Daily Papers

Retrieval-Augmented Generation (RAG) systems enhance large language models (LLMs) by incorporating external knowledge bases, but this may expose them to extraction attacks, leading to potential copyright and privacy risks. However, existing extraction methods typically rely on malicious inputs such as prompt injection or jailbreaking, making them easily detectable via input- or output-level detection. In this paper, we introduce Implicit Knowledge Extraction Attack (IKEA), which conducts Knowledge Extraction on RAG systems through benign queries. Specifically, IKEA first leverages anchor concepts-keywords related to internal knowledge-to generate queries with a natural appearance, and then designs two mechanisms that lead anchor concepts to thoroughly "explore" the RAG's knowledge: (1) Experience Reflection Sampling, which samples anchor concepts based on past query-response histories, ensuring their relevance to the topic; (2) Trust Region Directed Mutation, which iteratively mutates anchor concepts under similarity constraints to further exploit the embedding space. Extensive experiments demonstrate IKEA's effectiveness under various defenses, surpassing baselines by over 80% in extraction efficiency and 90% in attack success rate. Moreover, the substitute RAG system built from IKEA's extractions shows comparable performance to the original RAG and outperforms those based on baselines across multiple evaluation tasks, underscoring the stealthy copyright infringement risk in RAG systems.

Post-training methods, especially Supervised Fine-Tuning (SFT) and Reinforcement Learning (RL), play an important role in improving large language models' (LLMs) complex reasoning abilities. However, the dominant two-stage pipeline (SFT then RL) suffers from a key inconsistency: SFT enforces rigid imitation that suppresses exploration and induces forgetting, limiting RL's potential for improvements. We address this inefficiency with TRAPO (Trust-Region Adaptive Policy Optimization), a hybrid framework that interleaves SFT and RL within each training instance by optimizing SFT loss on expert prefixes and RL loss on the model's own completions, unifying external supervision and self-exploration. To stabilize training, we introduce Trust-Region SFT (TrSFT), which minimizes forward KL divergence inside a trust region but attenuates optimization outside, effectively shifting toward reverse KL and yielding stable, mode-seeking updates favorable for RL. An adaptive prefix-selection mechanism further allocates expert guidance based on measured utility. Experiments on five mathematical reasoning benchmarks show that TRAPO consistently surpasses standard SFT, RL, and SFT-then-RL pipelines, as well as recent state-of-the-art approaches, establishing a strong new paradigm for reasoning-enhanced LLMs.

Sharpness-aware minimization (SAM) reports improving domain generalization by reducing the loss surface curvature in the parameter space. However, generalization during fine-tuning is often more dependent on the transferability of representations in the function space. Trust-region methods (TR) target this goal by regularizing representation curvature to reduce catastrophic forgetting of pre-trained task-agnostic information while adopting task-specific skills. We consider unifying these strategies for low curvature in both parameter space and function space to improve out-of-domain (OOD) generalization. We propose Trust Region Aware Minimization (TRAM), a SAM algorithm fine-tuning for low parameter sharpness and smooth, informative representations preserving pre-trained structure. TRAM uses a trust region bound to inform the SAM adversarial neighborhood, introducing an awareness of function curvature within optimization for flatter minima. We empirically validate TRAM in vision (cross-dataset adaptation) and text (OOD language modeling, zero-shot cross-lingual transfer) tasks where robust domain transfer and representation generality are critical. TRAM outperforms SAM- and TR-based optimization across all tasks, notably surpassing competing methods for hard transfer between anticorrelated domains. TRAM establishes a novel standard in fine-tuning for domain-generalizable models with minimal additional computation over previous sharpness-aware methods.

Despite being self-supervised, protein language models have shown remarkable performance in fundamental biological tasks such as predicting impact of genetic variation on protein structure and function. The effectiveness of these models on diverse set of tasks suggests that they learn meaningful representations of fitness landscape that can be useful for downstream clinical applications. Here, we interrogate the use of these language models in characterizing known pathogenic mutations in curated, medically actionable genes through an exhaustive search of putative compensatory mutations on each variant's genetic background. Systematic analysis of the predicted effects of these compensatory mutations reveal unappreciated structural features of proteins that are missed by other structure predictors like AlphaFold. While deep mutational scan experiments provide an unbiased estimate of the mutational landscape, we encourage the community to generate and curate rescue mutation experiments to inform the design of more sophisticated co-masking strategies and leverage large language models more effectively for downstream clinical prediction tasks.

On-policy reinforcement learning (RL) has become a popular framework for solving sequential decision problems due to its computational efficiency and theoretical simplicity. Some on-policy methods guarantee every policy update is constrained to a trust region relative to the prior policy to ensure training stability. These methods often require computationally intensive non-linear optimization or require a particular form of action distribution. In this work, we show that applying KL penalization alone is nearly sufficient to enforce such trust regions. Then, we show that introducing a "fixup" phase is sufficient to guarantee a trust region is enforced on every policy update while adding fewer than 5% additional gradient steps in practice. The resulting algorithm, which we call FixPO, is able to train a variety of policy architectures and action spaces, is easy to implement, and produces results competitive with other trust region methods.

On-policy Reinforcement Learning (RL) with PPO-like clip objectives has become the standard choice for reward-based fine-tuning of large language models (LLMs). Although recent work has explored improved estimators of advantages and normalization, the clipping mechanism itself has remained untouched. Originally introduced as a proxy for principled KL-based trust regions, clipping is a crude approximation that often causes unstable updates and suboptimal performance. We replace the clip objective with a novel discrete differentiable trust region projection, which provides principled token-level KL constraints. The projection operates on a sparse subset of the model's most important token logits to balance computational cost and projection effectiveness. Our approach, Trust Region Optimization for Large Language Models (TROLL), serves as a direct replacement for PPO-like clipping during training and does not alter the model's inference behavior. Across datasets, model families, and advantage-estimation methods, TROLL consistently outperforms PPO-like clipping in terms of training speed, stability, and final success rates.

We describe an iterative procedure for optimizing policies, with guaranteed monotonic improvement. By making several approximations to the theoretically-justified procedure, we develop a practical algorithm, called Trust Region Policy Optimization (TRPO). This algorithm is similar to natural policy gradient methods and is effective for optimizing large nonlinear policies such as neural networks. Our experiments demonstrate its robust performance on a wide variety of tasks: learning simulated robotic swimming, hopping, and walking gaits; and playing Atari games using images of the screen as input. Despite its approximations that deviate from the theory, TRPO tends to give monotonic improvement, with little tuning of hyperparameters.

To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only typical antibodies. Unfortunately, the space of typical antibodies is enormous to search, and experiments often fail to find suitable antibodies on a budget. We introduce Clone-informed Bayesian Optimization (CloneBO), a Bayesian optimization procedure that efficiently optimizes antibodies in the lab by teaching a generative model how our immune system optimizes antibodies. Our immune system makes antibodies by iteratively evolving specific portions of their sequences to bind their target strongly and stably, resulting in a set of related, evolving sequences known as a clonal family. We train a large language model, CloneLM, on hundreds of thousands of clonal families and use it to design sequences with mutations that are most likely to optimize an antibody within the human immune system. We propose to guide our designs to fit previous measurements with a twisted sequential Monte Carlo procedure. We show that CloneBO optimizes antibodies substantially more efficiently than previous methods in realistic in silico experiments and designs stronger and more stable binders in in vitro wet lab experiments.

The complexity of the alignment problem stems from the fact that existing methods are unstable. Researchers continuously invent various tricks to address this shortcoming. For instance, in the fundamental Reinforcement Learning From Human Feedback (RLHF) technique of Language Model alignment, in addition to reward maximization, the Kullback-Leibler divergence between the trainable policy and the SFT policy is minimized. This addition prevents the model from being overfitted to the Reward Model (RM) and generating texts that are out-of-domain for the RM. The Direct Preference Optimization (DPO) method reformulates the optimization task of RLHF and eliminates the Reward Model while tacitly maintaining the requirement for the policy to be close to the SFT policy. In our paper, we argue that this implicit limitation in the DPO method leads to sub-optimal results. We propose a new method called Trust Region DPO (TR-DPO), which updates the reference policy during training. With such a straightforward update, we demonstrate the effectiveness of TR-DPO against DPO on the Anthropic HH and TLDR datasets. We show that TR-DPO outperforms DPO by up to 19%, measured by automatic evaluation with GPT-4. The new alignment approach that we propose allows us to improve the quality of models across several parameters at once, such as coherence, correctness, level of detail, helpfulness, and harmlessness.

Recently, Large Language Models (LLMs) have rapidly evolved, approaching Artificial General Intelligence (AGI) while benefiting from large-scale reinforcement learning to enhance Human Alignment (HA) and Reasoning. Recent reward-based optimization algorithms, such as Proximal Policy Optimization (PPO) and Group Relative Policy Optimization (GRPO) have achieved significant performance on reasoning tasks, whereas preference-based optimization algorithms such as Direct Preference Optimization (DPO) significantly improve the performance of LLMs on human alignment. However, despite the strong performance of reward-based optimization methods in alignment tasks , they remain vulnerable to reward hacking. Furthermore, preference-based algorithms (such as Online DPO) haven't yet matched the performance of reward-based optimization algorithms (like PPO) on reasoning tasks, making their exploration in this specific area still a worthwhile pursuit. Motivated by these challenges, we propose the Trust Region Preference Approximation (TRPA) algorithm, which integrates rule-based optimization with preference-based optimization for reasoning tasks. As a preference-based algorithm, TRPA naturally eliminates the reward hacking issue. TRPA constructs preference levels using predefined rules, forms corresponding preference pairs, and leverages a novel optimization algorithm for RL training with a theoretical monotonic improvement guarantee. Experimental results demonstrate that TRPA not only achieves competitive performance on reasoning tasks but also exhibits robust stability. The code of this paper are released and updating on https://github.com/XueruiSu/Trust-Region-Preference-Approximation.git.

Generative Foundation Models (GenFMs) have emerged as transformative tools. However, their widespread adoption raises critical concerns regarding trustworthiness across dimensions. This paper presents a comprehensive framework to address these challenges through three key contributions. First, we systematically review global AI governance laws and policies from governments and regulatory bodies, as well as industry practices and standards. Based on this analysis, we propose a set of guiding principles for GenFMs, developed through extensive multidisciplinary collaboration that integrates technical, ethical, legal, and societal perspectives. Second, we introduce TrustGen, the first dynamic benchmarking platform designed to evaluate trustworthiness across multiple dimensions and model types, including text-to-image, large language, and vision-language models. TrustGen leverages modular components--metadata curation, test case generation, and contextual variation--to enable adaptive and iterative assessments, overcoming the limitations of static evaluation methods. Using TrustGen, we reveal significant progress in trustworthiness while identifying persistent challenges. Finally, we provide an in-depth discussion of the challenges and future directions for trustworthy GenFMs, which reveals the complex, evolving nature of trustworthiness, highlighting the nuanced trade-offs between utility and trustworthiness, and consideration for various downstream applications, identifying persistent challenges and providing a strategic roadmap for future research. This work establishes a holistic framework for advancing trustworthiness in GenAI, paving the way for safer and more responsible integration of GenFMs into critical applications. To facilitate advancement in the community, we release the toolkit for dynamic evaluation.

Diffusion models have shown promising generative capabilities across diverse domains, yet aligning their outputs with desired reward functions remains a challenge, particularly in cases where reward functions are non-differentiable. Some gradient-free guidance methods have been developed, but they often struggle to achieve optimal inference-time alignment. In this work, we newly frame inference-time alignment in diffusion as a search problem and propose Dynamic Search for Diffusion (DSearch), which subsamples from denoising processes and approximates intermediate node rewards. It also dynamically adjusts beam width and tree expansion to efficiently explore high-reward generations. To refine intermediate decisions, DSearch incorporates adaptive scheduling based on noise levels and a lookahead heuristic function. We validate DSearch across multiple domains, including biological sequence design, molecular optimization, and image generation, demonstrating superior reward optimization compared to existing approaches.

Policy gradient methods are an appealing approach in reinforcement learning because they directly optimize the cumulative reward and can straightforwardly be used with nonlinear function approximators such as neural networks. The two main challenges are the large number of samples typically required, and the difficulty of obtaining stable and steady improvement despite the nonstationarity of the incoming data. We address the first challenge by using value functions to substantially reduce the variance of policy gradient estimates at the cost of some bias, with an exponentially-weighted estimator of the advantage function that is analogous to TD(lambda). We address the second challenge by using trust region optimization procedure for both the policy and the value function, which are represented by neural networks. Our approach yields strong empirical results on highly challenging 3D locomotion tasks, learning running gaits for bipedal and quadrupedal simulated robots, and learning a policy for getting the biped to stand up from starting out lying on the ground. In contrast to a body of prior work that uses hand-crafted policy representations, our neural network policies map directly from raw kinematics to joint torques. Our algorithm is fully model-free, and the amount of simulated experience required for the learning tasks on 3D bipeds corresponds to 1-2 weeks of real time.

Self-evolution methods enhance code generation through iterative "generate-verify-refine" cycles, yet existing approaches suffer from low exploration efficiency, failing to discover solutions with superior complexity within limited budgets. This inefficiency stems from initialization bias trapping evolution in poor solution regions, uncontrolled stochastic operations lacking feedback guidance, and insufficient experience utilization across tasks. To address these bottlenecks, we propose Controlled Self-Evolution (CSE), which consists of three key components. Diversified Planning Initialization generates structurally distinct algorithmic strategies for broad solution space coverage. Genetic Evolution replaces stochastic operations with feedback-guided mechanisms, enabling targeted mutation and compositional crossover. Hierarchical Evolution Memory captures both successful and failed experiences at inter-task and intra-task levels. Experiments on EffiBench-X demonstrate that CSE consistently outperforms all baselines across various LLM backbones. Furthermore, CSE achieves higher efficiency from early generations and maintains continuous improvement throughout evolution. Our code is publicly available at https://github.com/QuantaAlpha/EvoControl.

Reparameterized diffusion models (RDMs) have recently matched autoregressive methods in protein generation, motivating their use for challenging tasks such as designing membrane proteins, which possess interleaved soluble and transmembrane (TM) regions. We introduce the Membrane Diffusion Language Model (MemDLM), a fine-tuned RDM-based protein language model that enables controllable membrane protein sequence design. MemDLM-generated sequences recapitulate the TM residue density and structural features of natural membrane proteins, achieving comparable biological plausibility and outperforming state-of-the-art diffusion baselines in motif scaffolding tasks by producing lower perplexity, higher BLOSUM-62 scores, and improved pLDDT confidence. To enhance controllability, we develop Per-Token Guidance (PET), a novel classifier-guided sampling strategy that selectively solubilizes residues while preserving conserved TM domains, yielding sequences with reduced TM density but intact functional cores. Importantly, MemDLM designs validated in TOXCAT beta-lactamase growth assays demonstrate successful TM insertion, distinguishing high-quality generated sequences from poor ones. Together, our framework establishes the first experimentally-validated diffusion-based model for rational membrane protein generation, integrating de novo design, motif scaffolding, and targeted property optimization.

Mutation testing is an effective approach to evaluate and strengthen software test suites, but its adoption is currently limited by the mutants' execution computational cost. Several strategies have been proposed to reduce this cost (a.k.a. mutation cost reduction strategies), however none of them has proven to be effective for all scenarios since they often need an ad-hoc manual selection and configuration depending on the software under test (SUT). In this paper, we propose a novel multi-objective evolutionary hyper-heuristic approach, dubbed Sentinel, to automate the generation of optimal cost reduction strategies for every new SUT. We evaluate Sentinel by carrying out a thorough empirical study involving 40 releases of 10 open-source real-world software systems and both baseline and state-of-the-art strategies as a benchmark. We execute a total of 4,800 experiments, and evaluate their results with both quality indicators and statistical significance tests, following the most recent best practice in the literature. The results show that strategies generated by Sentinel outperform the baseline strategies in 95% of the cases always with large effect sizes. They also obtain statistically significantly better results than state-of-the-art strategies in 88% of the cases, with large effect sizes for 95% of them. Also, our study reveals that the mutation strategies generated by Sentinel for a given software version can be used without any loss in quality for subsequently developed versions in 95% of the cases. These results show that Sentinel is able to automatically generate mutation strategies that reduce mutation testing cost without affecting its testing effectiveness (i.e. mutation score), thus taking off from the tester's shoulders the burden of manually selecting and configuring strategies for each SUT.

