain text generation for the decoders. Extensive experiments conducted on four image-text tasks and four video-text tasks demonstrate the efficiency, effectiveness and transferability of our VL-PET framework. In particular, our VL-PET-large with lightweight PET module designs significantly outperforms VL-Adapter by 2.92% (3.41%) and LoRA by 3.37% (7.03%) with BART-base (T5-base) on image-text tasks. Furthermore, we validate the enhanced effect of employing our VL-PET designs on existing PET techniques, enabling them to achieve significant performance improvements. Our code is available at https://github.com/HenryHZY/VL-PET.

Protein homology search underlies function annotation, structure prediction, and evolutionary analysis, but remains challenging in the "twilight zone," where global sequence similarity is weak and classical alignment methods lose sensitivity. Protein language models provide context-aware representations that could improve alignment sensitivity in this regime. However, prior protein embedding-based retrieval pipelines often pool these representations into a single vector, potentially obscuring local motifs, domains, or conserved residues that reveal remote homology. We introduce ProtoCol, a model which represents proteins as sets of residue embeddings and uses ColBERT-style late interaction to test whether residue-level comparison improves homolog retrieval. ProtoCol encodes proteins independently, keeps candidate representations pre-computable, and scores candidates with MaxSim over residue embeddings. On SCOPe superfamily and Pfam clan benchmarks, ProtoCol outperforms sequence-composition, alignment-based, pooled PLM, and trained single-vector baselines, supporting late interaction as an effective retrieval layer for remote homology search.

Current alignment evaluation mostly measures whether models encode dangerous concepts and whether they refuse harmful requests. Both miss the layer where alignment often operates: routing from concept detection to behavioral policy. We study political censorship in Chinese-origin language models as a natural experiment, using probes, surgical ablations, and behavioral tests across nine open-weight models from five labs. Three findings follow. First, probe accuracy alone is non-diagnostic: political probes, null controls, and permutation baselines can all reach 100%, so held-out category generalization is the informative test. Second, surgical ablation reveals lab-specific routing. Removing the political-sensitivity direction eliminates censorship and restores accurate factual output in most models tested, while one model confabulates because its architecture entangles factual knowledge with the censorship mechanism. Cross-model transfer fails, indicating that routing geometry is model- and lab-specific. Third, refusal is no longer the dominant censorship mechanism. Within one model family, hard refusal falls to zero while narrative steering rises to the maximum, making censorship invisible to refusal-only benchmarks. These results support a three-stage descriptive framework: detect, route, generate. Models often retain the relevant knowledge; alignment changes how that knowledge is expressed. Evaluations that audit only detection or refusal therefore miss the routing mechanism that most directly determines behavior.

We introduce SteeringControl, a benchmark for evaluating representation steering methods across core alignment objectives--bias, harmful generation, and hallucination--and their effects on secondary behaviors such as sycophancy and commonsense morality. While prior alignment work often highlights truthfulness or reasoning ability to demonstrate the side effects of representation steering, we find there are many unexplored tradeoffs not yet understood in a systematic way. We collect a dataset of safety-relevant primary and secondary behaviors to evaluate steering effectiveness and behavioral entanglement centered around five popular steering methods. To enable this, we craft a modular steering framework based on unique components that serve as the building blocks of many existing methods. Our results on Qwen-2.5-7B and Llama-3.1-8B find that strong steering performance is dependent on the specific combination of steering method, model, and targeted behavior, and that severe concept entanglement can result from poor combinations of these three as well. We release our code here: https://github.com/wang-research-lab/SteeringControl.git.

