Antimicrobial peptides have emerged as promising molecules to combat antimicrobial resistance. However, fragmented datasets, inconsistent annotations, and the lack of standardized benchmarks hinder computational approaches and slow down the discovery of new candidates. To address these challenges, we present the Expanded Standardized Collection for Antimicrobial Peptide Evaluation (ESCAPE), an experimental framework integrating over 80000 peptides from 27 validated repositories. Our dataset separates antimicrobial peptides from negative sequences and incorporates their functional annotations into a biologically coherent multilabel hierarchy, capturing activities across antibacterial, antifungal, antiviral, and antiparasitic classes. Building on ESCAPE, we propose a transformer-based model that leverages sequence and structural information to predict multiple functional activities of peptides. Our method achieves up to a 2.56% relative average improvement in mean Average Precision over the second-best method adapted for this task, establishing a new state-of-the-art multilabel peptide classification. ESCAPE provides a comprehensive and reproducible evaluation framework to advance AI-driven antimicrobial peptide research.

Understanding what and how neural networks memorize during training is crucial, both from the perspective of unintentional memorization of potentially sensitive information and from the standpoint of effective knowledge acquisition for realworld, knowledge-intensive tasks. While previous studies primarily investigate memorization within a single modality, such as text memorization in large language models or image memorization in diffusion models, unified multimodal models are becoming increasingly prevalent in practical applications. In this work, we focus on the unique characteristics of cross-modality memorization and conduct a systematic study centered on vision-language models. To facilitate controlled experiments, we first introduce a synthetic persona dataset comprising diverse synthetic person images and textual descriptions. We quantify factual knowledge memorization and cross-modal transferability by training models on a single modality and evaluating their performance in the other. Our results reveal that facts learned in one modality transfer to the other, but a significant gap exists between recalling information in the "source" and "target" modalities. Furthermore, we observe that this gap exists across various scenarios, including more capable models, machine unlearning, and the multi-hop case. At the end, we propose a baseline method to mitigate this challenge. We hope our study can inspire future research on developing more robust multimodal learning techniques to enhance cross-modal transferability.

We study the problem of creating strong, yet narrow, AI systems. While recent AI progress has been driven by the training of large general-purpose foundation models, the creation of smaller models specialized for narrow domains could be valuable for both efficiency and safety. In this work, we explore two challenges involved in creating narrow AI systems, having to do with basic properties of how neural networks learn and structure their representations. The first challenge regards when it is possible to train narrow models from scratch. Through experiments on a synthetic task, we find that it is sometimes necessary to train networks on a wide distribution of data to learn certain narrow skills within that distribution.

Multi-agent AI systems powered by large language models (LLMs) are increasingly applied to solve complex tasks. However, these systems often rely on fragile, manually designed prompts and heuristics, making optimization difficult. A key challenge in optimizing multi-agent systems is acquiring suitable training data for specialized agents. We introduce SIRIUS, a self-improving, reasoning-driven optimization framework for multi-agent systems. Central to our approach is the construction of an experience library: a repository of high-quality reasoning trajectories. The library is built by retaining reasoning steps that lead to successful outcomes, providing a robust training set for optimizing multi-agent system. Additionally, we introduce a library augmentation procedure that refines unsuccessful trajectories, further enriching the library. SIRIUS boosts performance by 2.86% to 21.88% on reasoning and biomedical QA and enhances agent negotiation in competitive settings. Our results show that SIRIUS enhances multi-agent performance while generating reusable data for self-correction and self-play enhancement in the future.

Despite enthusiasm for Multi-Agent LLMSystems (MAS), their performance gains on popular benchmarks are often minimal. This gap highlights a critical need for a principled understanding of why MAS fail. Addressing this question requires systematic identification and analysis of failure patterns. We introduce MAST-Data, a comprehensive dataset of 1600+ annotated traces collected across 7 popular MAS frameworks. MAST-Data is the first multi-agent system dataset to outline the failure dynamics in MAS for guiding the development of better future systems.