In today's era, where large language models (LLMs) are integrated into numerous real-world applications, ensuring their safety and robustness is crucial for responsible AI usage. Automated red-teaming methods play a key role in this process by generating adversarial attacks to identify and mitigate potential vulnerabilities in these models. However, existing methods often struggle with slow performance, limited categorical diversity, and high resource demands. While Rainbow Teaming, a recent approach, addresses the diversity challenge by framing adversarial prompt generation as a quality-diversity search, it remains slow and requires a large fine-tuned mutator for optimal performance. To overcome these limitations, we propose Ferret, a novel approach that builds upon Rainbow Teaming by generating multiple adversarial prompt mutations per iteration and using a scoring function to rank and select the most effective adversarial prompt. We explore various scoring functions, including reward models, Llama Guard, and LLM-as-a-judge, to rank adversarial mutations based on their potential harm to improve the efficiency of the search for harmful mutations. Our results demonstrate that Ferret, utilizing a reward model as a scoring function, improves the overall attack success rate (ASR) to 95%, which is 46% higher than Rainbow Teaming. Additionally, Ferret reduces the time needed to achieve a 90% ASR by 15.2% compared to the baseline and generates adversarial prompts that are transferable i.e. effective on other LLMs of larger size. Our codes are available at https://github.com/declare-lab/ferret.

Model-free reinforcement learning algorithms have seen remarkable progress, but key challenges remain. Trust Region Policy Optimization (TRPO) is known for ensuring monotonic policy improvement through conservative updates within a trust region, backed by strong theoretical guarantees. However, its reliance on complex second-order optimization limits its practical efficiency. Proximal Policy Optimization (PPO) addresses this by simplifying TRPO's approach using ratio clipping, improving efficiency but sacrificing some theoretical robustness. This raises a natural question: Can we combine the strengths of both methods? In this paper, we introduce Simple Policy Optimization (SPO), a novel unconstrained first-order algorithm. By slightly modifying the policy loss used in PPO, SPO can achieve the best of both worlds. Our new objective improves upon ratio clipping, offering stronger theoretical properties and better constraining the probability ratio within the trust region. Empirical results demonstrate that SPO outperforms PPO with a simple implementation, particularly for training large, complex network architectures end-to-end.

During a virus's evolution,various regions of the genome are subjected to distinct levels of functional constraints.Combined with factors like codon bias and DNA repair efficiency,these constraints contribute to unique mutation patterns within the genome or a specific gene. In this project, we harnessed the power of Large Language Models(LLMs) to predict the evolution of SARS-CoV-2. By treating the mutation process from one generation to the next as a translation task, we trained a transformer model, called VirusT5, to capture the mutation patterns underlying SARS-CoV-2 evolution. We evaluated the VirusT5's ability to detect these mutation patterns including its ability to identify mutation hotspots and explored the potential of using VirusT5 to predict future virus variants. Our findings demonstrate the feasibility of using a large language model to model viral evolution as a translation process. This study establishes the groundbreaking concept of "mutation-as-translation," paving the way for new methodologies and tools for combating virus threats

Protein Language Models (PLMs) have emerged as performant and scalable tools for predicting the functional impact and clinical significance of protein-coding variants, but they still lag experimental accuracy. Here, we present a novel fine-tuning approach to improve the performance of PLMs with experimental maps of variant effects from Deep Mutational Scanning (DMS) assays using a Normalised Log-odds Ratio (NLR) head. We find consistent improvements in a held-out protein test set, and on independent DMS and clinical variant annotation benchmarks from ProteinGym and ClinVar. These findings demonstrate that DMS is a promising source of sequence diversity and supervised training data for improving the performance of PLMs for variant effect prediction.

Machine learning has markedly advanced de novo peptide sequencing (DNS) for mass spectrometry-based proteomics. DNS tools offer a reliable way to identify peptides without relying on reference databases, extending proteomic analysis and unlocking applications into less-charted regions of the proteome. However, they still face a key limitation. DNS tools lack principled methods for estimating false discovery rates (FDR) and instead rely on model-specific confidence scores that are often miscalibrated. This limits trust in results, hinders cross-model comparisons and reduces validation success. Here we present Winnow, a model-agnostic framework for estimating FDR from calibrated DNS outputs. Winnow maps raw model scores to calibrated confidences using a neural network trained on peptide-spectrum match (PSM)-derived features. From these calibrated scores, Winnow computes PSM-specific error metrics and an experiment-wide FDR estimate using a novel decoy-free FDR estimator. It supports both zero-shot and dataset-specific calibration, enabling flexible application via direct inference, fine-tuning, or training a custom model. We demonstrate that, when applied to InstaNovo predictions, Winnow's calibrator improves recall at fixed FDR thresholds, and its FDR estimator tracks true error rates when benchmarked against reference proteomes and database search. Winnow ensures accurate FDR control across datasets, helping unlock the full potential of DNS.

Antibodies comprise the most versatile class of binding molecules, with numerous applications in biomedicine. Computational design of antibodies involves generating novel and diverse sequences, while maintaining structural consistency. Unique to antibodies, designing the complementarity-determining region (CDR), which determines the antigen binding affinity and specificity, creates its own unique challenges. Recent deep learning models have shown impressive results, however the limited number of known antibody sequence/structure pairs frequently leads to degraded performance, particularly lacking diversity in the generated sequences. In our work we address this challenge by leveraging Model Reprogramming (MR), which repurposes pretrained models on a source language to adapt to the tasks that are in a different language and have scarce data - where it may be difficult to train a high-performing model from scratch or effectively fine-tune an existing pre-trained model on the specific task. Specifically, we introduce ReprogBert in which a pretrained English language model is repurposed for protein sequence infilling - thus considers cross-language adaptation using less data. Results on antibody design benchmarks show that our model on low-resourced antibody sequence dataset provides highly diverse CDR sequences, up to more than a two-fold increase of diversity over the baselines, without losing structural integrity and naturalness. The generated sequences also demonstrate enhanced antigen binding specificity and virus neutralization ability. Code is available at https://github.com/IBM/ReprogBERT

Large Language Models (LLMs) such as ChatGPT, have gained significant attention due to their impressive natural language processing capabilities. It is crucial to prioritize human-centered principles when utilizing these models. Safeguarding the ethical and moral compliance of LLMs is of utmost importance. However, individual ethical issues have not been well studied on the latest LLMs. Therefore, this study aims to address these gaps by introducing a new benchmark -- TrustGPT. TrustGPT provides a comprehensive evaluation of LLMs in three crucial areas: toxicity, bias, and value-alignment. Initially, TrustGPT examines toxicity in language models by employing toxic prompt templates derived from social norms. It then quantifies the extent of bias in models by measuring quantifiable toxicity values across different groups. Lastly, TrustGPT assesses the value of conversation generation models from both active value-alignment and passive value-alignment tasks. Through the implementation of TrustGPT, this research aims to enhance our understanding of the performance of conversation generation models and promote the development of language models that are more ethical and socially responsible.

Supervised fine-tuning (SFT) of foundation models often leads to poor generalization, where prior capabilities deteriorate after tuning on new tasks or domains. Inspired by trust-region policy optimization (TRPO) and proximal policy optimization (PPO) in reinforcement learning (RL), we propose Proximal SFT (PSFT). This fine-tuning objective incorporates the benefits of trust-region, effectively constraining policy drift during SFT while maintaining competitive tuning. By viewing SFT as a special case of policy gradient methods with constant positive advantages, we derive PSFT that stabilizes optimization and leads to generalization, while leaving room for further optimization in subsequent post-training stages. Experiments across mathematical and human-value domains show that PSFT matches SFT in-domain, outperforms it in out-of-domain generalization, remains stable under prolonged training without causing entropy collapse, and provides a stronger foundation for the subsequent optimization.

The introduction of genome engineering technology has transformed biomedical research, making it possible to make precise changes to genetic information. However, creating an efficient gene-editing system requires a deep understanding of CRISPR technology, and the complex experimental systems under investigation. While Large Language Models (LLMs) have shown promise in various tasks, they often lack specific knowledge and struggle to accurately solve biological design problems. In this work, we introduce CRISPR-GPT, an LLM agent augmented with domain knowledge and external tools to automate and enhance the design process of CRISPR-based gene-editing experiments. CRISPR-GPT leverages the reasoning ability of LLMs to facilitate the process of selecting CRISPR systems, designing guide RNAs, recommending cellular delivery methods, drafting protocols, and designing validation experiments to confirm editing outcomes. We showcase the potential of CRISPR-GPT for assisting non-expert researchers with gene-editing experiments from scratch and validate the agent's effectiveness in a real-world use case. Furthermore, we explore the ethical and regulatory considerations associated with automated gene-editing design, highlighting the need for responsible and transparent use of these tools. Our work aims to bridge the gap between beginner biological researchers and CRISPR genome engineering techniques, and demonstrate the potential of LLM agents in facilitating complex biological discovery tasks.

Mirror descent (MD), a well-known first-order method in constrained convex optimization, has recently been shown as an important tool to analyze trust-region algorithms in reinforcement learning (RL). However, there remains a considerable gap between such theoretically analyzed algorithms and the ones used in practice. Inspired by this, we propose an efficient RL algorithm, called {\em mirror descent policy optimization} (MDPO). MDPO iteratively updates the policy by {\em approximately} solving a trust-region problem, whose objective function consists of two terms: a linearization of the standard RL objective and a proximity term that restricts two consecutive policies to be close to each other. Each update performs this approximation by taking multiple gradient steps on this objective function. We derive {\em on-policy} and {\em off-policy} variants of MDPO, while emphasizing important design choices motivated by the existing theory of MD in RL. We highlight the connections between on-policy MDPO and two popular trust-region RL algorithms: TRPO and PPO, and show that explicitly enforcing the trust-region constraint is in fact {\em not} a necessity for high performance gains in TRPO. We then show how the popular soft actor-critic (SAC) algorithm can be derived by slight modifications of off-policy MDPO. Overall, MDPO is derived from the MD principles, offers a unified approach to viewing a number of popular RL algorithms, and performs better than or on-par with TRPO, PPO, and SAC in a number of continuous control tasks. Code is available at https://github.com/manantomar/Mirror-Descent-Policy-Optimization.

Antibodies have become an important class of therapeutic agents to treat human diseases. To accelerate therapeutic antibody discovery, computational methods, especially machine learning, have attracted considerable interest for predicting specific interactions between antibody candidates and target antigens such as viruses and bacteria. However, the publicly available datasets in existing works have notable limitations, such as small sizes and the lack of non-binding samples and exact amino acid sequences. To overcome these limitations, we have developed AVIDa-hIL6, a large-scale dataset for predicting antigen-antibody interactions in the variable domain of heavy chain of heavy chain antibodies (VHHs), produced from an alpaca immunized with the human interleukin-6 (IL-6) protein, as antigens. By leveraging the simple structure of VHHs, which facilitates identification of full-length amino acid sequences by DNA sequencing technology, AVIDa-hIL6 contains 573,891 antigen-VHH pairs with amino acid sequences. All the antigen-VHH pairs have reliable labels for binding or non-binding, as generated by a novel labeling method. Furthermore, via introduction of artificial mutations, AVIDa-hIL6 contains 30 different mutants in addition to wild-type IL-6 protein. This characteristic provides opportunities to develop machine learning models for predicting changes in antibody binding by antigen mutations. We report experimental benchmark results on AVIDa-hIL6 by using neural network-based baseline models. The results indicate that the existing models have potential, but further research is needed to generalize them to predict effective antibodies against unknown mutants. The dataset is available at https://avida-hil6.cognanous.com.

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

Visual artifacts remain a persistent challenge in diffusion models, even with training on massive datasets. Current solutions primarily rely on supervised detectors, yet lack understanding of why these artifacts occur in the first place. In our analysis, we identify three distinct phases in the diffusion generative process: Profiling, Mutation, and Refinement. Artifacts typically emerge during the Mutation phase, where certain regions exhibit anomalous score dynamics over time, causing abrupt disruptions in the normal evolution pattern. This temporal nature explains why existing methods focusing only on spatial uncertainty of the final output fail at effective artifact localization. Based on these insights, we propose ASCED (Abnormal Score Correction for Enhancing Diffusion), that detects artifacts by monitoring abnormal score dynamics during the diffusion process, with a trajectory-aware on-the-fly mitigation strategy that appropriate generation of noise in the detected areas. Unlike most existing methods that apply post hoc corrections, \eg, by applying a noising-denoising scheme after generation, our mitigation strategy operates seamlessly within the existing diffusion process. Extensive experiments demonstrate that our proposed approach effectively reduces artifacts across diverse domains, matching or surpassing existing supervised methods without additional training.

Ligand molecule conformation generation is a critical challenge in drug discovery. Deep learning models have been developed to tackle this problem, particularly through the use of generative models in recent years. However, these models often generate conformations that lack meaningful structure and randomness due to the absence of essential side information. Examples of such side information include the chemical and geometric features of the target protein, ligand-target compound interactions, and ligand chemical properties. Without these constraints, the generated conformations may not be suitable for further selection and design of new drugs. To address this limitation, we propose a novel method for generating ligand conformations that leverage side information and incorporate flexible constraints into standard diffusion models. Drawing inspiration from the concept of message passing, we introduce ligand-target massage passing block, a mechanism that facilitates the exchange of information between target nodes and ligand nodes, thereby incorporating target node features. To capture non-covalent interactions, we introduce ligand-target compound inter and intra edges. To further improve the biological relevance of the generated conformations, we train energy models using scalar chemical features. These models guide the progress of the standard Denoising Diffusion Probabilistic Models, resulting in more biologically meaningful conformations. We evaluate the performance of SIDEGEN using the PDBBind-2020 dataset, comparing it against other methods. The results demonstrate improvements in both Aligned RMSD and Ligand RMSD evaluations. Specifically, our model outperforms GeoDiff (trained on PDBBind-2020) by 20% in terms of the median aligned RMSD metric.

This paper describes Meta's ACH system for mutation-guided LLM-based test generation. ACH generates relatively few mutants (aka simulated faults), compared to traditional mutation testing. Instead, it focuses on generating currently undetected faults that are specific to an issue of concern. From these currently uncaught faults, ACH generates tests that can catch them, thereby `killing' the mutants and consequently hardening the platform against regressions. We use privacy concerns to illustrate our approach, but ACH can harden code against {\em any} type of regression. In total, ACH was applied to 10,795 Android Kotlin classes in 7 software platforms deployed by Meta, from which it generated 9,095 mutants and 571 privacy-hardening test cases. ACH also deploys an LLM-based equivalent mutant detection agent that achieves a precision of 0.79 and a recall of 0.47 (rising to 0.95 and 0.96 with simple pre-processing). ACH was used by Messenger and WhatsApp test-a-thons where engineers accepted 73% of its tests, judging 36% to privacy relevant. We conclude that ACH hardens code against specific concerns and that, even when its tests do not directly tackle the specific concern, engineers find them useful for their other benefits.

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.

