Since the advent of various pre-trained large language models, extracting structured knowledge from scientific text has experienced a revolutionary change compared with traditional machine learning or natural language processing techniques. Despite these advances, accessible automated tools that allow users to construct, validate, and visualise datasets from scientific literature extraction remain scarce. We therefore developed ComProScanner, an autonomous multi-agent platform that facilitates the extraction, validation, classification, and visualisation of machine-readable chemical compositions and properties, integrated with synthesis data from journal articles for comprehensive database creation. We evaluated our framework using 100 journal articles against 10 different LLMs, including both open-source and proprietary models, to extract highly complex compositions associated with ceramic piezoelectric materials and corresponding piezoelectric strain coefficients (d33), motivated by the lack of a large dataset for such materials. DeepSeek-V3-0324 outperformed all models with a significant overall accuracy of 0.82. This framework provides a simple, user-friendly, readily-usable package for extracting highly complex experimental data buried in the literature to build machine learning or deep learning datasets.

Three Chinese nationals have been arrested in Georgia on suspicion of attempting to illegally purchase 2kg of uranium. Lasha Maghradze, deputy head of the nation's State Security Service (SSG), told a news briefing the group planned to pay $400,000 (£300,570) for the nuclear material in the capital, Tblisi, before transporting it to China via Russia. The alleged plot was unearthed by intelligence agents while one member of the group was attempting to buy the radioactive substance on the black market, he said. The three pleaded not guilty at a court in Tblisi and have been placed in custody to prevent them fleeing the country, according to public broadcaster Georgia Today. They face up to five years in prison under a provision of Georgia's criminal code banning the purchasing of nuclear material.

The implicit solvent approach offers a computationally efficient framework to model solvation effects in molecular simulations. However, its accuracy often falls short compared to explicit solvent models, limiting its use in precise thermodynamic calculations. Recent advancements in machine learning (ML) present an opportunity to overcome these limitations by leveraging neural networks to develop more precise implicit solvent potentials for diverse applications. A major drawback of current ML-based methods is their reliance on force-matching alone, which can lead to energy predictions that differ by an arbitrary constant and are therefore unsuitable for absolute free energy comparisons. Here, we introduce a novel methodology with a graph neural network (GNN)-based implicit solvent model, dubbed Lambda Solvation Neural Network (LSNN). In addition to force-matching, this network was trained to match the derivatives of alchemical variables, ensuring that solvation free energies can be meaningfully compared across chemical species.. Trained on a dataset of approximately 300,000 small molecules, LSNN achieves free energy predictions with accuracy comparable to explicit-solvent alchemical simulations, while offering a computational speedup and establishing a foundational framework for future applications in drug discovery.

Deep Research (DR) agents built on Large Language Models (LLMs) can perform complex, multi-step research by decomposing tasks, retrieving online information, and synthesizing detailed reports. However, the misuse of LLMs with such powerful capabilities can lead to even greater risks. This is especially concerning in high-stakes and knowledge-intensive domains such as biosecurity, where DR can generate a professional report containing detailed forbidden knowledge. Unfortunately, we have found such risks in practice: simply submitting a harmful query, which a standalone LLM directly rejects, can elicit a detailed and dangerous report from DR agents. This highlights the elevated risks and underscores the need for a deeper safety analysis. Yet, jailbreak methods designed for LLMs fall short in exposing such unique risks, as they do not target the research ability of DR agents. To address this gap, we propose two novel jailbreak strategies: Plan Injection, which injects malicious sub-goals into the agent's plan; and Intent Hijack, which reframes harmful queries as academic research questions. We conducted extensive experiments across different LLMs and various safety benchmarks, including general and biosecurity forbidden prompts. These experiments reveal 3 key findings: (1) Alignment of the LLMs often fail in DR agents, where harmful prompts framed in academic terms can hijack agent intent; (2) Multi-step planning and execution weaken the alignment, revealing systemic vulnerabilities that prompt-level safeguards cannot address; (3) DR agents not only bypass refusals but also produce more coherent, professional, and dangerous content, compared with standalone LLMs. These results demonstrate a fundamental misalignment in DR agents and call for better alignment techniques tailored to DR agents. Code and datasets are available at https://chenxshuo.github.io/deeper-harm.

We got a sneak peek inside Found Energy's lab, just as it gears up to supply heat and hydrogen to its first customer. The crushed-up soda can disappears in a cloud of steam and--though it's not visible--hydrogen gas. "I can just keep this reaction going by adding more water," says Peter Godart, squirting some into the steaming beaker. "This is room-temperature water, and it's immediately boiling. Doing this on your stove would be slower than this." Godart is the founder and CEO of Found Energy, a startup in Boston that aims to harness the energy in scraps of aluminum metal to power industrial processes without fossil fuels.

Masked graph modeling (MGM) is a promising approach for molecular representation learning (MRL).However, extending the success of re-mask decoding from 2D to 3D MGM 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 3D Molecular Graph Auto-Encoder with Selective Re-mask Decoding. The core innovation of 3D-GSRD lies in its Selective Re-mask Decoding(SRD), which re-masks only 3D-relevant information from encoder representations while preserving the 2D graph structures. This SRD is synergistically integrated with a 3D Relational-Transformer(3D-ReTrans) encoder alongside a structure-independent decoder. We analyze that SRD, combined with the structure-independent decoder, enhances the encoder's role in MRL. Extensive experiments show that 3D-GSRD achieves strong downstream performance, setting a new state-of-the-art on 7 out of 8 targets in the widely used MD17 molecular property prediction benchmark. The code is released at https://github.com/WuChang0124/3D-GSRD.

