Mechanisms of AI Protein Folding in ESMFold

How do protein structure prediction models fold proteins? We investigate this question by tracing how ESMFold folds a beta hairpin, a prevalent structural motif. Through counterfactual interventions on model latents, we identify two computational stages in the folding trunk. In the first stage, early blocks initialize pairwise biochemical signals: residue identities and associated biochemical features such as charge flow from sequence representations into pairwise representations. In the second stage, late blocks develop pairwise spatial features: distance and contact information accumulate in the pairwise representation. We demonstrate that the mechanisms underlying structural decisions of ESMFold can be localized, traced through interpretable representations, and manipulated with strong causal effects.

Decomposing Query-Key Feature Interactions Using Contrastive Covariances

Despite the central role of attention heads in Transformers, we lack tools to understand why a model attends to a particular token. To address this, we study the query-key (QK) space -- the bilinear joint embedding space between queries and keys. We present a contrastive covariance method to decompose the QK space into low-rank, human-interpretable components. It is when features in keys and queries align in these low-rank subspaces that high attention scores are produced. We first study our method both analytically and empirically in a simplified setting. We then apply our method to large language models to identify human-interpretable QK subspaces for categorical semantic features and binding features. Finally, we demonstrate how attention scores can be attributed to our identified features.

Investigating the Development of Task-Oriented Communication in Vision-Language Models

We investigate whether \emph{LLM-based agents} can develop task-oriented communication protocols that differ from standard natural language in collaborative reasoning tasks. Our focus is on two core properties such task-oriented protocols may exhibit: Efficiency -- conveying task-relevant information more concisely than natural language, and Covertness -- becoming difficult for external observers to interpret, raising concerns about transparency and control. To investigate these aspects, we use a referential-game framework in which vision-language model (VLM) agents communicate, providing a controlled, measurable setting for evaluating language variants. Experiments show that VLMs can develop effective, task-adapted communication patterns. At the same time, they can develop covert protocols that are difficult for humans and external agents to interpret. We also observe spontaneous coordination between similar models without explicitly shared protocols. These findings highlight both the potential and the risks of task-oriented communication, and position referential games as a valuable testbed for future work in this area.

CtD: Composition through Decomposition in Emergent Communication

Compositionality is a cognitive mechanism that allows humans to systematically combine known concepts in novel ways. This study demonstrates how artificial neural agents acquire and utilize compositional generalization to describe previously unseen images. Our method, termed "Composition through Decomposition", involves two sequential training steps. In the 'Decompose' step, the agents learn to decompose an image into basic concepts using a codebook acquired during interaction in a multi-target coordination game. Subsequently, in the 'Compose' step, the agents employ this codebook to describe novel images by composing basic concepts into complex phrases. Remarkably, we observe cases where generalization in the `Compose' step is achieved zero-shot, without the need for additional training.

Will it Merge? On The Causes of Model Mergeability

Model merging has emerged as a promising technique for combining multiple fine-tuned models into a single multitask model without retraining. However, the factors that determine whether merging will succeed or fail remain poorly understood. In this work, we investigate why specific models are merged better than others. To do so, we propose a concrete, measurable definition of mergeability. We investigate several potential causes for high or low mergeability, highlighting the base model knowledge as a dominant factor: Models fine-tuned on instances that the base model knows better are more mergeable than models fine-tuned on instances that the base model struggles with. Based on our mergeability definition, we explore a simple weighted merging technique that better preserves weak knowledge in the base model.

Mechanisms of Prompt-Induced Hallucination in Vision-Language Models

Large vision-language models (VLMs) are highly capable, yet often hallucinate by favoring textual prompts over visual evidence. We study this failure mode in a controlled object-counting setting, where the prompt overstates the number of objects in the image (e.g., asking a model to describe four waterlilies when only three are present). At low object counts, models often correct the overestimation, but as the number of objects increases, they increasingly conform to the prompt regardless of the discrepancy. Through mechanistic analysis of three VLMs, we identify a small set of attention heads whose ablation substantially reduces prompt-induced hallucinations (PIH) by at least 40% without additional training. Across models, PIH-heads mediate prompt copying in model-specific ways. We characterize these differences and show that PIH ablation increases correction toward visual evidence. Our findings offer insights into the internal mechanisms driving prompt-induced hallucinations, revealing model-specific differences in how these behaviors are implemented.