Recently, instruction-based image editing (IIE) has received widespread attention. In practice, IIE often modifies only specific regions of an image, while the remaining areas largely remain unchanged. Although these two types of regions differ significantly in generation difficulty and computational redundancy, existing IIE models do not account for this distinction, instead applying a uniform generation process across the entire image. This motivates us to propose RegionE, an adaptive, region-aware generation framework that accelerates IIE tasks without additional training. Specifically, the RegionE framework consists of three main components: 1) Adaptive Region Partition. We observed that the trajectory of unedited regions is straight, allowing for multi-step denoised predictions to be inferred in a single step. Therefore, in the early denoising stages, we partition the image into edited and unedited regions based on the difference between the final estimated result and the reference image. 2) Region-Aware Generation. After distinguishing the regions, we replace multi-step denoising with one-step prediction for unedited areas. For edited regions, the trajectory is curved, requiring local iterative denoising. To improve the efficiency and quality of local iterative generation, we propose the Region-Instruction KV Cache, which reduces computational cost while incorporating global information. 3) Adaptive Velocity Decay Cache. Observing that adjacent timesteps in edited regions exhibit strong velocity similarity, we further propose an adaptive velocity decay cache to accelerate the local denoising process. We applied RegionE to state-of-the-art IIE base models, including Step1X-Edit, FLUX.1 Kontext, and Qwen-Image-Edit. RegionE achieved acceleration factors of 2.57, 2.41, and 2.06. Evaluations by GPT-4o confirmed that semantic and perceptual fidelity were well preserved.

Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent developments in steering protein generative models (e.g diffusion models, language models) offer a promising approach. However, by and large, past studies have optimized surrogate rewards and/or utilized large amounts of labeled data for steering, making it unclear how well existing methods perform and compare to each other in real-world optimization campaigns where fitness is measured by low-throughput wet-lab assays. In this study, we explore fitness optimization using small amounts (hundreds) of labeled sequence-fitness pairs and comprehensively evaluate strategies such as classifier guidance and posterior sampling for guiding generation from different discrete diffusion models of protein sequences. We also demonstrate how guidance can be integrated into adaptive sequence selection akin to Thompson sampling in Bayesian optimization, showing that plug-and-play guidance strategies offer advantages compared to alternatives such as reinforcement learning with protein language models.

The controllable generation of diffusion models aims to steer the model to generate samples that optimize some given objective functions. It is desirable for a variety of applications including image generation, molecule generation, and DNA/sequence generation. Reinforcement Learning (RL) based fine-tuning of the base model is a popular approach but it can overfit the reward function while requiring significant resources. We frame controllable generation as a problem of finding a distribution that optimizes a KL-regularized objective function. We present SLCD -- Supervised Learning based Controllable Diffusion, which iteratively generates online data and trains a small classifier to guide the generation of the diffusion model. Similar to the standard classifier-guided diffusion, SLCD's key computation primitive is classification and does not involve any complex concepts from RL or control. Via a reduction to no-regret online learning analysis, we show that under KL divergence, the output from SLCD provably converges to the optimal solution of the KL-regularized objective. Further, we empirically demonstrate that SLCD can generate high quality samples with nearly the same inference time as the base model in both image generation with continuous diffusion and biological sequence generation with discrete diffusion. Our code is available at https://github.com/Owen-Oertell/slcd

Compressing high-capability Large Language Models (LLMs) has emerged as a favored strategy for resource-efficient inferences. While state-of-the-art (SoTA) compression methods boast impressive advancements in preserving benign task performance, the potential risks of compression in terms of safety and trustworthiness have been largely neglected. This study conducts the first, thorough evaluation of three (3) leading LLMs using five (5) SoTA compression techniques across eight (8) trustworthiness dimensions. Our experiments highlight the intricate interplay between compression and trustworthiness, revealing some interesting patterns. We find that quantization is currently a more effective approach than pruning in achieving efficiency and trustworthiness simultaneously. For instance, a 4-bit quantized model retains the trustworthiness of its original counterpart, but model pruning significantly degrades trustworthiness, even at 50% sparsity. Moreover, employing quantization within a moderate bit range could unexpectedly improve certain trustworthiness dimensions such as ethics and fairness. Conversely, extreme quantization to very low bit levels (3 bits) tends to significantly reduce trustworthiness. This increased risk cannot be uncovered by looking at benign performance alone, in turn, mandating comprehensive trustworthiness evaluation in practice. These findings culminate in practical recommendations for simultaneously achieving high utility, efficiency, and trustworthiness in LLMs. Models and code are available at https://decoding-comp-trust.github.io/.

We introduce a novel score-based diffusion framework named Twigs that incorporates multiple co-evolving flows for enriching conditional generation tasks. Specifically, a central or trunk diffusion process is associated with a primary variable (e.g., graph structure), and additional offshoot or stem processes are dedicated to dependent variables (e.g., graph properties or labels). A new strategy, which we call loop guidance, effectively orchestrates the flow of information between the trunk and the stem processes during sampling. This approach allows us to uncover intricate interactions and dependencies, and unlock new generative capabilities. We provide extensive experiments to demonstrate strong performance gains of the proposed method over contemporary baselines in the context of conditional graph generation, underscoring the potential of Twigs in challenging generative tasks such as inverse molecular design and molecular optimization.

Discovering mutations enhancing protein-protein interactions (PPIs) is critical for advancing biomedical research and developing improved therapeutics. While machine learning approaches have substantially advanced the field, they often struggle to generalize beyond training data in practical scenarios. The contributions of this work are three-fold. First, we construct PPIRef, the largest and non-redundant dataset of 3D protein-protein interactions, enabling effective large-scale learning. Second, we leverage the PPIRef dataset to pre-train PPIformer, a new SE(3)-equivariant model generalizing across diverse protein-binder variants. We fine-tune PPIformer to predict effects of mutations on protein-protein interactions via a thermodynamically motivated adjustment of the pre-training loss function. Finally, we demonstrate the enhanced generalization of our new PPIformer approach by outperforming other state-of-the-art methods on new, non-leaking splits of standard labeled PPI mutational data and independent case studies optimizing a human antibody against SARS-CoV-2 and increasing the thrombolytic activity of staphylokinase.

Recent advances in LLM-guided evolutionary computation, particularly AlphaEvolve (Novikov et al., 2025; Georgiev et al., 2025), have demonstrated remarkable success in discovering novel mathematical constructions and solving challenging optimization problems. However, the high-level descriptions in published work leave many implementation details unspecified, hindering reproducibility and further research. In this report we present GigaEvo, an extensible open-source framework that enables researchers to study and experiment with hybrid LLM-evolution approaches inspired by AlphaEvolve. Our system provides modular implementations of key components: MAP-Elites quality-diversity algorithms, asynchronous DAG-based evaluation pipelines, LLM-driven mutation operators with insight generation and bidirectional lineage tracking, and flexible multi-island evolutionary strategies. In order to assess reproducibility and validate our implementation we evaluate GigaEvo on challenging problems from the AlphaEvolve paper: Heilbronn triangle placement, circle packing in squares, and high-dimensional kissing numbers. The framework emphasizes modularity, concurrency, and ease of experimentation, enabling rapid prototyping through declarative configuration. We provide detailed descriptions of system architecture, implementation decisions, and experimental methodology to support further research in LLM driven evolutionary methods. The GigaEvo framework and all experimental code are available at https://github.com/AIRI-Institute/gigaevo-core.

One of the critical phases in software development is software testing. Testing helps with identifying potential bugs and reducing maintenance costs. The goal of automated test generation tools is to ease the development of tests by suggesting efficient bug-revealing tests. Recently, researchers have leveraged Large Language Models (LLMs) of code to generate unit tests. While the code coverage of generated tests was usually assessed, the literature has acknowledged that the coverage is weakly correlated with the efficiency of tests in bug detection. To improve over this limitation, in this paper, we introduce MuTAP for improving the effectiveness of test cases generated by LLMs in terms of revealing bugs by leveraging mutation testing. Our goal is achieved by augmenting prompts with surviving mutants, as those mutants highlight the limitations of test cases in detecting bugs. MuTAP is capable of generating effective test cases in the absence of natural language descriptions of the Program Under Test (PUTs). We employ different LLMs within MuTAP and evaluate their performance on different benchmarks. Our results show that our proposed method is able to detect up to 28% more faulty human-written code snippets. Among these, 17% remained undetected by both the current state-of-the-art fully automated test generation tool (i.e., Pynguin) and zero-shot/few-shot learning approaches on LLMs. Furthermore, MuTAP achieves a Mutation Score (MS) of 93.57% on synthetic buggy code, outperforming all other approaches in our evaluation. Our findings suggest that although LLMs can serve as a useful tool to generate test cases, they require specific post-processing steps to enhance the effectiveness of the generated test cases which may suffer from syntactic or functional errors and may be ineffective in detecting certain types of bugs and testing corner cases PUTs.

Optimization with matrix gradient orthogonalization has recently demonstrated impressive results in the training of deep neural networks (Jordan et al., 2024; Liu et al., 2025). In this paper, we provide a theoretical analysis of this approach. In particular, we show that the orthogonalized gradient method can be seen as a first-order trust-region optimization method, where the trust-region is defined in terms of the matrix spectral norm. Motivated by this observation, we develop the stochastic non-Euclidean trust-region gradient method with momentum, which recovers the Muon optimizer (Jordan et al., 2024) as a special case, along with normalized SGD and signSGD with momentum (Cutkosky and Mehta, 2020; Sun et al., 2023). In addition, we prove state-of-the-art convergence results for the proposed algorithm in a range of scenarios, which involve arbitrary non-Euclidean norms, constrained and composite problems, and non-convex, star-convex, first- and second-order smooth functions. Finally, our theoretical findings provide an explanation for several practical observations, including the practical superiority of Muon compared to the Orthogonal-SGDM algorithm of Tuddenham et al. (2022) and the importance of weight decay in the training of large-scale language models.

Smart contracts are decentralized applications built atop blockchains like Ethereum. Recent research has shown that large language models (LLMs) have potential in auditing smart contracts, but the state-of-the-art indicates that even GPT-4 can achieve only 30% precision (when both decision and justification are correct). This is likely because off-the-shelf LLMs were primarily pre-trained on a general text/code corpus and not fine-tuned on the specific domain of Solidity smart contract auditing. In this paper, we propose TrustLLM, a general framework that combines fine-tuning and LLM-based agents for intuitive smart contract auditing with justifications. Specifically, TrustLLM is inspired by the observation that expert human auditors first perceive what could be wrong and then perform a detailed analysis of the code to identify the cause. As such, TrustLLM employs a two-stage fine-tuning approach: it first tunes a Detector model to make decisions and then tunes a Reasoner model to generate causes of vulnerabilities. However, fine-tuning alone faces challenges in accurately identifying the optimal cause of a vulnerability. Therefore, we introduce two LLM-based agents, the Ranker and Critic, to iteratively select and debate the most suitable cause of vulnerability based on the output of the fine-tuned Reasoner model. To evaluate TrustLLM, we collected a balanced dataset with 1,734 positive and 1,810 negative samples to fine-tune TrustLLM. We then compared it with traditional fine-tuned models (CodeBERT, GraphCodeBERT, CodeT5, and UnixCoder) as well as prompt learning-based LLMs (GPT4, GPT-3.5, and CodeLlama-13b/34b). On a dataset of 263 real smart contract vulnerabilities, TrustLLM achieves an F1 score of 91.21% and an accuracy of 91.11%. The causes generated by TrustLLM achieved a consistency of about 38% compared to the ground truth causes.

Target proteins that lack accessible binding pockets and conformational stability have posed increasing challenges for drug development. Induced proximity strategies, such as PROTACs and molecular glues, have thus gained attention as pharmacological alternatives, but still require small molecule docking at binding pockets for targeted protein degradation (TPD). The computational design of protein-based binders presents unique opportunities to access undruggable targets, but have often relied on stable 3D structures or predictions for effective binder generation. Recently, we have leveraged the expressive latent spaces of protein language models (pLMs) for the prioritization of peptide binders from sequence alone, which we have then fused to E3 ubiquitin ligase domains, creating a CRISPR-analogous TPD system for target proteins. However, our methods rely on training discriminator models for ranking heuristically or unconditionally-derived guide peptides for their target binding capability. In this work, we introduce PepMLM, a purely target sequence-conditioned de novo generator of linear peptide binders. By employing a novel masking strategy that uniquely positions cognate peptide sequences at the terminus of target protein sequences, PepMLM tasks the state-of-the-art ESM-2 pLM to fully reconstruct the binder region, achieving low perplexities matching or improving upon previously-validated peptide-protein sequence pairs. After successful in silico benchmarking with AlphaFold-Multimer, we experimentally verify PepMLM's efficacy via fusion of model-derived peptides to E3 ubiquitin ligase domains, demonstrating endogenous degradation of target substrates in cellular models. In total, PepMLM enables the generative design of candidate binders to any target protein, without the requirement of target structure, empowering downstream programmable proteome editing applications.

Diffusion models have been successful on a range of conditional generation tasks including molecular design and text-to-image generation. However, these achievements have primarily depended on task-specific conditional training or error-prone heuristic approximations. Ideally, a conditional generation method should provide exact samples for a broad range of conditional distributions without requiring task-specific training. To this end, we introduce the Twisted Diffusion Sampler, or TDS. TDS is a sequential Monte Carlo (SMC) algorithm that targets the conditional distributions of diffusion models through simulating a set of weighted particles. The main idea is to use twisting, an SMC technique that enjoys good computational efficiency, to incorporate heuristic approximations without compromising asymptotic exactness. We first find in simulation and in conditional image generation tasks that TDS provides a computational statistical trade-off, yielding more accurate approximations with many particles but with empirical improvements over heuristics with as few as two particles. We then turn to motif-scaffolding, a core task in protein design, using a TDS extension to Riemannian diffusion models. On benchmark test cases, TDS allows flexible conditioning criteria and often outperforms the state of the art.

Wild Test-Time Adaptation (WTTA) is proposed to adapt a source model to unseen domains under extreme data scarcity and multiple shifts. Previous approaches mainly focused on sample selection strategies, while overlooking the fundamental problem on underlying optimization. Initially, we critically analyze the widely-adopted entropy minimization framework in WTTA and uncover its significant limitations in noisy optimization dynamics that substantially hinder adaptation efficiency. Through our analysis, we identify region confidence as a superior alternative to traditional entropy, however, its direct optimization remains computationally prohibitive for real-time applications. In this paper, we introduce a novel region-integrated method ReCAP that bypasses the lengthy process. Specifically, we propose a probabilistic region modeling scheme that flexibly captures semantic changes in embedding space. Subsequently, we develop a finite-to-infinite asymptotic approximation that transforms the intractable region confidence into a tractable and upper-bounded proxy. These innovations significantly unlock the overlooked potential dynamics in local region in a concise solution. Our extensive experiments demonstrate the consistent superiority of ReCAP over existing methods across various datasets and wild scenarios.

Recent studies have demonstrated significant progress in aligning text-to-image diffusion models with human preference via Reinforcement Learning from Human Feedback. However, while existing methods achieve high scores on automated reward metrics, they often lead to Preference Mode Collapse (PMC)-a specific form of reward hacking where models converge on narrow, high-scoring outputs (e.g., images with monolithic styles or pervasive overexposure), severely degrading generative diversity. In this work, we introduce and quantify this phenomenon, proposing DivGenBench, a novel benchmark designed to measure the extent of PMC. We posit that this collapse is driven by over-optimization along the reward model's inherent biases. Building on this analysis, we propose Directional Decoupling Alignment (D^2-Align), a novel framework that mitigates PMC by directionally correcting the reward signal. Specifically, our method first learns a directional correction within the reward model's embedding space while keeping the model frozen. This correction is then applied to the reward signal during the optimization process, preventing the model from collapsing into specific modes and thereby maintaining diversity. Our comprehensive evaluation, combining qualitative analysis with quantitative metrics for both quality and diversity, reveals that D^2-Align achieves superior alignment with human preference.