The remarkable mechanical properties of spider silk, including its tensile strength and extensibility, are primarily governed by the repetitive regions of the proteins that constitute the fiber, the major ampullate spidroins (MaSps). However, establishing correlations between mechanical characteristics and repeat sequences is challenging due to the intricate sequence-structure-function relationships of MaSps and the limited availability of annotated datasets. In this study, we present a novel computational framework for designing MaSp repeat sequences with customizable mechanical properties. To achieve this, we developed a lightweight GPT-based generative model by distilling the pre-trained ProtGPT2 protein language model. The distilled model was subjected to multilevel fine-tuning using curated subsets of the Spider Silkome dataset. Specifically, we adapt the model for MaSp repeat generation using 6,000 MaSp repeat sequences and further refine it with 572 repeats associated with experimentally determined fiber-level mechanical properties. Our model generates biologically plausible MaSp repeat regions tailored to specific mechanical properties while also predicting those properties for given sequences. Validation includes sequence-level analysis, assessing physicochemical attributes and expected distribution of key motifs as well as secondary structure compositions. A correlation study using BLAST on the Spider Silkome dataset and a test set of MaSp repeats with known mechanical properties further confirmed the predictive accuracy of the model. This framework advances the rational design of spider silk-inspired biomaterials, offering a versatile tool for engineering protein sequences with tailored mechanical attributes.

Chemistry laboratory automation aims to increase throughput, reproducibility, and safety, yet many existing systems still depend on frequent human intervention. Advances in robotics have reduced this dependency, but without a structured representation of the required skills, autonomy remains limited to bespoke, task-specific solutions with little capacity to transfer beyond their initial design. Current experiment abstractions typically describe protocol-level steps without specifying the robotic actions needed to execute them. This highlights the lack of a systematic account of the manipulation skills required for robots in chemistry laboratories. To address this gap, we introduce TARMAC - a Taxonomy for Robot Manipulation in Chemistry - a domain-specific framework that defines and organizes the core manipulations needed in laboratory practice. Based on annotated teaching-lab demonstrations and supported by experimental validation, TARMAC categorizes actions according to their functional role and physical execution requirements. Beyond serving as a descriptive vocabulary, TARMAC can be instantiated as robot-executable primitives and composed into higher-level macros, enabling skill reuse and supporting scalable integration into long-horizon workflows. These contributions provide a structured foundation for more flexible and autonomous laboratory automation. More information is available at https://tarmac-paper.github.io/

The injection molding industry faces critical challenges in preserving and transferring field knowledge, particularly as experienced workers retire and multilingual barriers hinder effective communication. This study introduces IM-Chat, a multi-agent framework based on large language models (LLMs), designed to facilitate knowledge transfer in injection molding. IM-Chat integrates both limited documented knowledge (e.g., troubleshooting tables, manuals) and extensive field data modeled through a data-driven process condition generator that infers optimal manufacturing settings from environmental inputs such as temperature and humidity, enabling robust and context-aware task resolution. By adopting a retrieval-augmented generation (RAG) strategy and tool-calling agents within a modular architecture, IM-Chat ensures adaptability without the need for fine-tuning. Performance was assessed across 100 single-tool and 60 hybrid tasks for GPT-4o, GPT-4o-mini, and GPT-3.5-turbo by domain experts using a 10-point rubric focused on relevance and correctness, and was further supplemented by automated evaluation using GPT-4o guided by a domain-adapted instruction prompt. The evaluation results indicate that more capable models tend to achieve higher accuracy, particularly in complex, tool-integrated scenarios. In addition, compared with the fine-tuned single-agent LLM, IM-Chat demonstrated superior accuracy, particularly in quantitative reasoning, and greater scalability in handling multiple information sources. Overall, these findings demonstrate the viability of multi-agent LLM systems for industrial knowledge workflows and establish IM-Chat as a scalable and generalizable approach to AI-assisted decision support in manufacturing.

Large Language Models (LLMs) exhibit strong but shallow alignment: they directly refuse harmful queries when a refusal is expected at the very start of an assistant turn, yet this protection collapses once a harmful continuation is underway (either through the adversarial attacks or via harmful assistant-prefill attacks). This raises a fundamental question: Can the innate shallow alignment in LLMs be unlocked to ensure safety at arbitrary generation depths? To achieve this goal, we propose Any-Depth Alignment (ADA), an effective inference-time defense with negligible overhead. ADA is built based on our observation that alignment is concentrated in the assistant header tokens through repeated use in shallow-refusal training, and these tokens possess the model's strong alignment priors. By reintroducing these tokens mid-stream, ADA induces the model to reassess harmfulness and recover refusals at any point in generation. Across diverse open-source model families (Llama, Gemma, Mistral, Qwen, DeepSeek, and gpt-oss), ADA achieves robust safety performance without requiring any changes to the base model's parameters. It secures a near-100% refusal rate against challenging adversarial prefill attacks ranging from dozens to thousands of tokens. Furthermore, ADA reduces the average success rate of prominent adversarial prompt attacks (such as GCG, AutoDAN, PAIR, and TAP) to below 3%. This is all accomplished while preserving utility on benign tasks with minimal over-refusal. ADA maintains this resilience even after the base model undergoes subsequent instruction tuning (benign or adversarial).