Drug toxicity remains a major challenge in pharmaceutical development. Recent machine learning models have improved in silico toxicity prediction, but their reliance on annotated data and lack of interpretability limit their applicability. This limits their ability to capture organ-specific toxicities driven by complex biological mechanisms. Large language models (LLMs) offer a promising alternative through step-by-step reasoning and integration of textual data, yet prior approaches lack biological context and transparent rationale. To address this issue, we propose CoTox, a novel framework that integrates LLM with chain-of-thought (CoT) reasoning for multi-toxicity prediction. CoTox combines chemical structure data, biological pathways, and gene ontology (GO) terms to generate interpretable toxicity predictions through step-by-step reasoning. Using GPT-4o, we show that CoTox outperforms both traditional machine learning and deep learning model. We further examine its performance across various LLMs to identify where CoTox is most effective. Additionally, we find that representing chemical structures with IUPAC names, which are easier for LLMs to understand than SMILES, enhances the model's reasoning ability and improves predictive performance. To demonstrate its practical utility in drug development, we simulate the treatment of relevant cell types with drug and incorporated the resulting biological context into the CoTox framework. This approach allow CoTox to generate toxicity predictions aligned with physiological responses, as shown in case study. This result highlights the potential of LLM-based frameworks to improve interpretability and support early-stage drug safety assessment. The code and prompt used in this work are available at https://github.com/dmis-lab/CoTox.

The discipline of physics stands as a cornerstone of human intellect, driving the evolution of technology and deepening our understanding of the fundamental principles of the cosmos. Contemporary literature includes some works centered on the task of solving physics problems - a crucial domain of natural language reasoning. In this paper, we evaluate the performance of frontier LLMs in solving physics problems, both mathematical and descriptive. We also employ a plethora of inference-time techniques and agentic frameworks to improve the performance of the models. This includes the verification of proposed solutions in a cumulative fashion by other, smaller LLM agents, and we perform a comparative analysis of the performance that the techniques entail. There are significant improvements when the multi-agent framework is applied to problems that the models initially perform poorly on. Furthermore, we introduce a new evaluation benchmark for physics problems, ${\rm P{\small HYSICS}E{\small VAL}}$, consisting of 19,609 problems sourced from various physics textbooks and their corresponding correct solutions scraped from physics forums and educational websites. Our code and data are publicly available at https://github.com/areebuzair/PhysicsEval.

Recent progress in Multi-modal Large Language Models (MLLMs) has enabled step-by-step multi-modal mathematical reasoning by performing visual operations based on the textual instructions. A promising approach uses code as an intermediate representation to precisely express and manipulate the images in the reasoning steps. However, existing evaluations focus mainly on text-only reasoning outputs, leaving the MLLM's ability to perform accurate visual operations via code largely unexplored. This work takes a first step toward addressing that gap by evaluating MLLM's code-based capabilities in multi-modal mathematical reasoning.Specifically, our framework focuses on two key evaluation aspects: (1) Multi-modal Code Generation (MCG) evaluates the model's ability to accurately understand and construct visualizations from scratch. (2) Multi-modal Code Editing (MCE) assesses the model's capacity for fine-grained operations, which include three types: Deletion, Modification and Annotation. To evaluate the above tasks, we incorporate a dataset that covers the five most popular types of mathematical figures, including geometric diagrams, function plots, and three types of statistical charts, to provide a comprehensive and effective measurement of existing MLLMs. Our experimental evaluation involves nine mainstream MLLMs, and the results reveal that existing models still lag significantly behind human performance in performing fine-grained visual operations.

Most existing text-to-audio (TT A) generation methods produce mono outputs, neglecting essential spatial information for im-mersive auditory experiences. To address this issue, we propose a cascaded method for text-to-multisource binaural audio generation (TTMBA) with both temporal and spatial control. First, a pretrained large language model (LLM) segments the text into a structured format with time and spatial details for each sound event. Next, a pretrained mono audio generation network creates multiple mono audios with varying durations for each event. These mono audios are transformed into binaural audios using a binaural rendering neural network based on spatial data from the LLM. Finally, the binaural audios are arranged by their start times, resulting in multisource binaural audio. Experimental results demonstrate the superiority of the proposed method in terms of both audio generation quality and spatial perceptual accuracy.

Atomic commits, which address a single development concern, are a best practice in software development. In practice, however, developers often produce tangled commits that mix unrelated changes, complicating code review and maintenance. Prior untangling approaches (rule-based, feature-based, or graph-based) have made progress but typically rely on shallow signals and struggle to distinguish explicit dependencies (e.g., control/data flow) from implicit ones (e.g., semantic or conceptual relationships). In this paper, we propose ColaUntangle, a new collaborative consultation framework for commit untangling that models both explicit and implicit dependencies among code changes. ColaUntangle integrates Large Language Model (LLM)-driven agents in a multi-agent architecture: one agent specializes in explicit dependencies, another in implicit ones, and a reviewer agent synthesizes their perspectives through iterative consultation. To capture structural and contextual information, we construct Explicit and Implicit Contexts, enabling agents to reason over code relationships with both symbolic and semantic depth. We evaluate ColaUntangle on two widely-used datasets (1,612 C# and 14k Java tangled commits). Experimental results show that ColaUntangle outperforms the best-performing baseline, achieving an improvement of 44% on the C# dataset and 82% on the Java dataset. These findings highlight the potential of LLM-based collaborative frameworks for advancing automated commit untangling tasks.