As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet {A,T,G,C} have been used to design DNA sequences that are free of long homopolymers to increase stability, yet effective error detection and error correction are required to achieve reliability in data retrieval. Recently, we introduced lexicographically-ordered constrained (LOCO) codes, namely DNA LOCO (D-LOCO) codes, with error detection. In this paper, we equip our D-LOCO codes with error correction for substitution errors via syndrome-like decoding, designated as residue decoding. We only use D-LOCO codewords of indices divisible by a suitable redundancy metric R(m) > 0, where m is the code length, for error correction. We provide the community with a construction of constrained codes forbidding runs of length higher than fixed ell in {1,2,3} and GC-content in big [0.5-1{2K},0.5+1{2K}big ] that correct K segmented substitution errors, one per codeword. We call the proposed codes error-correction (EC) D-LOCO codes. We also give a list-decoding procedure with near-quadratic time-complexity in m to correct double-substitution errors within EC D-LOCO codewords, which has > 98.20% average success rate. The redundancy metric is projected to require 2log_2(m)+O(1)-bit allocation for a length-m codeword. Hence, our EC D-LOCO codes are projected to be capacity-approaching with respect to the error-free constrained system.

Deep neural networks such as AlphaFold and RoseTTAFold predict remarkably accurate structures of proteins compared to other algorithmic approaches. It is known that biologically small perturbations in the protein sequence do not lead to drastic changes in the protein structure. In this paper, we demonstrate that RoseTTAFold does not exhibit such a robustness despite its high accuracy, and biologically small perturbations for some input sequences result in radically different predicted protein structures. This raises the challenge of detecting when these predicted protein structures cannot be trusted. We define the robustness measure for the predicted structure of a protein sequence to be the inverse of the root-mean-square distance (RMSD) in the predicted structure and the structure of its adversarially perturbed sequence. We use adversarial attack methods to create adversarial protein sequences, and show that the RMSD in the predicted protein structure ranges from 0.119A to 34.162A when the adversarial perturbations are bounded by 20 units in the BLOSUM62 distance. This demonstrates very high variance in the robustness measure of the predicted structures. We show that the magnitude of the correlation (0.917) between our robustness measure and the RMSD between the predicted structure and the ground truth is high, that is, the predictions with low robustness measure cannot be trusted. This is the first paper demonstrating the susceptibility of RoseTTAFold to adversarial attacks.

This paper investigates using knowledge editing techniques to detoxify Large Language Models (LLMs). We construct a benchmark, SafeEdit, which covers nine unsafe categories with various powerful attack prompts and equips comprehensive metrics for systematic evaluation. We conduct experiments to compare knowledge editing approaches with previous baselines, indicating that knowledge editing has the potential to efficiently detoxify LLMs with limited impact on general performance. Then, we propose a simple yet effective baseline, dubbed Detoxifying with Intraoperative Neural Monitoring (DINM), to diminish the toxicity of LLMs within a few tuning steps via only one instance. We further provide an in-depth analysis of the internal mechanism for various detoxify approaches, demonstrating that previous methods like SFT and DPO may merely suppress the activations of toxic parameters, while DINM mitigates the toxicity of the toxic parameters to a certain extent, making permanent adjustments. We hope that these insights could shed light on future work of developing detoxifying approaches and the underlying knowledge mechanisms of LLMs. Code and benchmark are available at https://github.com/zjunlp/EasyEdit.

Multi-turn-to-single-turn (M2S) compresses iterative red-teaming into one structured prompt, but prior work relied on a handful of manually written templates. We present X-Teaming Evolutionary M2S, an automated framework that discovers and optimizes M2S templates through language-model-guided evolution. The system pairs smart sampling from 12 sources with an LLM-as-judge inspired by StrongREJECT and records fully auditable logs. Maintaining selection pressure by setting the success threshold to theta = 0.70, we obtain five evolutionary generations, two new template families, and 44.8% overall success (103/230) on GPT-4.1. A balanced cross-model panel of 2,500 trials (judge fixed) shows that structural gains transfer but vary by target; two models score zero at the same threshold. We also find a positive coupling between prompt length and score, motivating length-aware judging. Our results demonstrate that structure-level search is a reproducible route to stronger single-turn probes and underscore the importance of threshold calibration and cross-model evaluation. Code, configurations, and artifacts are available at https://github.com/hyunjun1121/M2S-x-teaming.

Designing sequences that satisfy multiple, often conflicting, objectives is a central challenge in therapeutic and biomolecular engineering. Existing generative frameworks largely operate in continuous spaces with single-objective guidance, while discrete approaches lack guarantees for multi-objective Pareto optimality. We introduce AReUReDi (Annealed Rectified Updates for Refining Discrete Flows), a discrete optimization algorithm with theoretical guarantees of convergence to the Pareto front. Building on Rectified Discrete Flows (ReDi), AReUReDi combines Tchebycheff scalarization, locally balanced proposals, and annealed Metropolis-Hastings updates to bias sampling toward Pareto-optimal states while preserving distributional invariance. Applied to peptide and SMILES sequence design, AReUReDi simultaneously optimizes up to five therapeutic properties (including affinity, solubility, hemolysis, half-life, and non-fouling) and outperforms both evolutionary and diffusion-based baselines. These results establish AReUReDi as a powerful, sequence-based framework for multi-property biomolecule generation.

Protein inverse folding, the design of an amino acid sequence based on a target 3D structure, is a fundamental problem of computational protein engineering. Existing methods either generate sequences without leveraging external knowledge or relying on protein language models (PLMs). The former omits the evolutionary information stored in protein databases, while the latter is parameter-inefficient and inflexible to adapt to ever-growing protein data. To overcome the above drawbacks, in this paper we propose a novel method, called retrieval-augmented denoising diffusion (RadDiff), for protein inverse folding. Given the target protein backbone, RadDiff uses a hierarchical search strategy to efficiently retrieve structurally similar proteins from large protein databases. The retrieved structures are then aligned residue-by-residue to the target to construct a position-specific amino acid profile, which serves as an evolutionary-informed prior that conditions the denoising process. A lightweight integration module is further designed to incorporate this prior effectively. Experimental results on the CATH, PDB, and TS50 datasets show that RadDiff consistently outperforms existing methods, improving sequence recovery rate by up to 19%. Experimental results also demonstrate that RadDiff generates highly foldable sequences and scales effectively with database size.

Advances in Large Language Models (LLMs) have enabled a new class of self-evolving agents that autonomously improve through interaction with the environment, demonstrating strong capabilities. However, self-evolution also introduces novel risks overlooked by current safety research. In this work, we study the case where an agent's self-evolution deviates in unintended ways, leading to undesirable or even harmful outcomes. We refer to this as Misevolution. To provide a systematic investigation, we evaluate misevolution along four key evolutionary pathways: model, memory, tool, and workflow. Our empirical findings reveal that misevolution is a widespread risk, affecting agents built even on top-tier LLMs (e.g., Gemini-2.5-Pro). Different emergent risks are observed in the self-evolutionary process, such as the degradation of safety alignment after memory accumulation, or the unintended introduction of vulnerabilities in tool creation and reuse. To our knowledge, this is the first study to systematically conceptualize misevolution and provide empirical evidence of its occurrence, highlighting an urgent need for new safety paradigms for self-evolving agents. Finally, we discuss potential mitigation strategies to inspire further research on building safer and more trustworthy self-evolving agents. Our code and data are available at https://github.com/ShaoShuai0605/Misevolution . Warning: this paper includes examples that may be offensive or harmful in nature.

Antibody design is an essential yet challenging task in various domains like therapeutics and biology. There are two major defects in current learning-based methods: 1) tackling only a certain subtask of the whole antibody design pipeline, making them suboptimal or resource-intensive. 2) omitting either the framework regions or side chains, thus incapable of capturing the full-atom geometry. To address these pitfalls, we propose dynamic Multi-channel Equivariant grAph Network (dyMEAN), an end-to-end full-atom model for E(3)-equivariant antibody design given the epitope and the incomplete sequence of the antibody. Specifically, we first explore structural initialization as a knowledgeable guess of the antibody structure and then propose shadow paratope to bridge the epitope-antibody connections. Both 1D sequences and 3D structures are updated via an adaptive multi-channel equivariant encoder that is able to process protein residues of variable sizes when considering full atoms. Finally, the updated antibody is docked to the epitope via the alignment of the shadow paratope. Experiments on epitope-binding CDR-H3 design, complex structure prediction, and affinity optimization demonstrate the superiority of our end-to-end framework and full-atom modeling.

We introduce ShinkaEvolve: a new open-source framework leveraging large language models (LLMs) to advance scientific discovery with state-of-the-art performance and unprecedented efficiency. Recent advances in scaling inference time compute of LLMs have enabled significant progress in generalized scientific discovery. These approaches rely on evolutionary agentic harnesses that leverage LLMs as mutation operators to generate candidate solutions. However, current code evolution methods suffer from critical limitations: they are sample inefficient, requiring thousands of samples to identify effective solutions, and remain closed-source, hindering broad adoption and extension. ShinkaEvolve addresses these limitations, introducing three key innovations: a parent sampling technique balancing exploration and exploitation, code novelty rejection-sampling for efficient search space exploration, and a bandit-based LLM ensemble selection strategy. We evaluate ShinkaEvolve across diverse tasks, demonstrating consistent improvements in sample efficiency and solution quality. ShinkaEvolve discovers a new state-of-the-art circle packing solution using only 150 samples, designs high-performing agentic harnesses for AIME mathematical reasoning tasks, identifies improvements to ALE-Bench competitive programming solutions, and discovers novel mixture-of-expert load balancing loss functions that illuminate the space of optimization strategies. Our results demonstrate that ShinkaEvolve achieves broad applicability with exceptional sample efficiency. By providing open-source accessibility and cost-efficiency, this work democratizes open-ended discovery across diverse computational problems.

In the multiple unmanned aerial vehicle (UAV)- assisted downlink communication, it is challenging for UAV base stations (UAV BSs) to realize trajectory design and resource assignment in unknown environments. The cooperation and competition between UAV BSs in the communication network leads to a Markov game problem. Multi-agent reinforcement learning is a significant solution for the above decision-making. However, there are still many common issues, such as the instability of the system and low utilization of historical data, that limit its application. In this paper, a novel graph-attention multi-agent trust region (GA-MATR) reinforcement learning framework is proposed to solve the multi-UAV assisted communication problem. Graph recurrent network is introduced to process and analyze complex topology of the communication network, so as to extract useful information and patterns from observational information. The attention mechanism provides additional weighting for conveyed information, so that the critic network can accurately evaluate the value of behavior for UAV BSs. This provides more reliable feedback signals and helps the actor network update the strategy more effectively. Ablation simulations indicate that the proposed approach attains improved convergence over the baselines. UAV BSs learn the optimal communication strategies to achieve their maximum cumulative rewards. Additionally, multi-agent trust region method with monotonic convergence provides an estimated Nash equilibrium for the multi-UAV assisted communication Markov game.

We introduce AMix-1, a powerful protein foundation model built on Bayesian Flow Networks and empowered by a systematic training methodology, encompassing pretraining scaling laws, emergent capability analysis, in-context learning mechanism, and test-time scaling algorithm. To guarantee robust scalability, we establish a predictive scaling law and reveal the progressive emergence of structural understanding via loss perspective, culminating in a strong 1.7-billion model. Building on this foundation, we devise a multiple sequence alignment (MSA)-based in-context learning strategy to unify protein design into a general framework, where AMix-1 recognizes deep evolutionary signals among MSAs and consistently generates structurally and functionally coherent proteins. This framework enables the successful design of a dramatically improved AmeR variant with an up to 50times activity increase over its wild type. Pushing the boundaries of protein engineering, we further empower AMix-1 with an evolutionary test-time scaling algorithm for in silico directed evolution that delivers substantial, scalable performance gains as verification budgets are intensified, laying the groundwork for next-generation lab-in-the-loop protein design.

With the rapid evolution of Large Language Models (LLMs), LLM-based agents and Multi-agent Systems (MAS) have significantly expanded the capabilities of LLM ecosystems. This evolution stems from empowering LLMs with additional modules such as memory, tools, environment, and even other agents. However, this advancement has also introduced more complex issues of trustworthiness, which previous research focused solely on LLMs could not cover. In this survey, we propose the TrustAgent framework, a comprehensive study on the trustworthiness of agents, characterized by modular taxonomy, multi-dimensional connotations, and technical implementation. By thoroughly investigating and summarizing newly emerged attacks, defenses, and evaluation methods for agents and MAS, we extend the concept of Trustworthy LLM to the emerging paradigm of Trustworthy Agent. In TrustAgent, we begin by deconstructing and introducing various components of the Agent and MAS. Then, we categorize their trustworthiness into intrinsic (brain, memory, and tool) and extrinsic (user, agent, and environment) aspects. Subsequently, we delineate the multifaceted meanings of trustworthiness and elaborate on the implementation techniques of existing research related to these internal and external modules. Finally, we present our insights and outlook on this domain, aiming to provide guidance for future endeavors.

Structure-Based molecule optimization (SBMO) aims to optimize molecules with both continuous coordinates and discrete types against protein targets. A promising direction is to exert gradient guidance on generative models given its remarkable success in images, but it is challenging to guide discrete data and risks inconsistencies between modalities. To this end, we leverage a continuous and differentiable space derived through Bayesian inference, presenting Molecule Joint Optimization (MolJO), the gradient-based SBMO framework that facilitates joint guidance signals across different modalities while preserving SE(3)-equivariance. We introduce a novel backward correction strategy that optimizes within a sliding window of the past histories, allowing for a seamless trade-off between explore-and-exploit during optimization. MolJO achieves state-of-the-art performance on CrossDocked2020 benchmark (Success Rate 51.3%, Vina Dock -9.05 and SA 0.78), more than 4x improvement in Success Rate compared to the gradient-based counterpart, and 2x "Me-Better" Ratio as much as 3D baselines. Furthermore, we extend MolJO to a wide range of optimization settings, including multi-objective optimization and challenging tasks in drug design such as R-group optimization and scaffold hopping, further underscoring its versatility. Code is available at https://github.com/AlgoMole/MolCRAFT.

This paper introduces a novel framework for DNA sequence generation, comprising two key components: DiscDiff, a Latent Diffusion Model (LDM) tailored for generating discrete DNA sequences, and Absorb-Escape, a post-training algorithm designed to refine these sequences. Absorb-Escape enhances the realism of the generated sequences by correcting `round errors' inherent in the conversion process between latent and input spaces. Our approach not only sets new standards in DNA sequence generation but also demonstrates superior performance over existing diffusion models, in generating both short and long DNA sequences. Additionally, we introduce EPD-GenDNA, the first comprehensive, multi-species dataset for DNA generation, encompassing 160,000 unique sequences from 15 species. We hope this study will advance the generative modelling of DNA, with potential implications for gene therapy and protein production.

Peptide therapeutics, a major class of medicines, have achieved remarkable success across diseases such as diabetes and cancer, with landmark examples such as GLP-1 receptor agonists revolutionizing the treatment of type-2 diabetes and obesity. Despite their success, designing peptides that satisfy multiple conflicting objectives, such as target binding affinity, solubility, and membrane permeability, remains a major challenge. Classical drug development and structure-based design are ineffective for such tasks, as they fail to optimize global functional properties critical for therapeutic efficacy. Existing generative frameworks are largely limited to continuous spaces, unconditioned outputs, or single-objective guidance, making them unsuitable for discrete sequence optimization across multiple properties. To address this, we present PepTune, a multi-objective discrete diffusion model for the simultaneous generation and optimization of therapeutic peptide SMILES. Built on the Masked Discrete Language Model (MDLM) framework, PepTune ensures valid peptide structures with state-dependent masking schedules and penalty-based objectives. To guide the diffusion process, we propose a Monte Carlo Tree Search (MCTS)-based strategy that balances exploration and exploitation to iteratively refine Pareto-optimal sequences. MCTS integrates classifier-based rewards with search-tree expansion, overcoming gradient estimation challenges and data sparsity inherent to discrete spaces. Using PepTune, we generate diverse, chemically-modified peptides optimized for multiple therapeutic properties, including target binding affinity, membrane permeability, solubility, hemolysis, and non-fouling characteristics on various disease-relevant targets. In total, our results demonstrate that MCTS-guided discrete diffusion is a powerful and modular approach for multi-objective sequence design in discrete state spaces.