Pretrained language models are remarkably effective in aligning with human brain responses elicited by natural language stimuli, positioning them as promising model organisms for studying language processing in the brain. However, existing approaches for both estimating and improving this brain alignment are participantdependent and highly affected by the amount of data available per participant, hindering both generalization to new participants and population-level analyses. In this work, we address these limitations by introducing a scalable, generalizable brain-tuning method, in which we fine-tune pretrained speech language models to jointly predict fMRI responses from multiple participants. We demonstrate that the resulting brain-tuned models exhibit strong individual brain alignment while generalizing across participants. Specifically, our method leads to 1) a 5-fold decrease in the amount of fMRI data needed to predict brain data from new participants, 2) up to a 50% increase in the overall brain alignment, and 3) strong generalization to new unseen datasets. Furthermore, this multi-participant brain-tuning additionally improves downstream performance on semantic tasks, suggesting that training using brain data from multiple participants leads to more generalizable semantic representations. Taken together, these findings demonstrate a bidirectional benefit between neuroscience and AI, helping bridge the gap between the two fields.

A multi-agent system (MAS) enhances its capacity to solve complex natural language processing (NLP) tasks through collaboration among multiple agents, where consensus-seeking serves as a fundamental mechanism. However, existing consensus-seeking approaches typically rely on voting mechanisms to judge consensus, overlooking contradictions in system-internal beliefs that destabilize the consensus. Moreover, these methods often involve agents updating their results through indiscriminate collaboration with every other agent. Such uniform interaction fails to identify the optimal collaborators for each agent, hindering the emergence of a stable consensus. To address these challenges, we provide a theoretical framework for selecting optimal collaborators that maximize consensus stability. Based on the theorems, we propose the Belief-Calibrated Consensus Seeking (BCCS) framework to facilitate stable consensus via selecting optimal collaborators and calibrating the consensus judgment by system-internal beliefs. Experimental results on the MATH and MMLU benchmark datasets demonstrate that the proposed BCCS framework outperforms the best existing results by 2.23% and 3.95% of accuracy on challenging tasks, respectively.

Estimating the Kullback-Leibler (KL) divergence between language models has many applications, e.g., reinforcement learning from human feedback (RLHF), interpretability, and knowledge distillation. However, computing the exact KL divergence between two arbitrary language models is intractable. Thus, practitioners often resort to sampling-based estimators. While it is easy to fashion a simple Monte Carlo (MC) estimator that provides an unbiased estimate of the KL divergence between language models, this estimator notoriously suffers from high variance and can even result in a negative estimate of the KL divergence, a non-negative quantity. In this paper, we introduce a Rao-Blackwellized estimator that is unbiased and provably has variance less than or equal to that of the standard Monte Carlo estimator. In an empirical study on sentiment-controlled fine-tuning, we show that our estimator provides more stable KL estimates and reduces variance substantially. Additionally, we derive an analogous Rao-Blackwellized estimator of the gradient of the KL divergence, which leads to more stable training and produces models that more frequently appear on the Pareto frontier of reward vs. KL compared to the ones trained with the MC estimator of the gradient.

The "right to be forgotten" and the data privacy laws that encode it have motivated machine unlearning since its earliest days. Now, some argue that an inbound wave of artificial intelligence regulations -- like the European Union's Artificial Intelligence Act (AIA) -- may offer important new use cases for machine unlearning. However, this position paper argues, this opportunity will only be realized if researchers proactively bridge the (sometimes sizable) gaps between machine unlearning's state of the art and its potential applications to AI regulation. To demonstrate this point, we use the AIA as our primary case study. Specifically, we deliver a "state of the union" as regards machine unlearning's current potential (or, in many cases, lack thereof) for aiding compliance with various provisions of the AIA. This starts with a precise cataloging of the potential applications of machine unlearning to AIA compliance. For each, we flag the technical gaps that exist between the potential application and the state of the art of machine unlearning. Finally, we end with a call to action: for machine learning researchers to solve the open technical questions that could unlock machine unlearning's potential to assist compliance with the AIA -- and other AI regulations like it.

Transformers have revolutionized nucleotide sequence analysis, yet capturing long-range dependencies remains challenging. Recent studies show that autoregressive transformers often exhibit Markovian behavior by relying on fixed-length context windows for next-token prediction. However, standard self-attention mechanisms are computationally inefficient for long sequences due to their quadratic complexity and do not explicitly enforce global transition consistency. We introduce CARMANIA (Context-Aware Regularization with Markovian Integration for Attention-Based Nucleotide Analysis), a self-supervised pretraining framework that augments next-token (NT) prediction with a transition-matrix (TM) loss. The TM loss aligns predicted token transitions with empirically derived ngram statistics from each input sequence, encouraging the model to capture higherorder dependencies beyond local context.