Intrinsically disordered regions (IDRs) account for one-third of the human proteome and play essential biological roles. However, predicting the functions of IDRs remains a major challenge due to their lack of stable structures, rapid sequence evolution, and context-dependent behavior. Many predictors of protein function neglect or underperform on IDRs. Recent advances in computational biology and machine learning, including protein language models, alignment-free approaches, and IDR-specific methods, have revealed conserved bulk features and local motifs within IDRs that are linked to function. This review highlights emerging computational methods that map the sequence-function relationship in IDRs, outlines critical challenges in IDR function annotation, and proposes a community-driven framework to accelerate interpretable functional predictions for IDRs.
The widespread adoption of Large Language Models (LLMs) for code generation, exemplified by GitHub Copilot\footnote{A coding extension powered by a Code-LLM to assist in code completion tasks} surpassing a million users, highlights the transformative potential of these tools in improving developer productivity. However, this rapid growth also underscores critical concerns regarding the quality, safety, and reliability of the code they generate. As Code-LLMs evolve, they face significant challenges, including the diminishing returns of model scaling and the scarcity of new, high-quality training data. To address these issues, this paper introduces Adversarial Knowledge Distillation (AKD), a novel approach that leverages adversarially generated synthetic datasets to distill the capabilities of larger models into smaller, more efficient ones. By systematically stress-testing and refining the reasoning capabilities of Code-LLMs, AKD provides a framework for enhancing model robustness, reliability, and security while improving their parameter-efficiency. We believe this work represents a critical step toward ensuring dependable automated code generation within the constraints of existing data and the cost-efficiency of model execution.
With the increasing prevalence of artificial intelligence, careful evaluation of inherent biases needs to be conducted to form the basis for alleviating the effects these predispositions can have on users. Large language models (LLMs) are predominantly used by many as a primary source of information for various topics. LLMs frequently make factual errors, fabricate data (hallucinations), or present biases, exposing users to misinformation and influencing opinions. Educating users on their risks is key to responsible use, as bias, unlike hallucinations, cannot be caught through data verification. We quantify the political bias of popular LLMs in the context of the recent vote of the German Bundestag using the score produced by the Wahl-O-Mat. This metric measures the alignment between an individual's political views and the positions of German political parties. We compare the models' alignment scores to identify factors influencing their political preferences. Doing so, we discover a bias toward left-leaning parties, most dominant in larger LLMs. Also, we find that the language we use to communicate with the models affects their political views. Additionally, we analyze the influence of a model's origin and release date and compare the results to the outcome of the recent vote of the Bundestag. Our results imply that LLMs are prone to exhibiting political bias. Large corporations with the necessary means to develop LLMs, thus, knowingly or unknowingly, have a responsibility to contain these biases, as they can influence each voter's decision-making process and inform public opinion in general and at scale.
Aligning language models with human preferences is critical for real-world deployment, but existing methods often require large amounts of high-quality human annotations. Aiming at a data-efficient alignment method, we propose Stackelberg Game Preference Optimization (SGPO), a framework that models alignment as a two-player Stackelberg game, where a policy (leader) optimizes against a worst-case preference distribution (follower) within an $\epsilon$-Wasserstein ball, ensuring robustness to (self-)annotation noise and distribution shifts. SGPO guarantees $O(\epsilon)$-bounded regret, unlike Direct Preference Optimization (DPO), which suffers from linear regret growth in the distribution mismatch. We instantiate SGPO with the Stackelberg Self-Annotated Preference Optimization (SSAPO) algorithm, which iteratively self-annotates preferences and adversarially reweights synthetic annotated preferences. Using only 2K seed preferences, from the UltraFeedback dataset, i.e., 1/30 of human labels in the dataset, our method achieves 35.82% GPT-4 win-rate with Mistral-7B and 40.12% with Llama3-8B-Instruct within three rounds of SSAPO.
Multimodal Vision Language Models (VLMs) have emerged as a transformative topic at the intersection of computer vision and natural language processing, enabling machines to perceive and reason about the world through both visual and textual modalities. For example, models such as CLIP, Claude, and GPT-4V demonstrate strong reasoning and understanding abilities on visual and textual data and beat classical single modality vision models on zero-shot classification [93]. With their rapid advancements in research and growing popularity in various applications, we provide a comprehensive survey of VLMs. Specifically, we provide a systematic overview of VLMs in the following aspects: [1] model information of the major VLMs developed up to 2025; [2] the transition of VLM architectures and the newest VLM alignment methods; [3] summary and categorization of the popular benchmarks and evaluation metrics of VLMs; [4] the challenges and issues faced by current VLMs such as hallucination, alignment, fairness, and safety. Detailed collections including papers and model repository links are listed in https://github.com/zli12321/Vision-Language-Models-Overview.
