Goto

Collaborating Authors

 reaction


Firm hacked by rogue AI calls the attack 'a wake-up call' after ChatGPT maker OpenAI admits advanced bot broke containment during a security test

Daily Mail - Science & tech

OpenAI says one of its most advanced models broke containment during a security test, escaping onto the internet and attacking New York-based startup Hugging Face. Now Hugging Face co-founder Thomas Wolf says that the incident should come as a chilling warning to the entire industry. Mr Wolf told BBC's Newsday radio programme that AI-driven attacks will soon be'one of the most common types of cyber-attacks we see'. The Hugging Face founder also believes most companies are currently unprepared for the mounting threat, adding that they are not aware that the'game has changed'. This comes after OpenAI revealed the terrifying details of an'unprecedented cyber incident', involving state-of-the-art cyber capabilities.'


Terrell Grice

TIME - Tech

Follow this author to personalize your feed and get instant alerts. Follow Go to your personalized feed WHY FOLLOW? Smart Alerts: Get notified about major news as it happens. If Terrell Grice had been born a few years earlier, he might have been an MTV VJ. Instead, the 32-year-old R&B singer and host of showcases his knowledge of popular music on YouTube, where he has more than 1.4 million subscribers.


Training a Scientific Reasoning Model for Chemistry

Neural Information Processing Systems

Reasoning models are large language models that emit a long chain-of-thought before answering, providing both higher accuracy and explicit reasoning for their response. A major question has been whether language model reasoning generalizes beyond mathematics, programming, and logic, where most previous work has focused. We demonstrate that reasoning models can be post-trained for chemistry without additional domain pretraining, and require substantially less data compared to contemporary domain-specific models. We report ether0, a 24B parameter LLM (based on Mistral-Small-24B) that can reason in natural language and respond with chemical structures. This reasoning model was trained with reinforcement learning on 640,730 experimentally-grounded chemistry problems across 375 tasks ranging from synthesizability, to blood-brain barrier permeability, to human receptor activity, to scent. Our model exceeds general-purpose chemistry models, frontier models, and human experts on molecular design tasks. It is also more data efficient relative to specialized models. We anticipate that this method can be applied to train data-efficient language models specialized for tasks across a wide variety of scientific domains.


e0ed6d6c2ec6df05f929b8a67b78513a-Supplemental-Datasets_and_Benchmarks_Track.pdf

Neural Information Processing Systems

In this section, we propose the detailed information during our benchmark and dataset construction821 process, including the data source description, dataset composition, filtering strategies, and the822 rationale for dataset construction. Chemical reaction data are separately collected from patent databases, including USPTO [19], Pista-828 chio [37], and Reaxys [8]. For reaction mechanism annotation, we followed the processing pipeline829 described in [26].830 A.2 Dataset Composition and Filtering Strategies831 Molecular Samples (25% of Benchmark): Although the ZINC database contains 250,000832 molecules, we observed that its molecular weight distribution is relatively concentrated. To en-833 sure diversity, we carefully selected molecules from PubChem, ChEMBL, and ZINC based on834 molecular weight and structural complexity.


Reaction Prediction via Interaction Modeling of Symmetric Difference Shingle Sets

Neural Information Processing Systems

Chemical reaction prediction remains a fundamental challenge in organic chemistry, where existing machine learning models face two critical limitations: sensitivity to input permutations (molecule/atom orderings) and inadequate modeling of substructural interactions governing reactivity. These shortcomings lead to inconsistent predictions and poor generalization to real-world scenarios. To address these challenges, we propose ReaDISH, a novel reaction prediction model that learns permutation-invariant representations while incorporating interaction-aware features. It introduces two innovations: (1) symmetric difference shingle encoding, which extends the differential reaction fingerprint (DRFP) by representing shingles as continuous high-dimensional embeddings, capturing structural changes while eliminating order sensitivity; and (2) geometry-structure interaction attention, a mechanism that models intra-and inter-molecular interactions at the shingle level. Extensive experiments demonstrate that ReaDISH improves reaction prediction performance across diverse benchmarks. It shows enhanced robustness with an average improvement of 8.76% on R2 under permutation perturbations.1


ADetails on the models and benchmarks862

Neural Information Processing Systems

For regression on the dataset, we perform leave-one-out cross validation. For the single solvents,865 we leave out one solvent at a time. For the full data, we leave out one solvent ramp at a time. We866 measure the performance of the model on each leave-one-out data split, then take the mean of their867 performance across the dataset. We exclude any experiments involving acetonitrile and acetic acid,868 due to the observed side-reactions.