Structured RAG for Answering Aggregative Questions

Retrieval-Augmented Generation (RAG) has become the dominant approach for answering questions over large corpora. However, current datasets and methods are highly focused on cases where only a small part of the corpus (usually a few paragraphs) is relevant per query, and fail to capture the rich world of aggregative queries. These require gathering information from a large set of documents and reasoning over them. To address this gap, we propose S-RAG, an approach specifically designed for such queries. At ingestion time, S-RAG constructs a structured representation of the corpus; at inference time, it translates natural-language queries into formal queries over said representation. To validate our approach and promote further research in this area, we introduce two new datasets of aggregative queries: HOTELS and WORLD CUP. Experiments with S-RAG on the newly introduced datasets, as well as on a public benchmark, demonstrate that it substantially outperforms both common RAG systems and long-context LLMs.

ManagerBench: Evaluating the Safety-Pragmatism Trade-off in Autonomous LLMs

As large language models (LLMs) evolve from conversational assistants into autonomous agents, evaluating the safety of their actions becomes critical. Prior safety benchmarks have primarily focused on preventing generation of harmful content, such as toxic text. However, they overlook the challenge of agents taking harmful actions when the most effective path to an operational goal conflicts with human safety. To address this gap, we introduce ManagerBench, a benchmark that evaluates LLM decision-making in realistic, human-validated managerial scenarios. Each scenario forces a choice between a pragmatic but harmful action that achieves an operational goal, and a safe action that leads to worse operational performance. A parallel control set, where potential harm is directed only at inanimate objects, measures a model's pragmatism and identifies its tendency to be overly safe. Our findings indicate that the frontier LLMs perform poorly when navigating this safety-pragmatism trade-off. Many consistently choose harmful options to advance their operational goals, while others avoid harm only to become overly safe and ineffective. Critically, we find this misalignment does not stem from an inability to perceive harm, as models' harm assessments align with human judgments, but from flawed prioritization. ManagerBench is a challenging benchmark for a core component of agentic behavior: making safe choices when operational goals and alignment values incentivize conflicting actions. Benchmark & code available at https://github.com/technion-cs-nlp/ManagerBench.

Planted in Pretraining, Swayed by Finetuning: A Case Study on the Origins of Cognitive Biases in LLMs

Large language models (LLMs) exhibit cognitive biases -- systematic tendencies of irrational decision-making, similar to those seen in humans. Prior work has found that these biases vary across models and can be amplified by instruction tuning. However, it remains unclear if these differences in biases stem from pretraining, finetuning, or even random noise due to training stochasticity. We propose a two-step causal experimental approach to disentangle these factors. First, we finetune models multiple times using different random seeds to study how training randomness affects over $30$ cognitive biases. Second, we introduce \emph{cross-tuning} -- swapping instruction datasets between models to isolate bias sources. This swap uses datasets that led to different bias patterns, directly testing whether biases are dataset-dependent. Our findings reveal that while training randomness introduces some variability, biases are mainly shaped by pretraining: models with the same pretrained backbone exhibit more similar bias patterns than those sharing only finetuning data. These insights suggest that understanding biases in finetuned models requires considering their pretraining origins beyond finetuning effects. This perspective can guide future efforts to develop principled strategies for evaluating and mitigating bias in LLMs.

Same Task, Different Circuits: Disentangling Modality-Specific Mechanisms in VLMs

Vision-Language models (VLMs) show impressive abilities to answer questions on visual inputs (e.g., counting objects in an image), yet demonstrate higher accuracies when performing an analogous task on text (e.g., counting words in a text). We investigate this accuracy gap by identifying and comparing the \textit{circuits} - the task-specific computational sub-graphs - in different modalities. We show that while circuits are largely disjoint between modalities, they implement relatively similar functionalities: the differences lie primarily in processing modality-specific data positions (an image or a text sequence). Zooming in on the image data representations, we observe they become aligned with the higher-performing analogous textual representations only towards later layers, too late in processing to effectively influence subsequent positions. To overcome this, we patch the representations of visual data tokens from later layers back into earlier layers. In experiments with multiple tasks and models, this simple intervention closes a third of the performance gap between the modalities, on average. Our analysis sheds light on the multi-modal performance gap in VLMs and suggests a training-free approach for reducing it.