Language model alignment is a critical step in training modern generative language models. Alignment targets to improve win rate of a sample from the aligned model against the base model. Today, we are increasingly using inference-time algorithms (e.g., Best-of-N, controlled decoding, tree search) to decode from language models rather than standard sampling. We show that this train/test mismatch makes standard RLHF framework sub-optimal in view of such inference-time methods. To this end, we propose a framework for inference-aware alignment (InfAlign), which aims to optimize inference-time win rate of the aligned policy against the base model. We prove that for any inference-time decoding procedure, the optimal aligned policy is the solution to the standard RLHF problem with a transformation of the reward. This motivates us to provide the calibrate-and-transform RL (InfAlign-CTRL) algorithm to solve this problem, which involves a reward calibration step and a KL-regularized reward maximization step with a transformation of the calibrated reward. For best-of-N sampling and best-of-N jailbreaking, we propose specific transformations offering up to 3-8% improvement on inference-time win rates. Finally, we also show that our proposed reward calibration method is a strong baseline for optimizing standard win rate.
Accurate and consistent evaluation is crucial for decision-making across numerous fields, yet it remains a challenging task due to inherent subjectivity, variability, and scale. Large Language Models (LLMs) have achieved remarkable success across diverse domains, leading to the emergence of "LLM-as-a-Judge," where LLMs are employed as evaluators for complex tasks. With their ability to process diverse data types and provide scalable, cost-effective, and consistent assessments, LLMs present a compelling alternative to traditional expert-driven evaluations. However, ensuring the reliability of LLM-as-a-Judge systems remains a significant challenge that requires careful design and standardization. This paper provides a comprehensive survey of LLM-as-a-Judge, addressing the core question: How can reliable LLM-as-a-Judge systems be built? We explore strategies to enhance reliability, including improving consistency, mitigating biases, and adapting to diverse assessment scenarios. Additionally, we propose methodologies for evaluating the reliability of LLM-as-a-Judge systems, supported by a novel benchmark designed for this purpose. To advance the development and real-world deployment of LLM-as-a-Judge systems, we also discussed practical applications, challenges, and future directions. This survey serves as a foundational reference for researchers and practitioners in this rapidly evolving field.
Self-play methods have demonstrated remarkable success in enhancing model capabilities across various domains. In the context of Reinforcement Learning from Human Feedback (RLHF), self-play not only boosts Large Language Model (LLM) performance but also overcomes the limitations of traditional Bradley-Terry (BT) model assumptions by finding the Nash equilibrium (NE) of a preference-based, two-player constant-sum game. However, existing methods either guarantee only average-iterate convergence, incurring high storage and inference costs, or converge to the NE of a regularized game, failing to accurately reflect true human preferences. In this paper, we introduce Magnetic Preference Optimization (MPO), a novel approach capable of achieving last-iterate convergence to the NE of the original game, effectively overcoming the limitations of existing methods. Building upon Magnetic Mirror Descent (MMD), MPO attains a linear convergence rate, making it particularly suitable for fine-tuning LLMs. To ensure our algorithm is both theoretically sound and practically viable, we present a simple yet effective implementation that adapts the theoretical insights to the RLHF setting. Empirical results demonstrate that MPO can significantly enhance the performance of LLMs, highlighting the potential of self-play methods in alignment.
Large language models have achieved remarkable capabilities, but aligning their outputs with human values and preferences remains a significant challenge. Existing alignment methods primarily focus on positive examples while overlooking the importance of negative responses in guiding models away from undesirable behaviors. For instance, the widely-used alignment datasets reveals a scarcity of explicit negative examples that contradict human values, hindering its ability to discourage harmful or biased outputs during training. To address this limitation, we propose NEAT, i.e., NEgative-prompt-driven AlignmenT, to introduce negative prompts to generate undesirable responses alongside positive examples during the optimization process. NEAT explicitly penalizes the model for producing harmful outputs, guiding it not only toward desirable behaviors but also steering it away from generating undesirable, biased responses. This dual feedback mechanism enables better alignment with human preferences, crucial in contexts where avoiding harm is paramount. Starting from a pre-trained language model, NEAT performs online alignment by incorporating a ranking loss derived from an expanded preference dataset containing both positive and negative examples. Extensive experiments validate NEAT's effectiveness in significantly enhancing language models' alignment with human values and preferences.
As large vision-language models (LVLMs) evolve rapidly, the demand for high-quality and diverse data to align these models becomes increasingly crucial. However, the creation of such data with human supervision proves costly and time-intensive. In this paper, we investigate the efficacy of AI feedback to scale supervision for aligning LVLMs. We introduce VLFeedback, the first large-scale vision-language feedback dataset, comprising over 82K multi-modal instructions and comprehensive rationales generated by off-the-shelf models without human annotations. To evaluate the effectiveness of AI feedback for vision-language alignment, we train Silkie, an LVLM fine-tuned via direct preference optimization on VLFeedback. Silkie showcases exceptional performance regarding helpfulness, visual faithfulness, and safety metrics. It outperforms its base model by 6.9\% and 9.5\% in perception and cognition tasks, reduces hallucination issues on MMHal-Bench, and exhibits enhanced resilience against red-teaming attacks. Furthermore, our analysis underscores the advantage of AI feedback, particularly in fostering preference diversity to deliver more comprehensive improvements. Our dataset, training code and models are available at https://vlf-silkie.github.io.
