Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in task transfer, they often struggle to accurately analyze molecular features due to limited knowledge and reasoning capabilities. To address this issue, we present Mol-LLaMA, a large molecular language model that grasps the general knowledge centered on molecules and exhibits explainability and reasoning ability. To this end, we design key data types that encompass the fundamental molecular features, taking into account the essential abilities for molecular reasoning. Further, to improve molecular understanding, we propose a module that integrates complementary information from different molecular encoders, leveraging the distinct advantages of molecular representations. Our experimental results demonstrate that Mol-LLaMA is capable of comprehending the general features of molecules and providing informative responses, implying its potential as a general-purpose assistant for molecular analysis. Our project page is at https://mol-llama.github.io/.

Evaluating the open-form textual responses generated by Large Language Models (LLMs) typically requires measuring the semantic similarity of the response to a (human generated) reference. However, there is evidence that current semantic similarity methods may capture syntactic or lexical forms over semantic content. While benchmarks exist for semantic equivalence, they often suffer from high generation costs due to reliance on subjective human judgment, limited availability for domain-specific applications, and unclear definitions of equivalence. This paper introduces a novel method for generating benchmarks to evaluate semantic similarity methods for LLM outputs, specifically addressing these limitations. Our approach leverages knowledge graphs (KGs) to generate pairs of naturallanguage statements that are semantically similar or dissimilar, with dissimilar pairs categorized into one of four sub-types. We generate benchmark datasets in four different domains (general knowledge, biomedicine, finance, biology), and conduct a comparative study of semantic similarity methods including traditional natural language processing scores and LLM-as-a-judge predictions. We observe that the sub-type of semantic variation, as well as the domain of the benchmark impact the performance of semantic similarity methods, with no method being consistently superior.

Evaluating the open-form textual responses generated by Large Language Models (LLMs) typically requires measuring the semantic similarity of the response to a (human generated) reference. However, there is evidence that current semantic similarity methods may capture syntactic or lexical forms over semantic content. While benchmarks exist for semantic equivalence, they often suffer from high generation costs due to reliance on subjective human judgment, limited availability for domain-specific applications, and unclear definitions of equivalence. This paper introduces a novel method for generating benchmarks to evaluate semantic similarity methods for LLM outputs, specifically addressing these limitations. Our approach leverages knowledge graphs (KGs) to generate pairs of naturallanguage statements that are semantically similar or dissimilar, with dissimilar pairs categorized into one of four sub-types. We generate benchmark datasets in four different domains (general knowledge, biomedicine, finance, biology), and conduct a comparative study of semantic similarity methods including traditional natural language processing scores and LLM-as-a-judge predictions. We observe that the sub-type of semantic variation, as well as the domain of the benchmark impact the performance of semantic similarity methods, with no method being consistently superior.

When instructed to place a floor lamp next to an armchair, humans can visually ground it in the scene, estimating its base diameter and height, imagining its precise alignment with the armchair, and judging whether it fits naturally within the 3D environment. Humans can naturally perceive, reason about, and localize expressions to "anywhere" in 3D scenes. Yet can today's 3D vision-language models ground free-form referring expressions to precise positions and dimensions in a 3D scene, especially when those expressions refer to regions beyond objects? Existing 3D visual grounding models, pretrained on large 3D scene datasets, excel at aligning expressions to objects in a scene [7, 58, 2, 63, 61, 26]. However, these models remain constrained to object-level alignment, with limited attention paid to the broader spatial regions beyond objects.

The growing importance of mRNA therapeutics and synthetic biology highlights the need for models that capture the latent structure of synonymous codon (different triplets encoding the same amino acid) usage, which subtly modulates translation efficiency and gene expression. While recent efforts incorporate codon-level inductive biases through auxiliary objectives, they often fall short of explicitly modeling the structured relationships that arise from the genetic code's inherent symmetries. We introduce Equi-mRNA, the first codon-level equivariant mRNA language model that explicitly encodes synonymous codon symmetries as cyclic subgroups of 2D Special Orthogonal matrix (SO(2)). By combining group-theoretic priors with an auxiliary equivariance loss and symmetry-aware pooling, Equi-mRNA learns biologically grounded representations that outperform vanilla baselines across multiple axes. On downstream property-prediction tasks including expression, stability, and riboswitch switching Equi-mRNA delivers up to 10% improvements in accuracy. In sequence generation, it produces mRNA constructs that are up to 4 more realistic under Fréchet BioDistance metrics and 28% better preserve functional properties compared to vanilla baseline. Interpretability analyses further reveal that learned codon-rotation distributions recapitulate known GC-content biases and tRNA abundance patterns, offering novel insights into codon usage. Equi-mRNA establishes a new biologically principled paradigm for mRNA modeling.