Post-training alignment is often shallow, eroding under fine-tuning. Whether midtraining interventions, cleanly isolated from post-training, can produce durable alignment remains untested. We test this via constitutional midtraining: inserting principled, values-based content into midtraining against a replay-only control at 120B scale. Our 394M-token constitutional corpus, built from Anthropic's Constitution, uses a 2x2 factorial design (curriculum ordering x deliberative reasoning) to produce four constitutionally midtrained conditions plus a control, evaluated on self-generated and established benchmarks including alignment under pressure, value conflict resolution, blackmail, and emergent misalignment across three stages: post-midtraining, post-SFT, and post-benign fine-tuning. Constitutionally midtrained models outperform the control on alignment generalization and durability, notably on blackmail: SFT instills a blackmail propensity in all models, but constitutional midtraining blunts it, with the advantage surviving benign fine-tuning (-17.5pp). This durability does not extend to settings requiring active resistance to in-context pressure or conflict, where the advantage attenuates after SFT. The presence of constitutional content at midtraining also matters more than its structure, and constitutional midtraining incurs no cost, on average, on the capabilities we test (MMLU, ARC-Easy, piqa, GSM8K) at any stage. A modest amount of constitutional content at midtraining could therefore yield broad, persistent alignment gains, offering a cheap, complementary addition to SFT-centered pipelines. Code, data, and models are available.

Neural networks can accurately forecast complex dynamical systems, yet how they internally represent underlying latent geometry remains poorly understood. We study neural forecasters through the lens of representational alignment, introducing anchor-based, geometry-agnostic relative embeddings that remove rotational and scaling ambiguities in latent spaces. Applying this framework across seven canonical dynamical systems - ranging from periodic to chaotic - we reveal reproducible family-level structure: multilayer perceptrons align with other MLPs, recurrent networks with RNNs, while transformers and echo-state networks achieve strong forecasts despite weaker alignment. Alignment generally correlates with forecasting accuracy, yet high accuracy can coexist with low alignment. Relative geometry thus provides a simple, reproducible foundation for comparing how model families internalize and represent dynamical structure.

Alignment in LLMs is more brittle than commonly assumed: misalignment can be triggered by adversarial prompts, benign fine-tuning, emergent misalignment, and goal misgeneralization. Recent evidence suggests that some misalignment behaviors are encoded as linear structure in activation space, making it tractable via steering, while safety alignment has been shown to govern the first few output tokens primarily, leaving subsequent generation unguarded. These findings motivate activation steering as a lightweight runtime defense that continuously corrects misaligned activations throughout generation. We evaluate three methods: Steer-With-Fixed-Coeff (SwFC), which applies uniform additive steering, and two novel projection-aware methods, Steer-to-Target-Projection (StTP) and Steer-to-Mirror-Projection (StMP), that use a logistic regression decision boundary to selectively intervene only on tokens whose activations fall below distributional thresholds. Using malicious system prompts as a controlled proxy for misalignment, we evaluate under two threat models (dishonesty and dismissiveness) and two architectures (Llama-3.3-70B-Instruct, Qwen3-32B). All methods substantially recover target traits (honesty and compassion) while preserving coherence. StTP and StMP better maintain general capabilities (MMLU, MT-Bench, AlpacaEval) and produce less repetition in multi-turn conversations.

Current genomic foundation models (GFMs) rely on extensive neural computation to implicitly approximate conserved biological motifs from single-nucleotide inputs. We propose Gengram, a conditional memory module that introduces an explicit and highly efficient lookup primitive for multi-base motifs via a genomic-specific hashing scheme, establishing genomic "syntax". Integrated into the backbone of state-of-the-art GFMs, Gengram achieves substantial gains (up to 14%) across several functional genomics tasks. The module demonstrates robust architectural generalization, while further inspection of Gengram's latent space reveals the emergence of meaningful representations that align closely with fundamental biological knowledge. By establishing structured motif memory as a modeling primitive, Gengram simultaneously boosts empirical performance and mechanistic interpretability, providing a scalable and biology-aligned pathway for the next generation of GFMs. The code is available at https://github.com/zhejianglab/Genos, and the model checkpoint is available at https://huggingface.co/ZhejiangLab/Gengram.