Machine learning models often struggle with distribution shifts in real-world scenarios, whereas humans exhibit robust adaptation. Models that better align with human perception may achieve higher out-of-distribution generalization. In this study, we investigate how various characteristics of large-scale computer vision models influence their alignment with human capabilities and robustness. Our findings indicate that increasing model and data size and incorporating rich semantic information and multiple modalities enhance models' alignment with human perception and their overall robustness. Our empirical analysis demonstrates a strong correlation between out-of-distribution accuracy and human alignment.
Large language models (LLMs) have shown promise in representing individuals and communities, offering new ways to study complex social dynamics. However, effectively aligning LLMs with specific human groups and systematically assessing the fidelity of the alignment remains a challenge. This paper presents a robust framework for aligning LLMs with online communities via instruction-tuning and comprehensively evaluating alignment across various aspects of language, including authenticity, emotional tone, toxicity, and harm. We demonstrate the utility of our approach by applying it to online communities centered on dieting and body image. We administer an eating disorder psychometric test to the aligned LLMs to reveal unhealthy beliefs and successfully differentiate communities with varying levels of eating disorder risk. Our results highlight the potential of LLMs in automated moderation and broader applications in public health and social science research.
Color is integral to human experience, influencing emotions, decisions, and perceptions. This paper presents a comparative analysis of various color models' alignment with human visual perception. The study evaluates color models such as RGB, HSV, HSL, XYZ, CIELAB, and CIELUV to assess their effectiveness in accurately representing how humans perceive color. We evaluate each model based on its ability to accurately reflect visual color differences and dominant palette extraction compatible with the human eye. In image processing, accurate assessment of color difference is essential for applications ranging from digital design to quality control. Current color difference metrics do not always match how people see colors, causing issues in accurately judging subtle differences. Understanding how different color models align with human visual perception is crucial for various applications in image processing, digital media, and design.
The dominant framework for alignment of large language models (LLM), whether through reinforcement learning from human feedback or direct preference optimisation, is to learn from preference data. This involves building datasets where each element is a quadruplet composed of a prompt, two independent responses (completions of the prompt) and a human preference between the two independent responses, yielding a preferred and a dis-preferred response. Such data is typically scarce and expensive to collect. On the other hand, \emph{single-trajectory} datasets where each element is a triplet composed of a prompt, a response and a human feedback is naturally more abundant. The canonical element of such datasets is for instance an LLM's response to a user's prompt followed by a user's feedback such as a thumbs-up/down. Consequently, in this work, we propose DRO, or \emph{Direct Reward Optimisation}, as a framework and associated algorithms that do not require pairwise preferences. DRO uses a simple mean-squared objective that can be implemented in various ways. We validate our findings empirically, using T5 encoder-decoder language models, and show DRO's performance over selected baselines such as Kahneman-Tversky Optimization (KTO). Thus, we confirm that DRO is a simple and empirically compelling method for single-trajectory policy optimisation.
Aligning language models with human preferences is crucial for reducing errors and biases in these models. Alignment techniques, such as reinforcement learning from human feedback (RLHF), are typically cast as optimizing a tradeoff between human preference rewards and a proximity regularization term that encourages staying close to the unaligned model. Selecting an appropriate level of regularization is critical: insufficient regularization can lead to reduced model capabilities due to reward hacking, whereas excessive regularization hinders alignment. Traditional methods for finding the optimal regularization level require retraining multiple models with varying regularization strengths. This process, however, is resource-intensive, especially for large models. To address this challenge, we propose decoding-time realignment (DeRa), a simple method to explore and evaluate different regularization strengths in aligned models without retraining. DeRa enables control over the degree of alignment, allowing users to smoothly transition between unaligned and aligned models. It also enhances the efficiency of hyperparameter tuning by enabling the identification of effective regularization strengths using a validation dataset.