Electronic Health Records (EHR) are time-series relational databases that record patient interactions and medical events over time, serving as a critical resource for healthcare research and applications. However, privacy concerns and regulatory restrictions limit the sharing and utilization of such sensitive data, necessitating the generation of synthetic EHR datasets. Unlike previous EHR synthesis methods--which typically generate medical records consisting of expert-chosen features (e.g., a few vital signs, structured codes only)--we introduce RawMed, the first framework to synthesize multi-table, time-series EHR data that closely resembles raw EHRs.

Process Reward Models (PRMs) have recently emerged as a powerful framework for supervising intermediate reasoning steps in large language models (LLMs). Previous PRMs are primarily trained on model final output responses and struggle to evaluate intermediate thinking trajectories robustly, especially in the emerging setting of trajectory-response outputs generated by frontier reasoning models like Deepseek-R1. In this work, we introduce ReasonFlux-PRM, a novel trajectory-aware PRM explicitly designed to evaluate the trajectory-response type of reasoning traces. ReasonFlux-PRM incorporates both step-level and trajectorylevel supervision, enabling fine-grained reward assignment aligned with structured chain-of-thought data. We adapt ReasonFlux-PRM to support reward supervision under both offline and online settings, including (i) selecting high-quality model distillation data for downstream supervised fine-tuning of smaller models, (ii) providing dense process-level rewards for policy optimization during reinforcement learning, and (iii) enabling reward-guided Best-of-N test-time scaling. Empirical results on challenging downstream benchmarks such as AIME, MATH500, and GPQA-Diamond demonstrate that ReasonFlux-PRM-7B selects higher quality data than strong PRMs (e.g., Qwen2.5-Math-PRM-72B) and human-curated baselines.

Explaining time series classification models is crucial, particularly in high-stakes applications such as healthcare and finance, where transparency and trust play a critical role. Although numerous time series classification methods have identified key subsequences, known as shapelets, as core features for achieving stateof-the-art performance and validating their pivotal role in classification outcomes, existing post-hoc time series explanation (PHTSE) methods primarily focus on timestep-level feature attribution. These explanation methods overlook the fundamental prior that classification outcomes are predominantly driven by key shapelets.

This paper addresses the problem of robust estimation in gossip algorithms over arbitrary communication graphs. Gossip algorithms are fully decentralized, relying only on local neighbor-to-neighbor communication, making them well-suited for situations where communication is constrained. A fundamental challenge in existing mean-based gossip algorithms is their vulnerability to malicious or corrupted nodes. In this paper, we show that an outlier-robust mean can be computed by globally estimating a robust statistic. More specifically, we propose a novel gossip algorithm for rank estimation, referred to as GORANK, and leverage it to design a gossip procedure dedicated to trimmed mean estimation, coined GOTRIM. In addition to a detailed description of the proposed methods, a key contribution of our work is a precise convergence analysis: we establish an O(1/t) rate for rank estimation and an O(1/t)rate for trimmed mean estimation, where by tis meant the number of iterations. Moreover, we provide a breakdown point analysis of GOTRIM.

Deep neural networks are vulnerable to adversarial examples that exhibit transferability across various models. Numerous approaches are proposed to enhance the transferability of adversarial examples, including advanced optimization, data augmentation, and model modifications. However, these methods still show limited transferability, particularly in cross-architecture scenarios, such as from CNN to ViT. To achieve high transferability, we propose a technique termed Spatial Adversarial Alignment (SAA), which employs an alignment loss and leverages a witness model to fine-tune the surrogate model. Specifically, SAA consists of two key parts: spatial-aware alignment and adversarial-aware alignment.