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).

The red palm mite infestation has become a serious concern, particularly in regions with extensive palm cultivation, leading to reduced productivity and economic losses. Accurate and early identification of mite-infested plants is critical for effective management. The current study focuses on evaluating and comparing the ML model for classifying the affected plants and detecting the infestation. TriggerNet is a novel interpretable AI framework that integrates Grad-CAM, RISE, FullGrad, and TCAV to generate novel visual explanations for deep learning models in plant classification and disease detection. This study applies TriggerNet to address red palm mite (Raoiella indica) infestation, a major threat to palm cultivation and agricultural productivity. A diverse set of RGB images across 11 plant species, Arecanut, Date Palm, Bird of Paradise, Coconut Palm, Ginger, Citrus Tree, Palm Oil, Orchid, Banana Palm, Avocado Tree, and Cast Iron Plant was utilized for training and evaluation. Advanced deep learning models like CNN, EfficientNet, MobileNet, ViT, ResNet50, and InceptionV3, alongside machine learning classifiers such as Random Forest, SVM, and KNN, were employed for plant classification. For disease classification, all plants were categorized into four classes: Healthy, Yellow Spots, Reddish Bronzing, and Silk Webbing. Snorkel was used to efficiently label these disease classes by leveraging heuristic rules and patterns, reducing manual annotation time and improving dataset reliability.

Synthesis procedures play a critical role in materials research, as they directly affect material properties. With data-driven approaches increasingly accelerating materials discovery, there is growing interest in extracting synthesis procedures from scientific literature as structured data. However, existing studies often rely on rigid, domain-specific schemas with predefined fields for structuring synthesis procedures or assume that synthesis procedures are linear sequences of operations, which limits their ability to capture the structural complexity of real-world procedures. To address these limitations, we adopt PROV-DM, an international standard for provenance information, which supports flexible, graph-based modeling of procedures. We present MatPROV, a dataset of PROV-DM-compliant synthesis procedures extracted from scientific literature using large language models. MatPROV captures structural complexities and causal relationships among materials, operations, and conditions through visually intuitive directed graphs. This representation enables machine-interpretable synthesis knowledge, opening opportunities for future research such as automated synthesis planning and optimization.

The pretraining-finetuning paradigm has powered major advances in domains such as natural language processing and computer vision, with representative examples including masked language modeling and next-token prediction. In molecular representation learning, however, pretraining tasks remain largely restricted to node-level denois-ing, which effectively captures local atomic environments but is often insufficient for encoding the global molecular structure critical to graph-level property prediction tasks such as energy estimation and molecular regression. To address this gap, we introduce Geo-Recon, a graph-level pretraining framework that shifts the focus from individual atoms to the molecule as an integrated whole. GeoRe-con formulates a graph-level reconstruction task: during pretraining, the model is trained to produce an informative graph representation that guides geometry reconstruction while inducing smoother and more transferable latent spaces. This encourages the learning of coherent, global structural features beyond isolated atomic details. Without relying on external supervision, GeoRecon achieves generally improves over backbones baselines on multiple molecular benchmarks including QM9, MD17, MD22, and 3BPA, demonstrating the effectiveness of graph-level reconstruction for holistic and geometry-aware molecular embeddings.