Sequential deep learning models excel in domains with temporal or sequential dependencies, but their complexity necessitates post-hoc feature attribution methods for understanding their predictions. While existing techniques quantify feature importance, they inherently assume fixed feature ordering - conflating the effects of (1) feature values and (2) their positions within input sequences. To address this gap, we introduce OrdShap, a novel attribution method that disentangles these effects by quantifying how a model's predictions change in response to permuting feature position. We establish a game-theoretic connection between OrdShap and Sanchez-Bergantiños values, providing a theoretically grounded approach to position-sensitive attribution. Empirical results from health, natural language, and synthetic datasets highlight OrdShap's effectiveness in capturing feature value and feature position attributions, and provide deeper insight into model behavior.

Contemporary large models often exhibit behaviors suggesting the presence of low-level primitives that compose into modules with richer functionality, but these fundamental building blocks remain poorly understood. We investigate this compositional structure in linear layers by asking: can we identify/synthesize linear transformations from a minimal set of geometric primitives? Using Clifford algebra, we show that linear layers can be expressed as compositions of bivectors -- geometric objects encoding oriented planes -- and introduce a differentiable algorithm that decomposes them into products of rotors. This construction uses only O(log^2 d) parameters, versus O(d^2) required by dense matrices. Applied to the key, query, and value projections in LLM attention layers, our rotor-based layers match the performance of strong baselines such as block-Hadamard and low-rank approximations. Our findings provide an algebraic perspective on how these geometric primitives can compose into higher-level functions within deep models.

Molecular structure elucidation from spectra is a fundamental challenge in molecular science. Conventional approaches rely heavily on expert interpretation and lack scalability, while retrieval-based machine learning approaches remain constrained by limited reference libraries. Generative models offer a promising alternative, yet most adopt autoregressive architectures that overlook 3D geometry and struggle to integrate diverse spectral modalities. In this work, we present DiffSpectra, a generative framework that formulates molecular structure elucidation as a conditional generation process, directly inferring 2D and 3D molecular structures from multi-modal spectra using diffusion models. Its denoising network is parameterized by the Diffusion Molecule Transformer, an SE(3)-equivariant architecture for geometric modeling, conditioned by SpecFormer, a Transformer-based spectral encoder capturing multi-modal spectral dependencies. Extensive experiments demonstrate that DiffSpectra accurately elucidates molecular structures, achieving 40.76% top-1 and 99.49% top-10 accuracy. Its performance benefits substantially from 3D geometric modeling, SpecFormer pre-training, and multi-modal conditioning. To our knowledge, DiffSpectra is the first framework that unifies multi-modal spectral reasoning and joint 2D/3D generative modeling for de novo molecular structure elucidation.

A common paradigm to improve the performance of large language models is optimizing for a reward model. Reward models assign a numerical score to an LLM's output that indicates, for example, how likely it is to align with user preferences or safety goals. However, reward models are never perfect. They inevitably function as proxies for complex desiderata such as correctness, helpfulness, and safety. By overoptimizing for a misspecified reward, we can subvert intended alignment goals and reduce overall performance, a phenomenon commonly referred to as reward hacking. In this work, we characterize reward hacking in inference-time alignment and demonstrate when and how we can mitigate it by hedging on the proxy reward. We study this phenomenon under Best-of-$n$ (BoN) and Soft Best-of-$n$ (SBoN), and we introduce Best-of-Poisson (BoP) that provides an efficient, near-exact approximation of the optimal reward-KL divergence policy at inference time. We show that the characteristic pattern of hacking as observed in practice (where the true reward first increases before declining) is an inevitable property of a broad class of inference-time mechanisms, including BoN and BoP. To counter this effect, we introduce HedgeTune, an efficient algorithm to find the optimal inference-time parameter. We demonstrate that hedging mitigates reward hacking and achieves superior reward-distortion tradeoffs on math, reasoning, and human-preference setups.

Sparse autoencoders (SAEs) are designed to extract interpretable features from language models by enforcing a sparsity constraint. Ideally, training an SAE would yield latents that are both sparse and semantically meaningful. However, many SAE latents activate frequently (i.e., are \emph{dense}), raising concerns that they may be undesirable artifacts of the training procedure. In this work, we systematically investigate the geometry, function, and origin of dense latents and show that they are not only persistent but often reflect meaningful model representations. We first demonstrate that dense latents tend to form antipodal pairs that reconstruct specific directions in the residual stream, and that ablating their subspace suppresses the emergence of new dense features in retrained SAEs -- suggesting that high density features are an intrinsic property of the residual space. We then introduce a taxonomy of dense latents, identifying classes tied to position tracking, context binding, entropy regulation, letter-specific output signals, part-of-speech, and principal component reconstruction. Finally, we analyze how these features evolve across layers, revealing a shift from structural features in early layers, to semantic features in mid layers, and finally to output-oriented signals in the last layers of the model. Our findings indicate that dense latents serve functional roles in language model computation and should not be dismissed as training noise.