Despite their impressive capabilities, aligned large language models (LLMs) often generate outputs that lack diversity. What drives this stability in the generation? We investigate this phenomenon through the lens of probability concentration in the model's output distribution. To quantify this concentration, we introduce the Branching Factor (BF) -- a token-invariant measure of the effective number of plausible next steps during generation. Our empirical analysis reveals two key findings: (1) BF often decreases as generation progresses, suggesting that LLMs become more predictable as they generate. (2) alignment tuning substantially sharpens the model's output distribution from the outset, reducing BF by nearly an order of magnitude (e.g., from 12 to 1.2) relative to base models. This stark reduction helps explain why aligned models often appear less sensitive to decoding strategies. Building on this insight, we find this stability has surprising implications for complex reasoning. Aligned Chain-of-Thought (CoT) models (e.g., DeepSeek-distilled models), for instance, leverage this effect; by generating longer reasoning chains, they push generation into later, more deterministic (lower BF) stages, resulting in more stable outputs. We hypothesize that alignment tuning does not fundamentally change a model's behavior, but instead steers it toward stylistic tokens (e.g., "Sure") that unlock low-entropy trajectories already present in the base model. This view is supported by nudging experiments, which show that prompting base models with such tokens can similarly reduce BF. Together, our findings establish BF as a powerful diagnostic for understanding and controlling LLM outputs - clarifying how alignment reduces variability, how CoT promotes stable generations, and how base models can be steered away from diversity.

The rapid development of large language models (LLMs) has not only provided numerous opportunities but also presented significant challenges. This becomes particularly evident when LLMs inadvertently generate harmful or toxic content, either unintentionally or because of intentional inducement. Existing alignment methods usually direct LLMs toward the favorable outcomes by utilizing human-annotated, flawless instruction-response pairs. Conversely, this study proposes a novel alignment technique based on mistake analysis, which deliberately exposes LLMs to erroneous content to learn the reasons for mistakes and how to avoid them. In this case, mistakes are repurposed into valuable data for alignment, effectively helping to avoid the production of erroneous responses. Without external models or human annotations, our method leverages a model's intrinsic ability to discern undesirable mistakes and improves the safety of its generated responses. Experimental results reveal that our method outperforms existing alignment approaches in enhancing model safety while maintaining the overall utility.

Alignment of large language models (LLMs) involves training models on preference-contrastive output pairs to adjust their responses according to human preferences. To obtain such contrastive pairs, traditional methods like RLHF and RLAIF rely on limited contrasting patterns, such as varying model variants or decoding temperatures. This singularity leads to two issues: (1) alignment is not comprehensive; and thereby (2) models are susceptible to jailbreaking attacks. To address these issues, we investigate how to construct more comprehensive and diversified contrasting patterns to enhance preference data (RQ1) and verify the impact of the diversification of contrasting patterns on model alignment (RQ2). For RQ1, we propose PopAlign, a framework that integrates diversified contrasting patterns across the prompt, model, and pipeline levels, introducing six contrasting strategies that do not require additional feedback labeling procedures. Regarding RQ2, we conduct thorough experiments demonstrating that PopAlign significantly outperforms existing methods, leading to more comprehensive alignment.

Aligned representations across languages is a desired property in multilingual large language models (mLLMs), as alignment can improve performance in cross-lingual tasks. Typically alignment requires fine-tuning a model, which is computationally expensive, and sizable language data, which often may not be available. A data-efficient alternative to fine-tuning is model interventions -- a method for manipulating model activations to steer generation into the desired direction. We analyze the effect of a popular intervention (finding experts) on the alignment of cross-lingual representations in mLLMs. We identify the neurons to manipulate for a given language and introspect the embedding space of mLLMs pre- and post-manipulation. We show that modifying the mLLM's activations changes its embedding space such that cross-lingual alignment is enhanced. Further, we show that the changes to the embedding space translate into improved downstream performance on retrieval tasks, with up to 2x improvements in top-1 accuracy on cross-lingual retrieval.