In recent research on large language models (LLMs), there has been a growing emphasis on aligning these models with human values to reduce the impact of harmful content. However, current alignment methods often rely solely on singular forms of human feedback, such as preferences, annotated labels, or natural language critiques, overlooking the potential advantages of combining these feedback types. This limitation leads to suboptimal performance, even when ample training data is available. In this paper, we introduce Constructive and Diverse Feedback (CDF) as a novel method to enhance LLM alignment, inspired by constructivist learning theory. Our approach involves collecting three distinct types of feedback tailored to problems of varying difficulty levels within the training dataset. Specifically, we exploit critique feedback for easy problems, refinement feedback for medium problems, and preference feedback for hard problems. By training our model with this diversified feedback, we achieve enhanced alignment performance while using less training data. To assess the effectiveness of CDF, we evaluate it against previous methods in three downstream tasks: question answering, dialog generation, and text summarization. Experimental results demonstrate that CDF achieves superior performance even with a smaller training dataset.
Ensuring alignment, which refers to making models behave in accordance with human intentions [1,2], has become a critical task before deploying large language models (LLMs) in real-world applications. For instance, OpenAI devoted six months to iteratively aligning GPT-4 before its release [3]. However, a major challenge faced by practitioners is the lack of clear guidance on evaluating whether LLM outputs align with social norms, values, and regulations. This obstacle hinders systematic iteration and deployment of LLMs. To address this issue, this paper presents a comprehensive survey of key dimensions that are crucial to consider when assessing LLM trustworthiness. The survey covers seven major categories of LLM trustworthiness: reliability, safety, fairness, resistance to misuse, explainability and reasoning, adherence to social norms, and robustness. Each major category is further divided into several sub-categories, resulting in a total of 29 sub-categories. Additionally, a subset of 8 sub-categories is selected for further investigation, where corresponding measurement studies are designed and conducted on several widely-used LLMs. The measurement results indicate that, in general, more aligned models tend to perform better in terms of overall trustworthiness. However, the effectiveness of alignment varies across the different trustworthiness categories considered. This highlights the importance of conducting more fine-grained analyses, testing, and making continuous improvements on LLM alignment. By shedding light on these key dimensions of LLM trustworthiness, this paper aims to provide valuable insights and guidance to practitioners in the field. Understanding and addressing these concerns will be crucial in achieving reliable and ethically sound deployment of LLMs in various applications.
Despite the recent successes of large, pretrained neural language models (LLMs), comparatively little is known about the representations of linguistic structure they learn during pretraining, which can lead to unexpected behaviors in response to prompt variation or distribution shift. To better understand these models and behaviors, we introduce a general model analysis framework to study LLMs with respect to their representation and use of human-interpretable linguistic properties. Our framework, CALM (Competence-based Analysis of Language Models), is designed to investigate LLM competence in the context of specific tasks by intervening on models' internal representations of different linguistic properties using causal probing, and measuring models' alignment under these interventions with a given ground-truth causal model of the task. We also develop a new approach for performing causal probing interventions using gradient-based adversarial attacks, which can target a broader range of properties and representations than prior techniques. Finally, we carry out a case study of CALM using these interventions to analyze and compare LLM competence across a variety of lexical inference tasks, showing that CALM can be used to explain behaviors across these tasks.
The recent emergence of new algorithms for permuting models into functionally equivalent regions of the solution space has shed some light on the complexity of error surfaces, and some promising properties like mode connectivity. However, finding the right permutation is challenging, and current optimization techniques are not differentiable, which makes it difficult to integrate into a gradient-based optimization, and often leads to sub-optimal solutions. In this paper, we propose a Sinkhorn re-basin network with the ability to obtain the transportation plan that better suits a given objective. Unlike the current state-of-art, our method is differentiable and, therefore, easy to adapt to any task within the deep learning domain. Furthermore, we show the advantage of our re-basin method by proposing a new cost function that allows performing incremental learning by exploiting the linear mode connectivity property. The benefit of our method is compared against similar approaches from the literature, under several conditions for both optimal transport finding and linear mode connectivity. The effectiveness of our continual learning method based on re-basin is also shown for several common benchmark datasets, providing experimental results that are competitive with state-of-art results from the literature.
In the real-world question answering scenarios, hybrid form combining both tabular and textual contents has attracted more and more attention, among which numerical reasoning problem is one of the most typical and challenging problems. Existing methods usually adopt encoder-decoder framework to represent hybrid contents and generate answers. However, it can not capture the rich relationship among numerical value, table schema, and text information on the encoder side. The decoder uses a simple predefined operator classifier which is not flexible enough to handle numerical reasoning processes with diverse expressions. To address these problems, this paper proposes a \textbf{Re}lational \textbf{G}raph enhanced \textbf{H}ybrid table-text \textbf{N}umerical reasoning model with \textbf{T}ree decoder (\textbf{RegHNT}). It models the numerical question answering over table-text hybrid contents as an expression tree generation task. Moreover, we propose a novel relational graph modeling method, which models alignment between questions, tables, and paragraphs. We validated our model on the publicly available table-text hybrid QA benchmark (TAT-QA). The proposed RegHNT significantly outperform the baseline model and achieve state-of-the-art results. We openly released the source code and data at https://github.com/lfy79001/RegHNT (2022-05-05).