Masked graph modeling (MGM) is a promising approach for molecular representation learning (MRL). However, extending the success of re-mask decoding from 2D to 3DMGM is non-trivial, primarily due to two conflicting challenges: avoiding 2D structure leakage to the decoder, while still providing sufficient 2D context for reconstructing re-masked atoms. To address these challenges, we propose 3D-GSRD: a 3DMolecular Graph Auto-Encoder with Selective Re-mask Decoding.

Scientific embodied agents play a crucial role in modern laboratories by automating complex experimental workflows. Compared to typical household environments, laboratory settings impose significantly higher demands on perception of physicalchemical transformations and long-horizon planning, making them an ideal testbed for advancing embodied intelligence. However, its development has been long hampered by the lack of suitable simulator and benchmarks. In this paper, we address this gap by introducing LabUtopia, a comprehensive simulation and benchmarking suite designed to facilitate the development of generalizable, reasoning-capable embodied agents in laboratory settings.

Molecular Relational Learning (MRL) is a rapidly growing field that focuses on understanding the interaction dynamics between molecules, which is crucial for applications ranging from catalyst engineering to drug discovery. Despite recent progress, ture of molecules, earlier MRL as obtaining approaches the are 3D limited interaction to using geometry only the remains 2D topological prohibiti strucvely expensive. This paper introduces a novel 3D geometric pre-training strategy for MRL (3DMRL) that incorporates a 3D virtual interaction environment, overcoming the the constructe limitations d of 3D costly virtual tradit interaction ional quantum environment, mechanical 3DMRL calculation trains 2D methods. MRL model With to learn the global and local 3D geometric information of molecular interaction. Extensive experiments on various tasks using real-world datasets, including out-ofdistribution and extrapolation scenarios, demonstrate the effectiveness of 3DMRL, sho publicly wing a up vailable to a 24.93% at https://github.com/

Large language models (LLMs) and vision-language models (LVLMs) have driven the paradigm shift towards general-purpose foundation models. However, both of them are prone to hallucinations, which compromise their factual accuracy and reliability. While existing research primarily focuses on isolated textual-or visual-centric errors, a critical yet underexplored phenomenon persists in LVLMs: Even neither of textual-or visual centric errors occur, LVLMs often struggle with a new and subtle hallucination mode that arising from composition of them. In this paper, we define this issue as Simple Compositional Hallucination (SCHall). Through an preliminary analysis, we present two key findings: (1) visual abstraction fails under compositional questioning, and (2) visual inputs induce degradation in language processing, leading to hallucinations. To facilitate future research on this phenomenon, we introduce a custom benchmark, SCBench, and propose a novel VLR-distillation method, which serves as the first baseline to effectively mitigate SCHall. Furthermore, experiment results on publicly available benchmarks, including both hallucination-specific and general-purpose ones, demonstrate the effectiveness of our VLR-distillation method.

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/.

LLMs have made impressive progress, but their growing capabilities also expose them to highly flexible jailbreaking attacks designed to bypass safety alignment. While many existing defenses focus on known types of attacks, it is more critical to prepare LLMs for unseen attacks that may arise during deployment. To address this, we propose a lifelong safety alignment framework that enables LLMs to continuously adapt to new and evolving jailbreaking strategies. Our framework introduces a competitive setup between two components: a Meta-Attacker, trained to actively discover novel jailbreaking strategies, and a Defender, trained to resist them. To effectively warm up the Meta-Attacker, we first leverage the GPT-4o API to extract key insights from a large collection of jailbreak-related research papers. Through iterative training, the first iteration Meta-Attacker achieves a 73% attack success rate (ASR) on RR [80] and a 57% transfer ASR on LAT [53] using only single-turn attacks. Meanwhile, the Defender progressively improves its robustness and ultimately reduces the Meta-Attacker's success rate to just 7%, enabling safer and more reliable deployment of LLMs in open-ended environments.

We investigate fingerprints in pretraining datasets for large language models (LLMs) through dataset classification experiments. Building on prior work demonstrating the existence of fingerprints or biases in popular computer vision datasets, we analyze popular open-source pretraining datasets for LLMs derived from CommonCrawl including C4, RefinedWeb, DolmaCC, RedPajama-V2, FineWeb, and DCLM-Baseline. Despite those datasets being obtained with similar curation steps, neural networks can classify surprisingly well which dataset a single text sequence belongs to, significantly better than a human can. This indicates that small differences in filtering and processing pipelines induce fingerprints, that we find are evident in formatting, vocabulary, and content distributions. Such fingerprints can negatively impact cross-dataset generalization. Additionally, we show that these fingerprints propagate through training: sequences generated by models trained on those datasets can be accurately classified by a classifier trained on the original datasets. This can offer insights into data characteristics that are typically undisclosed by LLM developers, including pretraining mixture proportions and finetuning data sources.

Structure-guided molecular generation is pivotal in early-stage drug discovery, enabling the design of compounds tailored to specific protein targets. However, despite recent advances in 3D generative modeling, particularly in improving docking scores, these methods often produce uncommon and intrinsically unreasonable molecular structures that deviate from drug-like chemical space. To quantify this issue, we propose a novel metric, the Molecule Reasonable Ratio (MRR), which measures structural rationality and reveals a critical gap between existing models and real-world approved drugs. To address this, we introduce the Collaborative Intelligence Drug Design (CIDD) framework, the first approach to unify the 3D interaction modeling capabilities of generative models with the general knowledge and reasoning power of large language models (LLMs). By leveraging LLMbased Chain-of-Thought reasoning, CIDD generates molecules that are not only compatible with protein pockets but also exhibit favorable drug-likeness, structural rationality, and synthetic accessibility. On the CrossDocked2020 benchmark, CIDD consistently improves drug-likeness metrics, including QED, SA, and MRR, across different base generative models, while maintaining competitive binding affinity. Notably, it raises the combined success rate (balancing drug-likeness and binding) from 15.72% to 34.59%, more than doubling previous results. These findings demonstrate the value of integrating knowledge reasoning with geometric generation to advance AI-driven drug design.3

Accurate prediction of ionic conductivity in electrolyte systems is crucial for advancing numerous scientific and technological applications. While significant progress has been made, current research faces two fundamental challenges: (1) the lack of high-quality standardized benchmarks, and (2) inadequate modeling of geometric structure and intermolecular interactions in mixture systems. To address these limitations, we first reorganize and enhance the CALiSol and DiffMix electrolyte datasets by incorporating geometric graph representations of molecules. We then propose GeoMix, a novel geometry-aware framework that preserves Set-SE(3) equivariance--an essential but challenging property for mixture systems. At the heart of GeoMix lies the Geometric Interaction Network (GIN), an equivariant module specifically designed for intermolecular geometric message passing. Comprehensive experiments demonstrate that GeoMix consistently outperforms diverse baselines (including MLPs, GNNs, and geometric GNNs) across both datasets, validating the importance of cross-molecular geometric interactions and equivariant message passing for accurate property prediction. This work not only establishes new benchmarks for electrolyte research but also provides a general geometric learning framework that advances modeling of mixture systems in energy materials, pharmaceutical development, and beyond.

Information on trees at the individual level is crucial for monitoring forest ecosystems and planning forest management. Current monitoring methods involve ground measurements, requiring extensive cost, time and labor.