This article introduces contrastive alignment instructions (AlignInstruct) to address two challenges in machine translation (MT) on large language models (LLMs). One is the expansion of supported languages to previously unseen ones. The second relates to the lack of data in low-resource languages. Model fine-tuning through MT instructions (MTInstruct) is a straightforward approach to the first challenge. However, MTInstruct is limited by weak cross-lingual signals inherent in the second challenge. AlignInstruct emphasizes cross-lingual supervision via a cross-lingual discriminator built using statistical word alignments. Our results based on fine-tuning the BLOOMZ models (1b1, 3b, and 7b1) in up to 24 unseen languages showed that: (1) LLMs can effectively translate unseen languages using MTInstruct; (2) AlignInstruct led to consistent improvements in translation quality across 48 translation directions involving English; (3) Discriminator-based instructions outperformed their generative counterparts as cross-lingual instructions; (4) AlignInstruct improved performance in 30 zero-shot directions.

Recent research has evidenced the significant potentials of Large Language Models (LLMs) in handling challenging tasks within 3D scenes. However, current models are constrained to addressing object-centric tasks, where each question-answer pair focuses solely on an individual object. In real-world applications, users may pose queries involving multiple objects or expect for answers that precisely reference various objects. We introduce the use of object identifiers to freely reference objects during a conversation. While this solution appears straightforward, it presents two main challenges: 1) How to establish a reliable one-to-one correspondence between each object and its identifier? 2) How to incorporate complex spatial relationships among dozens of objects into the embedding space of the LLM? To address these challenges, we propose a two-stage alignment method, which involves learning an attribute-aware token and a relation-aware token for each object. These tokens capture the object's attributes and spatial relationships with surrounding objects in the 3D scene. Once the alignment is established, we can fine-tune our model on various downstream tasks using instruction tuning. Experiments conducted on traditional datasets like ScanQA, ScanRefer, and Nr3D/Sr3D showcase the effectiveness of our proposed method. Additionally, we create a 3D scene captioning dataset annotated with rich object identifiers, with the assistant of GPT-4. This dataset aims to further explore the capability of object identifiers in effective object referencing and precise scene understanding.

With the rapid development of large language models (LLMs), they are not only used as general-purpose AI assistants but are also customized through further fine-tuning to meet the requirements of different applications. A pivotal factor in the success of current LLMs is the alignment process. Current alignment methods, such as supervised fine-tuning (SFT) and reinforcement learning from human feedback (RLHF), focus on training-time alignment and are often complex and cumbersome to implement. Therefore, we develop InferAligner, a novel inference-time alignment method that utilizes cross-model guidance for harmlessness alignment. InferAligner utilizes safety steering vectors extracted from safety-aligned model to modify the activations of the target model when responding to harmful inputs, thereby guiding the target model to provide harmless responses. Experimental results show that our method can be very effectively applied to domain-specific models in finance, medicine, and mathematics, as well as to multimodal large language models (MLLMs) such as LLaVA. It significantly diminishes the Attack Success Rate (ASR) of both harmful instructions and jailbreak attacks, while maintaining almost unchanged performance in downstream tasks.

Long-context large language models (LLMs) are prone to be distracted by irrelevant contexts. The reason for distraction remains poorly understood. In this paper, we first identify the contextual heads, a special group of attention heads that control the overall attention of the LLM. Then, we demonstrate that distraction arises when contextual heads fail to allocate sufficient attention to relevant contexts and can be mitigated by increasing attention to these contexts. We further identify focus directions, located at the key and query activations of these heads, which enable them to allocate more attention to relevant contexts without explicitly specifying which context is relevant. We comprehensively evaluate the effect of focus direction on various long-context tasks and find out focus directions could help to mitigate the poor task alignment of the long-context LLMs. We believe our findings could promote further research on long-context LLM alignment.