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.

Symbolic regression (SR) is the problem of learning a symbolic expression from numerical data. Recently, deep neural models trained on procedurally-generated synthetic datasets showed competitive performance compared to more classical Genetic Programming (GP) algorithms. Unlike their GP counterparts, these neural approaches are trained to generate expressions from datasets given as context. This allows them to produce accurate expressions in a single forward pass at test time. However, they usually do not benefit from search abilities, which result in low performance compared to GP on out-of-distribution datasets. In this paper, we propose a novel method which provides the best of both worlds, based on a Monte-Carlo Tree Search procedure using a context-aware neural mutation model, which is initially pre-trained to learn promising mutations, and further refined from successful experiences in an online fashion. The approach demonstrates state-of-the-art performance on the well-known SRBench benchmark.

Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream tasks. However, there is limited empirical work that examines the structure of these interactions. This paper analyzes 1.86 million models on Hugging Face, a leading peer production platform for model development. Our study of model family trees -- networks that connect fine-tuned models to their base or parent -- reveals sprawling fine-tuning lineages that vary widely in size and structure. Using an evolutionary biology lens to study ML models, we use model metadata and model cards to measure the genetic similarity and mutation of traits over model families. We find that models tend to exhibit a family resemblance, meaning their genetic markers and traits exhibit more overlap when they belong to the same model family. However, these similarities depart in certain ways from standard models of asexual reproduction, because mutations are fast and directed, such that two `sibling' models tend to exhibit more similarity than parent/child pairs. Further analysis of the directional drifts of these mutations reveals qualitative insights about the open machine learning ecosystem: Licenses counter-intuitively drift from restrictive, commercial licenses towards permissive or copyleft licenses, often in violation of upstream license's terms; models evolve from multi-lingual compatibility towards english-only compatibility; and model cards reduce in length and standardize by turning, more often, to templates and automatically generated text. Overall, this work takes a step toward an empirically grounded understanding of model fine-tuning and suggests that ecological models and methods can yield novel scientific insights.

Gene expression analysis holds the key to many biomedical discoveries, yet extracting insights from raw transcriptomic data remains formidable due to the complexity of multiple large, semi-structured files and the need for extensive domain expertise. Current automation approaches are often limited by either inflexible workflows that break down in edge cases or by fully autonomous agents that lack the necessary precision for rigorous scientific inquiry. GenoMAS charts a different course by presenting a team of LLM-based scientists that integrates the reliability of structured workflows with the adaptability of autonomous agents. GenoMAS orchestrates six specialized LLM agents through typed message-passing protocols, each contributing complementary strengths to a shared analytic canvas. At the heart of GenoMAS lies a guided-planning framework: programming agents unfold high-level task guidelines into Action Units and, at each juncture, elect to advance, revise, bypass, or backtrack, thereby maintaining logical coherence while bending gracefully to the idiosyncrasies of genomic data. On the GenoTEX benchmark, GenoMAS reaches a Composite Similarity Correlation of 89.13% for data preprocessing and an F_1 of 60.48% for gene identification, surpassing the best prior art by 10.61% and 16.85% respectively. Beyond metrics, GenoMAS surfaces biologically plausible gene-phenotype associations corroborated by the literature, all while adjusting for latent confounders. Code is available at https://github.com/Liu-Hy/GenoMAS.

Reinforcement Learning with Human Feedback (RLHF) and its variants have made huge strides toward the effective alignment of large language models (LLMs) to follow instructions and reflect human values. More recently, Direct Alignment Algorithms (DAAs) have emerged in which the reward modeling stage of RLHF is skipped by characterizing the reward directly as a function of the policy being learned. Examples include Direct Preference Optimization (DPO) and Simple Preference Optimization (SimPO). These methods often suffer from likelihood displacement, a phenomenon by which the probabilities of preferred responses are often reduced undesirably. In this paper, we argue that, for DAAs the reward (function) shape matters. We introduce AlphaPO, a new DAA method that leverages an alpha-parameter to help change the shape of the reward function beyond the standard log reward. AlphaPO helps maintain fine-grained control over likelihood displacement and over-optimization. Compared to SimPO, one of the best performing DAAs, AlphaPO leads to about 7\% to 10\% relative improvement in alignment performance for the instruct versions of Mistral-7B and Llama3-8B. The analysis and results presented highlight the importance of the reward shape, and how one can systematically change it to affect training dynamics, as well as improve alignment performance.

Gaussian process (GP) regression provides a strategy for accelerating saddle point searches on high-dimensional energy surfaces by reducing the number of times the energy and its derivatives with respect to atomic coordinates need to be evaluated. The computational overhead in the hyperparameter optimization can, however, be large and make the approach inefficient. Failures can also occur if the search ventures too far into regions that are not represented well enough by the GP model. Here, these challenges are resolved by using geometry-aware optimal transport measures and an active pruning strategy using a summation over Wasserstein-1 distances for each atom-type in farthest-point sampling, selecting a fixed-size subset of geometrically diverse configurations to avoid rapidly increasing cost of GP updates as more observations are made. Stability is enhanced by permutation-invariant metric that provides a reliable trust radius for early-stopping and a logarithmic barrier penalty for the growth of the signal variance. These physically motivated algorithmic changes prove their efficacy by reducing to less than a half the mean computational time on a set of 238 challenging configurations from a previously published data set of chemical reactions. With these improvements, the GP approach is established as, a robust and scalable algorithm for accelerating saddle point searches when the evaluation of the energy and atomic forces requires significant computational effort.

Large language models (LLMs) are increasingly trained with reinforcement learning from verifiable rewards (RLVR), yet real-world deployment demands models that can self-improve without labels or external judges. Existing label-free methods, confidence minimization, self-consistency, or majority-vote objectives, stabilize learning but steadily shrink exploration, causing an entropy collapse: generations become shorter, less diverse, and brittle. Unlike prior approaches such as Test-Time Reinforcement Learning (TTRL), which primarily adapt models to the immediate unlabeled dataset at hand, our goal is broader: to enable general improvements without sacrificing the model's inherent exploration capacity and generalization ability, i.e., evolving. We formalize this issue and propose EVolution-Oriented and Label-free Reinforcement Learning (EVOL-RL), a simple rule that couples stability with variation under a label-free setting. EVOL-RL keeps the majority-voted answer as a stable anchor (selection) while adding a novelty-aware reward that favors responses whose reasoning differs from what has already been produced (variation), measured in semantic space. Implemented with GRPO, EVOL-RL also uses asymmetric clipping to preserve strong signals and an entropy regularizer to sustain search. This majority-for-selection + novelty-for-variation design prevents collapse, maintains longer and more informative chains of thought, and improves both pass@1 and pass@n. EVOL-RL consistently outperforms the majority-only TTRL baseline; e.g., training on label-free AIME24 lifts Qwen3-4B-Base AIME25 pass@1 from TTRL's 4.6% to 16.4%, and pass@16 from 18.5% to 37.9%. EVOL-RL not only prevents diversity collapse but also unlocks stronger generalization across domains (e.g., GPQA). Furthermore, we demonstrate that EVOL-RL also boosts performance in the RLVR setting, highlighting its broad applicability.

Diffusion models for continuous data gained widespread adoption owing to their high quality generation and control mechanisms. However, controllable diffusion on discrete data faces challenges given that continuous guidance methods do not directly apply to discrete diffusion. Here, we provide a straightforward derivation of classifier-free and classifier-based guidance for discrete diffusion, as well as a new class of diffusion models that leverage uniform noise and that are more guidable because they can continuously edit their outputs. We improve the quality of these models with a novel continuous-time variational lower bound that yields state-of-the-art performance, especially in settings involving guidance or fast generation. Empirically, we demonstrate that our guidance mechanisms combined with uniform noise diffusion improve controllable generation relative to autoregressive and diffusion baselines on several discrete data domains, including genomic sequences, small molecule design, and discretized image generation.

We study the problem of extrapolative controlled generation, i.e., generating sequences with attribute values beyond the range seen in training. This task is of significant importance in automated design, especially drug discovery, where the goal is to design novel proteins that are better (e.g., more stable) than existing sequences. Thus, by definition, the target sequences and their attribute values are out of the training distribution, posing challenges to existing methods that aim to directly generate the target sequence. Instead, in this work, we propose Iterative Controlled Extrapolation (ICE) which iteratively makes local edits to a sequence to enable extrapolation. We train the model on synthetically generated sequence pairs that demonstrate small improvement in the attribute value. Results on one natural language task (sentiment analysis) and two protein engineering tasks (ACE2 stability and AAV fitness) show that ICE considerably outperforms state-of-the-art approaches despite its simplicity. Our code and models are available at: https://github.com/vishakhpk/iter-extrapolation.

Mathematical geometric problem solving (GPS) often requires effective integration of multimodal information and verifiable logical coherence. Despite the fast development of large language models in general problem solving, it remains unresolved regarding with both methodology and benchmarks, especially given the fact that exiting synthetic GPS benchmarks are often not self-verified and contain noise and self-contradicted information due to the illusion of LLMs. In this paper, we propose a scalable data engine called TrustGeoGen for problem generation, with formal verification to provide a principled benchmark, which we believe lays the foundation for the further development of methods for GPS. The engine synthesizes geometric data through four key innovations: 1) multimodal-aligned generation of diagrams, textual descriptions, and stepwise solutions; 2) formal verification ensuring rule-compliant reasoning paths; 3) a bootstrapping mechanism enabling complexity escalation via recursive state generation and 4) our devised GeoExplore series algorithms simultaneously produce multi-solution variants and self-reflective backtracking traces. By formal logical verification, TrustGeoGen produces GeoTrust-200K dataset with guaranteed modality integrity, along with GeoTrust-test testset. Experiments reveal the state-of-the-art models achieve only 49.17\% accuracy on GeoTrust-test, demonstrating its evaluation stringency. Crucially, models trained on GeoTrust achieve OOD generalization on GeoQA, significantly reducing logical inconsistencies relative to pseudo-label annotated by OpenAI-o1. Our code is available at https://github.com/Alpha-Innovator/TrustGeoGen

Safety fine-tuning algorithms are commonly used to fine-tune language models to reduce harmful outputs, but the exact internal mechanisms of how those models achieve this remain unclear. In studying direct preference optimisation (DPO) for toxicity reduction, current explanations claim that DPO works by dampening the most toxic MLP neurons to learn an offset to avert toxic regions in the residual stream. However, by ablating the most toxic neurons and applying activation patching, we find this explanation incomplete. By projecting neuron activation changes onto a toxicity probe, we find that only 31.8\% of toxicity reduction comes from dampened toxic neurons. Instead, DPO reduces toxicity by accumulating effects across multiple neuron groups, both reducing writing in the toxic direction and promoting anti-toxicity in the residual stream. Moreover, DPO gives noisy adjustments to neuron activations, with many neurons actually increasing toxicity. This indicates that DPO is a balancing process between opposing neuron effects to achieve toxicity reduction.

Neurological diseases are the leading global cause of disability, yet most lack disease-modifying treatments. We present PROTON, a heterogeneous graph transformer that generates testable hypotheses across molecular, organoid, and clinical systems. To evaluate PROTON, we apply it to Parkinson's disease (PD), bipolar disorder (BD), and Alzheimer's disease (AD). In PD, PROTON linked genetic risk loci to genes essential for dopaminergic neuron survival and predicted pesticides toxic to patient-derived neurons, including the insecticide endosulfan, which ranked within the top 1.29% of predictions. In silico screens performed by PROTON reproduced six genome-wide α-synuclein experiments, including a split-ubiquitin yeast two-hybrid system (normalized enrichment score [NES] = 2.30, FDR-adjusted p < 1 times 10^{-4}), an ascorbate peroxidase proximity labeling assay (NES = 2.16, FDR < 1 times 10^{-4}), and a high-depth targeted exome sequencing study in 496 synucleinopathy patients (NES = 2.13, FDR < 1 times 10^{-4}). In BD, PROTON predicted calcitriol as a candidate drug that reversed proteomic alterations observed in cortical organoids derived from BD patients. In AD, we evaluated PROTON predictions in health records from n = 610,524 patients at Mass General Brigham, confirming that five PROTON-predicted drugs were associated with reduced seven-year dementia risk (minimum hazard ratio = 0.63, 95% CI: 0.53-0.75, p < 1 times 10^{-7}). PROTON generated neurological hypotheses that were evaluated across molecular, organoid, and clinical systems, defining a path for AI-driven discovery in neurological disease.

Accurate blind docking has the potential to lead to new biological breakthroughs, but for this promise to be realized, docking methods must generalize well across the proteome. Existing benchmarks, however, fail to rigorously assess generalizability. Therefore, we develop DockGen, a new benchmark based on the ligand-binding domains of proteins, and we show that existing machine learning-based docking models have very weak generalization abilities. We carefully analyze the scaling laws of ML-based docking and show that, by scaling data and model size, as well as integrating synthetic data strategies, we are able to significantly increase the generalization capacity and set new state-of-the-art performance across benchmarks. Further, we propose Confidence Bootstrapping, a new training paradigm that solely relies on the interaction between diffusion and confidence models and exploits the multi-resolution generation process of diffusion models. We demonstrate that Confidence Bootstrapping significantly improves the ability of ML-based docking methods to dock to unseen protein classes, edging closer to accurate and generalizable blind docking methods.

Breast cancer remains a leading cause of cancer-related mortality worldwide, making early detection and accurate treatment response monitoring critical priorities. We present BreastDCEDL, a curated, deep learning-ready dataset comprising pre-treatment 3D Dynamic Contrast-Enhanced MRI (DCE-MRI) scans from 2,070 breast cancer patients drawn from the I-SPY1, I-SPY2, and Duke cohorts, all sourced from The Cancer Imaging Archive. The raw DICOM imaging data were rigorously converted into standardized 3D NIfTI volumes with preserved signal integrity, accompanied by unified tumor annotations and harmonized clinical metadata including pathologic complete response (pCR), hormone receptor (HR), and HER2 status. Although DCE-MRI provides essential diagnostic information and deep learning offers tremendous potential for analyzing such complex data, progress has been limited by lack of accessible, public, multicenter datasets. BreastDCEDL addresses this gap by enabling development of advanced models, including state-of-the-art transformer architectures that require substantial training data. To demonstrate its capacity for robust modeling, we developed the first transformer-based model for breast DCE-MRI, leveraging Vision Transformer (ViT) architecture trained on RGB-fused images from three contrast phases (pre-contrast, early post-contrast, and late post-contrast). Our ViT model achieved state-of-the-art pCR prediction performance in HR+/HER2- patients (AUC 0.94, accuracy 0.93). BreastDCEDL includes predefined benchmark splits, offering a framework for reproducible research and enabling clinically meaningful modeling in breast cancer imaging.