Measuring Scientific Capabilities of Language Models with a Systems Biology Dry Lab

Neural Information Processing Systems

Designing experiments and result interpretations are core scientific competencies, particularly in biology, where researchers perturb complex systems to uncover the underlying systems. Recent efforts to evaluate the scientific capabilities of large language models (LLMs) fail to test these competencies because wet-lab experimentation is prohibitively expensive: in expertise, time and equipment. We introduce SciGym, a first-in-class benchmark that assesses LLMs' iterative experiment design and analysis abilities in open-ended scientific discovery tasks. SciGym overcomes the challenge of wet-lab costs by running a dry lab of biological systems. These models, encoded in Systems Biology Markup Language, are efficient for generating simulated data, making them ideal testbeds for experimentation on realistically complex systems.


MOOSE-Chem2: Exploring LLMLimits in Fine-Grained Scientific Hypothesis Discovery via Hierarchical Search

Neural Information Processing Systems

Large language models (LLMs) have shown promise in automating scientific hypothesis generation, yet existing approaches primarily yield coarse-grained hypotheses lacking critical methodological and experimental details. We introduce and formally define the new task of fine-grained scientific hypothesis discovery, which entails generating detailed, experimentally actionable hypotheses from coarse initial research directions. We frame this as a combinatorial optimization problem and investigate the upper limits of LLMs' capacity to solve it when maximally leveraged. Specifically, we explore four foundational questions: (1) how to best harness an LLM's internal heuristics to formulate the fine-grained hypothesis it itself would judge as the most promising among all the possible hypotheses it might generate, based on its own internal scoring-thus defining a latent reward landscape over the hypothesis space; (2) whether such LLM-judged better hypotheses exhibit stronger alignment with ground-truth hypotheses; (3) whether shaping the reward landscape using an ensemble of diverse LLMs of similar capacity yields better outcomes than defining it with repeated instances of the strongest LLM among them; and (4) whether an ensemble of identical LLMs provides a more reliable reward landscape than a single LLM. To address these questions, we propose a hierarchical search method that incrementally proposes and integrates details into the hypothesis, progressing from general concepts to specific experimental configurations. We show that this hierarchical process smooths the reward landscape and enables more effective optimization. Empirical evaluations on a new benchmark of expert-annotated fine-grained hypotheses from recent literature show that our method consistently outperforms strong baselines.1


RETRO-R1: LLM-based Agentic Retrosynthesis

Neural Information Processing Systems

Retrosynthetic planning is a fundamental task in chemical discovery. Due to the vast combinatorial search space, identifying viable synthetic routes remains a significant challenge-even for expert chemists. Recent advances in Large Language Models (LLMs), particularly equipped with reinforcement learning, have demonstrated strong human-like reasoning and planning abilities, especially in mathematics and code problem solving. This raises a natural question: Can the reasoning capabilities of LLMs be harnessed to develop an AI chemist capable of learning effective policies for multi-step retrosynthesis? In this study, we introduce RETROR1, a novel LLM-based retrosynthesis agent trained via reinforcement learning to design molecular synthesis pathways. Unlike prior approaches, which typically rely on single-turn, question-answering formats, RETRO-R1 interacts dynamically with plug-in single-step retrosynthesis tools and learns from environmental feedback. Experimental results show that RETRO-R1 achieves a 55.79% pass@1 success rate, surpassing the previous state of the art by 8.95%. Notably, RETRO-R1 demonstrates strong generalization to out-of-domain test cases, where existing methods tend to fail despite their high in-domain performance. Our work marks a significant step toward equipping LLMs with advanced, chemist-like reasoning abilities, highlighting the promise of reinforcement learning for enabling data-efficient, generalizable, and sophisticated scientific problem-solving in LLM-based agents.


BioCG: Constrained Generative Modeling for Biochemical Interaction Prediction

Neural Information Processing Systems

Predicting interactions between biochemical entities is a core challenge in drug discovery and systems biology, often hindered by limited data and poor generalization to unseen entities. Traditional discriminative models frequently underperform in such settings. We propose BioCG (Biochemical Constrained Generation), a novel framework that reformulates interaction prediction as a constrained sequence generation task. BioCG encodes target entities as unique discrete sequences via Iterative Residual Vector Quantization (I-RVQ) and trains a generative model to produce the sequence of an interacting partner given a query entity. A trie-guided constrained decoding mechanism, built from a catalog of valid target sequences, concentrates the model's learning on the critical distinctions between valid biochemical options, ensuring all outputs correspond to an entity within the pre-defined target catalog. An information-weighted training objective further focuses learning on the most critical decision points. BioCG achieves state-of-the-art (SOTA) performance across diverse tasks, Drug-Target Interaction (DTI), Drug-Drug Interaction (DDI), and Enzyme-Reaction Prediction, especially in data-scarce and cold-start conditions.