We introduce DanmakuTPPBench, a comprehensive benchmark designed to advance multi-modal Temporal Point Process (TPP) modeling in the era of Large Language Models (LLMs). While TPPs have been widely studied for modeling temporal event sequences, existing datasets are predominantly unimodal, hindering progress in models that require joint reasoning over temporal, textual, and visual information. To address this gap, DanmakuTPPBench comprises two complementary components: (1) DanmakuTPP-Events, a novel dataset derived from the Bilibili video platform, where user-generated bullet comments (Danmaku) naturally form multi-modal events annotated with precise timestamps, rich textual content, and corresponding video frames; (2) DanmakuTPP-QA, a challenging question-answering dataset constructed via a novel multi-agent pipeline powered by state-of-the-art LLMs and multi-modal LLMs (MLLMs), targeting complex temporal-textual-visual reasoning. We conduct extensive evaluations using both classical TPP models and recent MLLMs, revealing significant performance gaps and limitations in current methods' ability to model multi-modal event dynamics. Our benchmark establishes strong baselines and calls for further integration of TPP modeling into the multi-modal language modeling landscape.

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/.

Existing post-hoc approaches can remove undesired concepts but often degrade useful signals. We introduce SPLINCE--Simultaneous Projection for LINear concept removal and Covariance prEservation--which eliminates sensitive concepts from representations while exactly preserving their covariance with a target label. SPLINCE achieves this via an oblique projection that "splices out" the unwanted direction yet protects important label correlations. Theoretically, it is the unique solution that removes linear concept predictability and maintains target covariance with minimal embedding distortion. Empirically, SPLINCE outperforms baselines on benchmarks such as Bias in Bios and Winobias, removing protected attributes while minimally damaging main-task information.

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.

Large language models (LLMS) have shown increasing effectiveness in Textto-SQL tasks. However, another closely related problem, Cross-System SQL Translation (a.k.a., SQL-to-SQL), which adapts a query written for one database system (e.g., MySQL) into its equivalent one for another system (e.g., ClickHouse), is of great practical importance but remains underexplored. Existing SQL benchmarks are not well-suited for SQL-to-SQL evaluation, which (1) focus on a limited set of database systems (often just SQLite) and (2) cannot capture many system-specific SQL dialects (e.g., customized functions, data types, and syntax rules). Thus, in this paper, we introduce PARROT, a Practical And Realistic BenchmaRk for CrOss-System SQLTranslation. PARROT comprises 598 translation pairs from 38 open-source benchmarks and real-world business services, specifically prepared to challenge system-specific SQL understanding (e.g., LLMS achieve lower than 38.53% accuracy on average). We also provide multiple benchmark variants, including PARROT-Diverse with 28,003 translations (for extensive syntax testing) and PARROT-Simple with 5,306 representative samples (for focused stress testing), covering 22 production-grade database systems.

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.