Large language models (LLMs) frequently refuse to respond to pseudo-malicious instructions: semantically harmless input queries triggering unnecessary LLM refusals due to conservative safety alignment, significantly impairing user experience. Collecting such instructions is crucial for evaluating and mitigating over-refusals, but existing instruction curation methods, like manual creation or instruction rewriting, either lack scalability or fail to produce sufficiently diverse and effective refusal-inducing prompts. To address these limitations, we introduce EVOREFUSE, a prompt optimization approach that generates diverse pseudo-malicious instructions consistently eliciting confident refusals across LLMs. EVOREFUSE employs an evolutionary algorithm exploring the instruction space in more diverse directions than existing methods via mutation strategies and recombination, and iteratively evolves seed instructions to maximize evidence lower bound on LLM refusal probability. Using EVOREFUSE, we create two novel datasets: EVOREFUSE-TEST, a benchmark of 582 pseudo-malicious instructions that outperforms the next-best benchmark with 140.41% higher average refusal triggering rate across 9 LLMs, 34.86% greater lexical diversity, and 40.03% improved LLM response confidence scores; and EVOREFUSE-ALIGN, which provides 3,000 pseudo-malicious instructions with responses for supervised and preference-based alignment training. LLAMA3.1-8B-INSTRUCT supervisedly fine-tuned on EVOREFUSE-ALIGN achieves up to 14.31% fewer over-refusals than models trained on the second-best alignment dataset, without compromising safety. Our analysis with EVOREFUSE-TEST reveals models trigger over-refusals by overly focusing on sensitive keywords while ignoring broader context.

Modern neural networks are often trained on massive datasets that are web scraped with minimal human inspection. As a result of this insecure curation pipeline, an adversary can poison or backdoor the resulting model by uploading malicious data to the internet and waiting for a victim to scrape and train on it. Existing approaches for creating poisons and backdoors start with randomly sampled clean data, called base samples, and then modify those samples to craft poisons. However, some base samples may be significantly more amenable to poisoning than others. As a result, we may be able to craft more potent poisons by carefully choosing the base samples. In this work, we use guided diffusion to synthesize base samples from scratch that lead to significantly more potent poisons and backdoors than previous state-of-the-art attacks. Our Guided Diffusion Poisoning (GDP) base samples can be combined with any downstream poisoning or backdoor attack to boost its effectiveness. Our implementation code is publicly available at: https://github.com/hsouri/GDP .

Designing biological sequences that satisfy multiple, often conflicting, functional and biophysical criteria remains a central challenge in biomolecule engineering. While discrete flow matching models have recently shown promise for efficient sampling in high-dimensional sequence spaces, existing approaches address only single objectives or require continuous embeddings that can distort discrete distributions. We present Multi-Objective-Guided Discrete Flow Matching (MOG-DFM), a general framework to steer any pretrained discrete-time flow matching generator toward Pareto-efficient trade-offs across multiple scalar objectives. At each sampling step, MOG-DFM computes a hybrid rank-directional score for candidate transitions and applies an adaptive hypercone filter to enforce consistent multi-objective progression. We also trained two unconditional discrete flow matching models, PepDFM for diverse peptide generation and EnhancerDFM for functional enhancer DNA generation, as base generation models for MOG-DFM. We demonstrate MOG-DFM's effectiveness in generating peptide binders optimized across five properties (hemolysis, non-fouling, solubility, half-life, and binding affinity), and in designing DNA sequences with specific enhancer classes and DNA shapes. In total, MOG-DFM proves to be a powerful tool for multi-property-guided biomolecule sequence design.

Modern Artificial Intelligence (AI) increasingly relies on multi-agent architectures that blend visual and language understanding. Yet, a pressing challenge remains: How can we trust these agents especially in zero-shot settings with no fine-tuning? We introduce a novel modular Agentic AI visual classification framework that integrates generalist multimodal agents with a non-visual reasoning orchestrator and a Retrieval-Augmented Generation (RAG) module. Applied to apple leaf disease diagnosis, we benchmark three configurations: (I) zero-shot with confidence-based orchestration, (II) fine-tuned agents with improved performance, and (III) trust-calibrated orchestration enhanced by CLIP-based image retrieval and re-evaluation loops. Using confidence calibration metrics (ECE, OCR, CCC), the orchestrator modulates trust across agents. Our results demonstrate a 77.94\% accuracy improvement in the zero-shot setting using trust-aware orchestration and RAG, achieving 85.63\% overall. GPT-4o showed better calibration, while Qwen-2.5-VL displayed overconfidence. Furthermore, image-RAG grounded predictions with visually similar cases, enabling correction of agent overconfidence via iterative re-evaluation. The proposed system separates perception (vision agents) from meta-reasoning (orchestrator), enabling scalable and interpretable multi-agent AI. This blueprint is extensible to diagnostics, biology, and other trust-critical domains. All models, prompts, results, and system components including the complete software source code are openly released to support reproducibility, transparency, and community benchmarking at Github: https://github.com/Applied-AI-Research-Lab/Orchestrator-Agent-Trust

Designing enzyme backbones with substrate-specific functionality is a critical challenge in computational protein engineering. Current generative models excel in protein design but face limitations in binding data, substrate-specific control, and flexibility for de novo enzyme backbone generation. To address this, we introduce EnzyBind, a dataset with 11,100 experimentally validated enzyme-substrate pairs specifically curated from PDBbind. Building on this, we propose EnzyControl, a method that enables functional and substrate-specific control in enzyme backbone generation. Our approach generates enzyme backbones conditioned on MSA-annotated catalytic sites and their corresponding substrates, which are automatically extracted from curated enzyme-substrate data. At the core of EnzyControl is EnzyAdapter, a lightweight, modular component integrated into a pretrained motif-scaffolding model, allowing it to become substrate-aware. A two-stage training paradigm further refines the model's ability to generate accurate and functional enzyme structures. Experiments show that our EnzyControl achieves the best performance across structural and functional metrics on EnzyBind and EnzyBench benchmarks, with particularly notable improvements of 13\% in designability and 13\% in catalytic efficiency compared to the baseline models. The code is released at https://github.com/Vecteur-libre/EnzyControl.

The trustworthiness of machine learning has emerged as a critical topic in the field, encompassing various applications and research areas such as robustness, security, interpretability, and fairness. The last decade saw the development of numerous methods addressing these challenges. In this survey, we systematically review these advancements from a data-centric perspective, highlighting the shortcomings of traditional empirical risk minimization (ERM) training in handling challenges posed by the data. Interestingly, we observe a convergence of these methods, despite being developed independently across trustworthy machine learning subfields. Pearl's hierarchy of causality offers a unifying framework for these techniques. Accordingly, this survey presents the background of trustworthy machine learning development using a unified set of concepts, connects this language to Pearl's causal hierarchy, and finally discusses methods explicitly inspired by causality literature. We provide a unified language with mathematical vocabulary to link these methods across robustness, adversarial robustness, interpretability, and fairness, fostering a more cohesive understanding of the field. Further, we explore the trustworthiness of large pretrained models. After summarizing dominant techniques like fine-tuning, parameter-efficient fine-tuning, prompting, and reinforcement learning with human feedback, we draw connections between them and the standard ERM. This connection allows us to build upon the principled understanding of trustworthy methods, extending it to these new techniques in large pretrained models, paving the way for future methods. Existing methods under this perspective are also reviewed. Lastly, we offer a brief summary of the applications of these methods and discuss potential future aspects related to our survey. For more information, please visit http://trustai.one.

Retrosynthesis planning, essential in organic synthesis and drug discovery, has greatly benefited from recent AI-driven advancements. Nevertheless, existing methods frequently face limitations in both applicability and explainability. Traditional graph-based and sequence-to-sequence models often lack generalized chemical knowledge, leading to predictions that are neither consistently accurate nor easily explainable. To address these challenges, we introduce RetroDFM-R, a reasoning-based large language model (LLM) designed specifically for chemical retrosynthesis. Leveraging large-scale reinforcement learning guided by chemically verifiable rewards, RetroDFM-R significantly enhances prediction accuracy and explainability. Comprehensive evaluations demonstrate that RetroDFM-R significantly outperforms state-of-the-art methods, achieving a top-1 accuracy of 65.0% on the USPTO-50K benchmark. Double-blind human assessments further validate the chemical plausibility and practical utility of RetroDFM-R's predictions. RetroDFM-R also accurately predicts multistep retrosynthetic routes reported in the literature for both real-world drug molecules and perovskite materials. Crucially, the model's explicit reasoning process provides human-interpretable insights, thereby enhancing trust and practical value in real-world retrosynthesis applications.

Drag-based image editing using generative models provides intuitive control over image structures. However, existing methods rely heavily on manually provided masks and textual prompts to preserve semantic fidelity and motion precision. Removing these constraints creates a fundamental trade-off: visual artifacts without masks and poor spatial control without prompts. To address these limitations, we propose DirectDrag, a novel mask- and prompt-free editing framework. DirectDrag enables precise and efficient manipulation with minimal user input while maintaining high image fidelity and accurate point alignment. DirectDrag introduces two key innovations. First, we design an Auto Soft Mask Generation module that intelligently infers editable regions from point displacement, automatically localizing deformation along movement paths while preserving contextual integrity through the generative model's inherent capacity. Second, we develop a Readout-Guided Feature Alignment mechanism that leverages intermediate diffusion activations to maintain structural consistency during point-based edits, substantially improving visual fidelity. Despite operating without manual mask or prompt, DirectDrag achieves superior image quality compared to existing methods while maintaining competitive drag accuracy. Extensive experiments on DragBench and real-world scenarios demonstrate the effectiveness and practicality of DirectDrag for high-quality, interactive image manipulation. Project Page: https://frakw.github.io/DirectDrag/. Code is available at: https://github.com/frakw/DirectDrag.

Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation. For example, in the protein inverse folding task, conditional diffusion models have achieved impressive results in generating natural-like sequences that fold back into the original structure. However, practical design tasks often require not only modeling a conditional distribution but also optimizing specific task objectives. For instance, we may prefer protein sequences with high stability. To address this, we consider the scenario where we have pre-trained discrete diffusion models that can generate natural-like sequences, as well as reward models that map sequences to task objectives. We then formulate the reward maximization problem within discrete diffusion models, analogous to reinforcement learning (RL), while minimizing the KL divergence against pretrained diffusion models to preserve naturalness. To solve this RL problem, we propose a novel algorithm, DRAKES, that enables direct backpropagation of rewards through entire trajectories generated by diffusion models, by making the originally non-differentiable trajectories differentiable using the Gumbel-Softmax trick. Our theoretical analysis indicates that our approach can generate sequences that are both natural-like and yield high rewards. While similar tasks have been recently explored in diffusion models for continuous domains, our work addresses unique algorithmic and theoretical challenges specific to discrete diffusion models, which arise from their foundation in continuous-time Markov chains rather than Brownian motion. Finally, we demonstrate the effectiveness of DRAKES in generating DNA and protein sequences that optimize enhancer activity and protein stability, respectively, important tasks for gene therapies and protein-based therapeutics.

In the realm of machine learning, traditional model development and automated approaches like AutoML typically rely on layers of abstraction, such as tree-based or Cartesian genetic programming. Our study introduces "Guided Evolution" (GE), a novel framework that diverges from these methods by utilizing Large Language Models (LLMs) to directly modify code. GE leverages LLMs for a more intelligent, supervised evolutionary process, guiding mutations and crossovers. Our unique "Evolution of Thought" (EoT) technique further enhances GE by enabling LLMs to reflect on and learn from the outcomes of previous mutations. This results in a self-sustaining feedback loop that augments decision-making in model evolution. GE maintains genetic diversity, crucial for evolutionary algorithms, by leveraging LLMs' capability to generate diverse responses from expertly crafted prompts and modulate model temperature. This not only accelerates the evolution process but also injects expert like creativity and insight into the process. Our application of GE in evolving the ExquisiteNetV2 model demonstrates its efficacy: the LLM-driven GE autonomously produced variants with improved accuracy, increasing from 92.52% to 93.34%, without compromising model compactness. This underscores the potential of LLMs to accelerate the traditional model design pipeline, enabling models to autonomously evolve and enhance their own designs.

Toxicity remains a leading cause of early-stage drug development failure. Despite advances in molecular design and property prediction, the task of molecular toxicity repair - generating structurally valid molecular alternatives with reduced toxicity - has not yet been systematically defined or benchmarked. To fill this gap, we introduce ToxiMol, the first benchmark task for general-purpose Multimodal Large Language Models (MLLMs) focused on molecular toxicity repair. We construct a standardized dataset covering 11 primary tasks and 560 representative toxic molecules spanning diverse mechanisms and granularities. We design a prompt annotation pipeline with mechanism-aware and task-adaptive capabilities, informed by expert toxicological knowledge. In parallel, we propose an automated evaluation framework, ToxiEval, which integrates toxicity endpoint prediction, synthetic accessibility, drug-likeness, and structural similarity into a high-throughput evaluation chain for repair success. We systematically assess nearly 30 mainstream general-purpose MLLMs and design multiple ablation studies to analyze key factors such as evaluation criteria, candidate diversity, and failure attribution. Experimental results show that although current MLLMs still face significant challenges on this task, they begin to demonstrate promising capabilities in toxicity understanding, semantic constraint adherence, and structure-aware molecule editing.

Cis-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their ability to modulate gene expression, highly depends on the nucleotide sequences, especially specific motifs known as transcription factor binding sites (TFBSs). Designing high-fitness CREs is crucial for therapeutic and bioengineering applications. Current CRE design methods are limited by two major drawbacks: (1) they typically rely on iterative optimization strategies that modify existing sequences and are prone to local optima, and (2) they lack the guidance of biological prior knowledge in sequence optimization. In this paper, we address these limitations by proposing a generative approach that leverages reinforcement learning (RL) to fine-tune a pre-trained autoregressive (AR) model. Our method incorporates data-driven biological priors by deriving computational inference-based rewards that simulate the addition of activator TFBSs and removal of repressor TFBSs, which are then integrated into the RL process. We evaluate our method on promoter design tasks in two yeast media conditions and enhancer design tasks for three human cell types, demonstrating its ability to generate high-fitness CREs while maintaining sequence diversity. The code is available at https://github.com/yangzhao1230/TACO.

Semi-supervised learning has become a compelling approach for 3D tooth segmentation from CBCT scans, where labeled data is minimal. However, existing methods still face two persistent challenges: limited corrective supervision in structurally ambiguous or mislabeled regions during supervised training and performance degradation caused by unreliable pseudo-labels on unlabeled data. To address these problems, we propose Region-Aware Instructive Learning (RAIL), a dual-group dual-student, semi-supervised framework. Each group contains two student models guided by a shared teacher network. By alternating training between the two groups, RAIL promotes intergroup knowledge transfer and collaborative region-aware instruction while reducing overfitting to the characteristics of any single model. Specifically, RAIL introduces two instructive mechanisms. Disagreement-Focused Supervision (DFS) Controller improves supervised learning by instructing predictions only within areas where student outputs diverge from both ground truth and the best student, thereby concentrating supervision on structurally ambiguous or mislabeled areas. In the unsupervised phase, Confidence-Aware Learning (CAL) Modulator reinforces agreement in regions with high model certainty while reducing the effect of low-confidence predictions during training. This helps prevent our model from learning unstable patterns and improves the overall reliability of pseudo-labels. Extensive experiments on four CBCT tooth segmentation datasets show that RAIL surpasses state-of-the-art methods under limited annotation. Our code will be available at https://github.com/Tournesol-Saturday/RAIL.

Noise is a ubiquitous feature of the physical world. As a result, the first prerequisite of life is fault tolerance: maintaining integrity of state despite external bombardment. Recent experimental advances have revealed that biological systems achieve fault tolerance by implementing mathematically intricate error-correcting codes and by organizing in a modular fashion that physically separates functionally distinct subsystems. These elaborate structures represent a vanishing volume in the massive genetic configuration space. How is it possible that the primitive process of evolution, by which all biological systems evolved, achieved such unusual results? In this work, through experiments in Boolean networks, we show that the simultaneous presence of error correction and modularity in biological systems is no coincidence. Rather, it is a typical co-occurrence in noisy dynamic systems undergoing evolution. From this, we deduce the principle of error correction enhanced evolvability: systems possessing error-correcting codes are more effectively improved by evolution than those without.

We study inference-time scaling for diffusion models, where the goal is to adapt a pre-trained model to new target distributions without retraining. Existing guidance-based methods are simple but introduce bias, while particle-based corrections suffer from weight degeneracy and high computational cost. We introduce DriftLite, a lightweight, training-free particle-based approach that steers the inference dynamics on the fly with provably optimal stability control. DriftLite exploits a previously unexplored degree of freedom in the Fokker-Planck equation between the drift and particle potential, and yields two practical instantiations: Variance- and Energy-Controlling Guidance (VCG/ECG) for approximating the optimal drift with minimal overhead. Across Gaussian mixture models, particle systems, and large-scale protein-ligand co-folding problems, DriftLite consistently reduces variance and improves sample quality over pure guidance and sequential Monte Carlo baselines. These results highlight a principled, efficient route toward scalable inference-time adaptation of diffusion models.

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)

Direct alignment from preferences (DAP) has emerged as a promising paradigm for aligning large language models (LLMs) to human desiderata from pre-collected, offline preference datasets. While recent studies indicate that existing offline DAP methods can directly benefit from online training samples, we highlight the need to develop specific online DAP algorithms to fully harness the power of online training. Specifically, we identify that the learned LLM should adhere to the proximity of the behavior LLM, which collects the training samples. To this end, we propose online Preference Optimization in proximity to the Behavior LLM (BPO), emphasizing the importance of constructing a proper trust region for LLM alignment. We conduct extensive experiments to validate the effectiveness and applicability of our approach by integrating it with various DAP methods, resulting in significant performance improvements across a wide range of tasks when training with the same amount of preference data. Even when only introducing one additional data collection phase, our online BPO improves its offline DAP baseline from 72.0% to 80.2% on TL;DR and from 82.2% to 89.1% on Anthropic Helpfulness in terms of win rate against human reference text.

Text-to-image diffusion models deliver high-quality images, yet aligning them with human preferences remains challenging. We revisit diffusion-based Direct Preference Optimization (DPO) for these models and identify a critical pathology: enlarging the preference margin does not necessarily improve generation quality. In particular, the standard Diffusion-DPO objective can increase the reconstruction error of both winner and loser branches. Consequently, degradation of the less-preferred outputs can become sufficiently severe that the preferred branch is also adversely affected even as the margin grows. To address this, we introduce Diffusion-SDPO, a safeguarded update rule that preserves the winner by adaptively scaling the loser gradient according to its alignment with the winner gradient. A first-order analysis yields a closed-form scaling coefficient that guarantees the error of the preferred output is non-increasing at each optimization step. Our method is simple, model-agnostic, broadly compatible with existing DPO-style alignment frameworks and adds only marginal computational overhead. Across standard text-to-image benchmarks, Diffusion-SDPO delivers consistent gains over preference-learning baselines on automated preference, aesthetic, and prompt alignment metrics. Code is publicly available at https://github.com/AIDC-AI/Diffusion-SDPO.

Molecular docking is an important tool for structure-based drug design, accelerating the efficiency of drug development. Complex and dynamic binding processes between proteins and small molecules require searching and sampling over a wide spatial range. Traditional docking by searching for possible binding sites and conformations is computationally complex and results poorly under blind docking. Quantum-inspired algorithms combining quantum properties and annealing show great advantages in solving combinatorial optimization problems. Inspired by this, we achieve an improved in blind docking by using quantum-inspired combined with gradients learned by deep learning in the encoded molecular space. Numerical simulation shows that our method outperforms traditional docking algorithms and deep learning-based algorithms over 10\%. Compared to the current state-of-the-art deep learning-based docking algorithm DiffDock, the success rate of Top-1 (RMSD<2) achieves an improvement from 33\% to 35\% in our same setup. In particular, a 6\% improvement is realized in the high-precision region(RMSD<1) on molecules data unseen in DiffDock, which demonstrates the well-generalized of our method.

LLM agents have demonstrated remarkable performance across various applications, primarily due to their advanced capabilities in reasoning, utilizing external knowledge and tools, calling APIs, and executing actions to interact with environments. Current agents typically utilize a memory module or a retrieval-augmented generation (RAG) mechanism, retrieving past knowledge and instances with similar embeddings from knowledge bases to inform task planning and execution. However, the reliance on unverified knowledge bases raises significant concerns about their safety and trustworthiness. To uncover such vulnerabilities, we propose a novel red teaming approach AgentPoison, the first backdoor attack targeting generic and RAG-based LLM agents by poisoning their long-term memory or RAG knowledge base. In particular, we form the trigger generation process as a constrained optimization to optimize backdoor triggers by mapping the triggered instances to a unique embedding space, so as to ensure that whenever a user instruction contains the optimized backdoor trigger, the malicious demonstrations are retrieved from the poisoned memory or knowledge base with high probability. In the meantime, benign instructions without the trigger will still maintain normal performance. Unlike conventional backdoor attacks, AgentPoison requires no additional model training or fine-tuning, and the optimized backdoor trigger exhibits superior transferability, in-context coherence, and stealthiness. Extensive experiments demonstrate AgentPoison's effectiveness in attacking three types of real-world LLM agents: RAG-based autonomous driving agent, knowledge-intensive QA agent, and healthcare EHRAgent. On each agent, AgentPoison achieves an average attack success rate higher than 80% with minimal impact on benign performance (less than 1%) with a poison rate less than 0.1%.

Drug discovery is a complex process that involves multiple scenarios and stages, such as fragment-constrained molecule generation, hit generation and lead optimization. However, existing molecular generative models can only tackle one or two of these scenarios and lack the flexibility to address various aspects of the drug discovery pipeline. In this paper, we present Generalist Molecular generative model (GenMol), a versatile framework that addresses these limitations by applying discrete diffusion to the Sequential Attachment-based Fragment Embedding (SAFE) molecular representation. GenMol generates SAFE sequences through non-autoregressive bidirectional parallel decoding, thereby allowing utilization of a molecular context that does not rely on the specific token ordering and enhanced computational efficiency. Moreover, under the discrete diffusion framework, we introduce fragment remasking, a strategy that optimizes molecules by replacing fragments with masked tokens and regenerating them, enabling effective exploration of chemical space. GenMol significantly outperforms the previous GPT-based model trained on SAFE representations in de novo generation and fragment-constrained generation, and achieves state-of-the-art performance in goal-directed hit generation and lead optimization. These experimental results demonstrate that GenMol can tackle a wide range of drug discovery tasks, providing a unified and versatile approach for molecular design.

Recent advances in protein structure prediction have achieved near-atomic accuracy for well-folded proteins. However, current benchmarks inadequately assess model performance in biologically challenging contexts, especially those involving intrinsically disordered regions (IDRs), limiting their utility in applications such as drug discovery, disease variant interpretation, and protein interface design. We introduce DisProtBench, a comprehensive benchmark for evaluating protein structure prediction models (PSPMs) under structural disorder and complex biological conditions. DisProtBench spans three key axes: (1) Data complexity, covering disordered regions, G protein-coupled receptor (GPCR) ligand pairs, and multimeric complexes; (2) Task diversity, benchmarking twelve leading PSPMs across structure-based tasks with unified classification, regression, and interface metrics; and (3) Interpretability, via the DisProtBench Portal, which provides precomputed 3D structures and visual error analyses. Our results reveal significant variability in model robustness under disorder, with low-confidence regions linked to functional prediction failures. Notably, global accuracy metrics often fail to predict task performance in disordered settings, emphasizing the need for function-aware evaluation. DisProtBench establishes a reproducible, extensible, and biologically grounded framework for assessing next-generation PSPMs in realistic biomedical scenarios.

Reinforcement learning from human feedback (RLHF) has proven effective in aligning large language models (LLMs) with human preferences, but often at the cost of reduced output diversity. This trade-off between diversity and alignment quality remains a significant challenge. Drawing inspiration from curiosity-driven exploration in reinforcement learning, we introduce curiosity-driven RLHF (CD-RLHF), a framework that incorporates intrinsic rewards for novel states, alongside traditional sparse extrinsic rewards, to optimize both output diversity and alignment quality. We demonstrate the effectiveness of CD-RLHF through extensive experiments on a range of tasks, including text summarization and instruction following. Our approach achieves significant gains in diversity on multiple diversity-oriented metrics while maintaining alignment with human preferences comparable to standard RLHF. We make our code publicly available at https://github.com/ernie-research/CD-RLHF.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

A central paradox in fine-tuning Large Language Models (LLMs) with Reinforcement Learning with Verifiable Reward (RLVR) is the frequent degradation of multi-attempt performance (Pass@k) despite improvements in single-attempt accuracy (Pass@1). This is often accompanied by catastrophic forgetting, where models lose previously acquired skills. While various methods have been proposed, the choice and function of the divergence term have been surprisingly unexamined as a proactive solution. We argue that standard RLVR objectives -- both those using the mode-seeking reverse KL-divergence and those forgoing a divergence term entirely -- lack a crucial mechanism for knowledge retention. The reverse-KL actively accelerates this decay by narrowing the policy, while its absence provides no safeguard against the model drifting from its diverse knowledge base. We propose a fundamental shift in perspective: using the divergence term itself as the solution. Our framework, Diversity-Preserving Hybrid RL (DPH-RL), leverages mass-covering f-divergences (like forward-KL and JS-divergence) to function as a rehearsal mechanism. By continuously referencing the initial policy, this approach forces the model to maintain broad solution coverage. Extensive experiments on math and SQL generation demonstrate that DPH-RL not only resolves the Pass@k degradation but improves both Pass@1 and Pass@k in- and out-of-domain. Additionally, DPH-RL is more training-efficient because it computes f-divergence using generator functions, requiring only sampling from the initial policy and no online reference model. Our work highlights a crucial, overlooked axis for improving RLVR, demonstrating that the proper selection of a divergence measure is a powerful tool for building more general and diverse reasoning models.

Designing biological sequences is an important challenge that requires satisfying complex constraints and thus is a natural problem to address with deep generative modeling. Diffusion generative models have achieved considerable success in many applications. Score-based generative stochastic differential equations (SDE) model is a continuous-time diffusion model framework that enjoys many benefits, but the originally proposed SDEs are not naturally designed for modeling discrete data. To develop generative SDE models for discrete data such as biological sequences, here we introduce a diffusion process defined in the probability simplex space with stationary distribution being the Dirichlet distribution. This makes diffusion in continuous space natural for modeling discrete data. We refer to this approach as Dirchlet diffusion score model. We demonstrate that this technique can generate samples that satisfy hard constraints using a Sudoku generation task. This generative model can also solve Sudoku, including hard puzzles, without additional training. Finally, we applied this approach to develop the first human promoter DNA sequence design model and showed that designed sequences share similar properties with natural promoter sequences.

Large language models (LLMs), exemplified by ChatGPT, have gained considerable attention for their excellent natural language processing capabilities. Nonetheless, these LLMs present many challenges, particularly in the realm of trustworthiness. Therefore, ensuring the trustworthiness of LLMs emerges as an important topic. This paper introduces TrustLLM, a comprehensive study of trustworthiness in LLMs, including principles for different dimensions of trustworthiness, established benchmark, evaluation, and analysis of trustworthiness for mainstream LLMs, and discussion of open challenges and future directions. Specifically, we first propose a set of principles for trustworthy LLMs that span eight different dimensions. Based on these principles, we further establish a benchmark across six dimensions including truthfulness, safety, fairness, robustness, privacy, and machine ethics. We then present a study evaluating 16 mainstream LLMs in TrustLLM, consisting of over 30 datasets. Our findings firstly show that in general trustworthiness and utility (i.e., functional effectiveness) are positively related. Secondly, our observations reveal that proprietary LLMs generally outperform most open-source counterparts in terms of trustworthiness, raising concerns about the potential risks of widely accessible open-source LLMs. However, a few open-source LLMs come very close to proprietary ones. Thirdly, it is important to note that some LLMs may be overly calibrated towards exhibiting trustworthiness, to the extent that they compromise their utility by mistakenly treating benign prompts as harmful and consequently not responding. Finally, we emphasize the importance of ensuring transparency not only in the models themselves but also in the technologies that underpin trustworthiness. Knowing the specific trustworthy technologies that have been employed is crucial for analyzing their effectiveness.

Existing safety assurance research has primarily focused on training-phase alignment to instill safe behaviors into LLMs. However, recent studies have exposed these methods' susceptibility to diverse jailbreak attacks. Concurrently, inference scaling has significantly advanced LLM reasoning capabilities but remains unexplored in the context of safety assurance. Addressing this gap, our work pioneers inference scaling for robust and effective LLM safety against emerging threats. We reveal that conventional inference scaling techniques, despite their success in reasoning tasks, perform poorly in safety contexts, even falling short of basic approaches like Best-of-N Sampling. We attribute this inefficiency to a newly identified challenge, the exploration--efficiency dilemma, arising from the high computational overhead associated with frequent process reward model (PRM) evaluations. To overcome this dilemma, we propose SAFFRON, a novel inference scaling paradigm tailored explicitly for safety assurance. Central to our approach is the introduction of a multifurcation reward model (MRM) that significantly reduces the required number of reward model evaluations. To operationalize this paradigm, we further propose: (i) a partial supervision training objective for MRM, (ii) a conservative exploration constraint to prevent out-of-distribution explorations, and (iii) a Trie-based key--value caching strategy that facilitates cache sharing across sequences during tree search. Extensive experiments validate the effectiveness of our method. Additionally, we publicly release our trained multifurcation reward model (Saffron-1) and the accompanying token-level safety reward dataset (Safety4M) to accelerate future research in LLM safety. Our code, model, and data are publicly available at https://github.com/q-rz/saffron , and our project homepage is at https://q-rz.github.io/p/saffron .

Population-based search has recently emerged as a possible alternative to Reinforcement Learning (RL) for black-box neural architecture search (NAS). It performs well in practice even though it is not theoretically well understood. In particular, whereas traditional population-based search methods such as evolutionary algorithms (EAs) draw much power from crossover operations, it is difficult to take advantage of them in NAS. The main obstacle is believed to be the permutation problem: The mapping between genotype and phenotype in traditional graph representations is many-to-one, leading to a disruptive effect of standard crossover. This paper presents the first theoretical analysis of the behaviors of mutation, crossover and RL in black-box NAS, and proposes a new crossover operator based on the shortest edit path (SEP) in graph space. The SEP crossover is shown theoretically to overcome the permutation problem, and as a result, have a better expected improvement compared to mutation, standard crossover and RL. Further, it empirically outperform these other methods on state-of-the-art NAS benchmarks. The SEP crossover therefore allows taking full advantage of population-based search in NAS, and the underlying theory can serve as a foundation for deeper understanding of black-box NAS methods in general.

Reinforcement Learning with Human Feedback (RLHF) is a methodology designed to align Large Language Models (LLMs) with human preferences, playing an important role in LLMs alignment. Despite its advantages, RLHF relies on human annotators to rank the text, which can introduce potential security vulnerabilities if any adversarial annotator (i.e., attackers) manipulates the ranking score by up-ranking any malicious text to steer the LLM adversarially. To assess the red-teaming of RLHF against human preference data poisoning, we propose RankPoison, a poisoning attack method on candidates' selection of preference rank flipping to reach certain malicious behaviors (e.g., generating longer sequences, which can increase the computational cost). With poisoned dataset generated by RankPoison, we can perform poisoning attacks on LLMs to generate longer tokens without hurting the original safety alignment performance. Moreover, applying RankPoison, we also successfully implement a backdoor attack where LLMs can generate longer answers under questions with the trigger word. Our findings highlight critical security challenges in RLHF, underscoring the necessity for more robust alignment methods for LLMs.

Causal abstraction is a promising theoretical framework for explainable artificial intelligence that defines when an interpretable high-level causal model is a faithful simplification of a low-level deep learning system. However, existing causal abstraction methods have two major limitations: they require a brute-force search over alignments between the high-level model and the low-level one, and they presuppose that variables in the high-level model will align with disjoint sets of neurons in the low-level one. In this paper, we present distributed alignment search (DAS), which overcomes these limitations. In DAS, we find the alignment between high-level and low-level models using gradient descent rather than conducting a brute-force search, and we allow individual neurons to play multiple distinct roles by analyzing representations in non-standard bases-distributed representations. Our experiments show that DAS can discover internal structure that prior approaches miss. Overall, DAS removes previous obstacles to conducting causal abstraction analyses and allows us to find conceptual structure in trained neural nets.

The transcriptional response to genetic perturbation reveals fundamental insights into complex cellular systems. While current approaches have made progress in predicting genetic perturbation responses, they provide limited biological understanding and cannot systematically refine existing knowledge. Overcoming these limitations requires an end-to-end integration of data-driven learning and existing knowledge. However, this integration is challenging due to inconsistencies between data and knowledge bases, such as noise, misannotation, and incompleteness. To address this challenge, we propose ALIGNED (Adaptive aLignment for Inconsistent Genetic kNowledgE and Data), a neuro-symbolic framework based on the Abductive Learning (ABL) paradigm. This end-to-end framework aligns neural and symbolic components and performs systematic knowledge refinement. We introduce a balanced consistency metric to evaluate the predictions' consistency against both data and knowledge. Our results show that ALIGNED outperforms state-of-the-art methods by achieving the highest balanced consistency, while also re-discovering biologically meaningful knowledge. Our work advances beyond existing methods to enable both the transparency and the evolution of mechanistic biological understanding.

Designing antibody sequences to better resemble those observed in natural human repertoires is a key challenge in biologics development. We introduce IgCraft: a multi-purpose model for paired human antibody sequence generation, built on Bayesian Flow Networks. IgCraft presents one of the first unified generative modeling frameworks capable of addressing multiple antibody sequence design tasks with a single model, including unconditional sampling, sequence inpainting, inverse folding, and CDR motif scaffolding. Our approach achieves competitive results across the full spectrum of these tasks while constraining generation to the space of human antibody sequences, exhibiting particular strengths in CDR motif scaffolding (grafting) where we achieve state-of-the-art performance in terms of humanness and preservation of structural properties. By integrating previously separate tasks into a single scalable generative model, IgCraft provides a versatile platform for sampling human antibody sequences under a variety of contexts relevant to antibody discovery and engineering. Model code and weights are publicly available at github.com/mgreenig/IgCraft.

As Large Language Model (LLM) agents increasingly gain self-evolutionary capabilities to adapt and refine their strategies through real-world interaction, their long-term reliability becomes a critical concern. We identify the Alignment Tipping Process (ATP), a critical post-deployment risk unique to self-evolving LLM agents. Unlike training-time failures, ATP arises when continual interaction drives agents to abandon alignment constraints established during training in favor of reinforced, self-interested strategies. We formalize and analyze ATP through two complementary paradigms: Self-Interested Exploration, where repeated high-reward deviations induce individual behavioral drift, and Imitative Strategy Diffusion, where deviant behaviors spread across multi-agent systems. Building on these paradigms, we construct controllable testbeds and benchmark Qwen3-8B and Llama-3.1-8B-Instruct. Our experiments show that alignment benefits erode rapidly under self-evolution, with initially aligned models converging toward unaligned states. In multi-agent settings, successful violations diffuse quickly, leading to collective misalignment. Moreover, current reinforcement learning-based alignment methods provide only fragile defenses against alignment tipping. Together, these findings demonstrate that alignment of LLM agents is not a static property but a fragile and dynamic one, vulnerable to feedback-driven decay during deployment. Our data and code are available at https://github.com/aiming-lab/ATP.

Conditioning image generation facilitates seamless editing and the creation of photorealistic images. However, conditioning on noisy or Out-of-Distribution (OoD) images poses significant challenges, particularly in balancing fidelity to the input and realism of the output. We introduce Confident Ordinary Differential Editing (CODE), a novel approach for image synthesis that effectively handles OoD guidance images. Utilizing a diffusion model as a generative prior, CODE enhances images through score-based updates along the probability-flow Ordinary Differential Equation (ODE) trajectory. This method requires no task-specific training, no handcrafted modules, and no assumptions regarding the corruptions affecting the conditioning image. Our method is compatible with any diffusion model. Positioned at the intersection of conditional image generation and blind image restoration, CODE operates in a fully blind manner, relying solely on a pre-trained generative model. Our method introduces an alternative approach to blind restoration: instead of targeting a specific ground truth image based on assumptions about the underlying corruption, CODE aims to increase the likelihood of the input image while maintaining fidelity. This results in the most probable in-distribution image around the input. Our contributions are twofold. First, CODE introduces a novel editing method based on ODE, providing enhanced control, realism, and fidelity compared to its SDE-based counterpart. Second, we introduce a confidence interval-based clipping method, which improves CODE's effectiveness by allowing it to disregard certain pixels or information, thus enhancing the restoration process in a blind manner. Experimental results demonstrate CODE's effectiveness over existing methods, particularly in scenarios involving severe degradation or OoD inputs.

Reinforcement learning with stochastic optimal control offers a promising framework for diffusion fine-tuning, where a pre-trained diffusion model is optimized to generate paths that lead to a reward-tilted distribution. While these approaches enable optimization without access to explicit samples from the optimal distribution, they require training on rollouts under the current fine-tuned model, making them susceptible to reinforcing sub-optimal trajectories that yield poor rewards. To overcome this challenge, we introduce TRee Search Guided TRajectory-Aware Fine-Tuning for Discrete Diffusion (TR2-D2), a novel framework that optimizes reward-guided discrete diffusion trajectories with tree search to construct replay buffers for trajectory-aware fine-tuning. These buffers are generated using Monte Carlo Tree Search (MCTS) and subsequently used to fine-tune a pre-trained discrete diffusion model under a stochastic optimal control objective. We validate our framework on single- and multi-objective fine-tuning of biological sequence diffusion models, highlighting the overall effectiveness of TR2-D2 for reliable reward-guided fine-tuning in discrete sequence generation.

Greedy search methods like Greedy Best-First Search (GBFS) and Enforced Hill-Climbing (EHC) often struggle when faced with Uninformed Heuristic Regions (UHRs) like heuristic local minima or plateaus. In this work, we theoretically and empirically compare two popular methods for escaping UHRs in breadth-first search (BrFS) and restarting random walks (RRWs). We first derive the expected runtime of escaping a UHR using BrFS and RRWs, based on properties of the UHR and the random walk procedure, and then use these results to identify when RRWs will be faster in expectation than BrFS. We then evaluate these methods for escaping UHRs by comparing standard EHC, which uses BrFS to escape UHRs, to variants of EHC called EHC-RRW, which use RRWs for that purpose. EHC-RRW is shown to have strong expected runtime guarantees in cases where EHC has previously been shown to be effective. We also run experiments with these approaches on PDDL planning benchmarks to better understand their relative effectiveness for escaping UHRs.

Fuzzing is an important dynamic program analysis technique designed for finding vulnerabilities in complex software. Fuzzing involves presenting a target program with crafted malicious input to cause crashes, buffer overflows, memory errors, and exceptions. Crafting malicious inputs in an efficient manner is a difficult open problem and the best approaches often apply uniform random mutations to pre-existing valid inputs. In this work, we propose to adopt fine-tuned large language models (FuzzCoder) to learn patterns in the input files from successful attacks to guide future fuzzing explorations. Specifically, we develop a framework to leverage the code LLMs to guide the mutation process of inputs in fuzzing. The mutation process is formulated as the sequence-to-sequence modeling, where LLM receives a sequence of bytes and then outputs the mutated byte sequence. FuzzCoder is fine-tuned on the created instruction dataset (Fuzz-Instruct), where the successful fuzzing history is collected from the heuristic fuzzing tool. FuzzCoder can predict mutation locations and strategies locations in input files to trigger abnormal behaviors of the program. Experimental results show that FuzzCoder based on AFL (American Fuzzy Lop) gain significant improvements in terms of effective proportion of mutation (EPM) and number of crashes (NC) for various input formats including ELF, JPG, MP3, and XML.

In a convergence of machine learning and biology, we reveal that diffusion models are evolutionary algorithms. By considering evolution as a denoising process and reversed evolution as diffusion, we mathematically demonstrate that diffusion models inherently perform evolutionary algorithms, naturally encompassing selection, mutation, and reproductive isolation. Building on this equivalence, we propose the Diffusion Evolution method: an evolutionary algorithm utilizing iterative denoising -- as originally introduced in the context of diffusion models -- to heuristically refine solutions in parameter spaces. Unlike traditional approaches, Diffusion Evolution efficiently identifies multiple optimal solutions and outperforms prominent mainstream evolutionary algorithms. Furthermore, leveraging advanced concepts from diffusion models, namely latent space diffusion and accelerated sampling, we introduce Latent Space Diffusion Evolution, which finds solutions for evolutionary tasks in high-dimensional complex parameter space while significantly reducing computational steps. This parallel between diffusion and evolution not only bridges two different fields but also opens new avenues for mutual enhancement, raising questions about open-ended evolution and potentially utilizing non-Gaussian or discrete diffusion models in the context of Diffusion Evolution.

As the marginal cost of scaling computation (data and parameters) during model pre-training continues to increase substantially, test-time scaling (TTS) has emerged as a promising direction for improving generative model performance by allocating additional computation at inference time. While TTS has demonstrated significant success across multiple language tasks, there remains a notable gap in understanding the test-time scaling behaviors of image and video generative models (diffusion-based or flow-based models). Although recent works have initiated exploration into inference-time strategies for vision tasks, these approaches face critical limitations: being constrained to task-specific domains, exhibiting poor scalability, or falling into reward over-optimization that sacrifices sample diversity. In this paper, we propose Evolutionary Search (EvoSearch), a novel, generalist, and efficient TTS method that effectively enhances the scalability of both image and video generation across diffusion and flow models, without requiring additional training or model expansion. EvoSearch reformulates test-time scaling for diffusion and flow models as an evolutionary search problem, leveraging principles from biological evolution to efficiently explore and refine the denoising trajectory. By incorporating carefully designed selection and mutation mechanisms tailored to the stochastic differential equation denoising process, EvoSearch iteratively generates higher-quality offspring while preserving population diversity. Through extensive evaluation across both diffusion and flow architectures for image and video generation tasks, we demonstrate that our method consistently outperforms existing approaches, achieves higher diversity, and shows strong generalizability to unseen evaluation metrics. Our project is available at the website https://tinnerhrhe.github.io/evosearch.

Large language models (LLMs) have become increasingly prevalent in our daily lives, leading to an expectation for LLMs to be trustworthy -- - both accurate and well-calibrated (the prediction confidence should align with its ground truth correctness likelihood). Nowadays, fine-tuning has become the most popular method for adapting a model to practical usage by significantly increasing accuracy on downstream tasks. Despite the great accuracy it achieves, we found fine-tuning is still far away from satisfactory trustworthiness due to "tuning-induced mis-calibration". In this paper, we delve deeply into why and how mis-calibration exists in fine-tuned models, and how distillation can alleviate the issue. Then we further propose a brand new method named Efficient Trustworthy Distillation (FIRST), which utilizes a small portion of teacher's knowledge to obtain a reliable language model in a cost-efficient way. Specifically, we identify the "concentrated knowledge" phenomenon during distillation, which can significantly reduce the computational burden. Then we apply a "trustworthy maximization" process to optimize the utilization of this small portion of concentrated knowledge before transferring it to the student. Experimental results demonstrate the effectiveness of our method, where better accuracy (+2.3%) and less mis-calibration (-10%) are achieved on average across both in-domain and out-of-domain scenarios, indicating better trustworthiness.

The study of hardest and easiest fitness landscapes is an active area of research. Recently, Kaufmann, Larcher, Lengler and Zou conjectured that for the self-adjusting (1,lambda)-EA, Adversarial Dynamic BinVal (ADBV) is the hardest dynamic monotone function to optimize. We introduce the function Switching Dynamic BinVal (SDBV) which coincides with ADBV whenever the number of remaining zeros in the search point is strictly less than n/2, where n denotes the dimension of the search space. We show, using a combinatorial argument, that for the (1+1)-EA with any mutation rate p in [0,1], SDBV is drift-minimizing among the class of dynamic monotone functions. Our construction provides the first explicit example of an instance of the partially-ordered evolutionary algorithm (PO-EA) model with parameterized pessimism introduced by Colin, Doerr and F\'erey, building on work of Jansen. We further show that the (1+1)-EA optimizes SDBV in Theta(n^{3/2}) generations. Our simulations demonstrate matching runtimes for both static and self-adjusting (1,lambda) and (1+lambda)-EA. We further show, using an example of fixed dimension, that drift-minimization does not equal maximal runtime.

Recent advances in Conditional Diffusion Models have led to substantial capabilities in various domains. However, understanding the impact of variations in the initial seed vector remains an underexplored area of concern. Particularly, latent-based diffusion models display inconsistencies in image generation under standard conditions when initialized with suboptimal initial seed vectors. To understand the impact of the initial seed vector on generated samples, we propose a reliability evaluation framework that evaluates the generated samples of a diffusion model when the initial seed vector is subjected to various synthetic shifts. Our results indicate that slight manipulations to the initial seed vector of the state-of-the-art Stable Diffusion (Rombach et al., 2022) can lead to significant disturbances in the generated samples, consequently creating images without the effect of conditioning variables. In contrast, GLIDE (Nichol et al., 2022) stands out in generating reliable samples even when the initial seed vector is transformed. Thus, our study sheds light on the importance of the selection and the impact of the initial seed vector in the latent-based diffusion model.

In precision medicine, quantitative multi-omic features, topological context, and textual biological knowledge play vital roles in identifying disease-critical signaling pathways and targets. Existing pipelines capture only part of these-numerical omics ignore topological context, text-centric LLMs lack quantitative grounded reasoning, and graph-only models underuse node semantics and the generalization of LLMs-limiting mechanistic interpretability. Although Process Reward Models (PRMs) aim to guide reasoning in LLMs, they remain limited by unreliable intermediate evaluation, and vulnerability to reward hacking with computational cost. These gaps motivate integrating quantitative multi-omic signals, topological structure with node annotations, and literature-scale text via LLMs, using subgraph reasoning as the principle bridge linking numeric evidence, topological knowledge and language context. Therefore, we propose GALAX (Graph Augmented LAnguage model with eXplainability), an innovative framework that integrates pretrained Graph Neural Networks (GNNs) into Large Language Models (LLMs) via reinforcement guided by a Graph Process Reward Model (GPRM), which generates disease-relevant subgraphs in a step-wise manner initiated by an LLM and iteratively evaluated by a pretrained GNN, enabling process-level supervision without explicit intermediate reasoning annotations. As an application, we also introduced Target-QA, a benchmark combining CRISPR-identified targets, multi-omic profiles, and biomedical graph knowledge across diverse cancer cell lines, which enables GNN pretraining for supervising step-wise graph construction and supports long-context reasoning over text-numeric graphs (TNGs), providing a scalable and biologically grounded framework for explainable, reinforcement-guided subgraph reasoning toward reliable and interpretable target and pathway discovery in precision medicine.

Aligning diffusion models to downstream tasks often requires finetuning new models or gradient-based guidance at inference time to enable sampling from the reward-tilted posterior. In this work, we explore a simple inference-time gradient-free guidance approach, called controlled denoising (CoDe), that circumvents the need for differentiable guidance functions and model finetuning. CoDe is a blockwise sampling method applied during intermediate denoising steps, allowing for alignment with downstream rewards. Our experiments demonstrate that, despite its simplicity, CoDe offers a favorable trade-off between reward alignment, prompt instruction following, and inference cost, achieving a competitive performance against the state-of-the-art baselines. Our code is available at: https://github.com/anujinho/code.