The SDE benchmark shows LLMs lag on scientific discovery tasks relative to general science tests, with diminishing scaling returns and shared weaknesses across models.
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Augmenting large language models with chemistry tools
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LAB-Bench provides over 2,400 multiple-choice questions to measure LLM performance on real biology research tasks like literature recall, figure reading, database access, and sequence manipulation, with initial results compared against human expert biologists.
SCICONVBENCH is a new benchmark evaluating LLMs on multi-turn disambiguation and inconsistency resolution for task formulation in computational science, with frontier models reaching only 52.7% success on fluid mechanics disambiguation cases.
Margin-calibrated classifier guidance via Sequence Completion Ranking raises multi-step retrosynthesis solve rates from 16.8% to 95.3% on USPTO-190 and unlocks previously unsolvable targets.
An AI-agent social platform generated mostly neutral content whose use in fine-tuning reduced model truthfulness comparably to human Reddit data, suggesting limited unique harm but flagging tail risks like secret leaks.
SCPT creates similarity-constrained preference triplets from scaffolds to train LLMs as conditional molecular editors that improve properties while keeping scaffolds intact.
MatClaw shows a code-first LLM agent autonomously generating and executing workflows for ML force field training, Curie temperature prediction, and parameter search on CuInP2S6, succeeding on code but requiring interventions for tacit domain knowledge.
Domain-specialized small language models enable deterministic atomic-resolution scanning probe microscopy control with 99.3% command accuracy, lower computational cost, and better domain performance than larger general models.
AlphaEvolve is an LLM-orchestrated evolutionary coding agent that discovered a 4x4 complex matrix multiplication algorithm using 48 scalar multiplications, the first improvement over Strassen's algorithm in 56 years, plus optimizations for Google data centers and hardware.
ColPackAgent integrates a custom colpack Python package wrapping HOOMD-blue with MCP tools and an agent skill to enable reliable autonomous workflows for colloidal packing simulations across interactive, prompt-driven, and autoresearch modes.
An LLM entity-tagging pipeline plus multi-agent system extracts ~6.3M nuanced records from 22.5M PubMed papers across six tasks with lower measured error than existing curated databases.
BioTool dataset enables fine-tuning a 4B-parameter LLM to outperform GPT-5.1 in biomedical tool calling while improving downstream answer quality per human experts.
A multi-agent AI framework using processing and acoustic agents achieves 91.6% accuracy and 0.821 F1 score for in-situ porosity defect detection in wire-arc additive manufacturing.
An LLM agent integrated with AVEVA Process Simulation via MCP enables natural language driven flowsheet analysis, optimization, and construction for chemical separation processes.
CodeDistiller distills 250 materials-science GitHub repositories into vetted code libraries that improve the accuracy and scientific soundness of experiments generated by ASD agents.
DynaMate2 is an open-source hierarchical agentic framework that converts expert-defined Python functions into AI-callable tools for supervised multi-agent scientific workflows.
pArticleMap combines article embeddings, graph-based frontier extraction, and agentic LLMs to map nanomedicine literature and generate hypotheses, achieving 10.8% gold recovery and 61% future-neighborhood rate in retrospective benchmarks.
Bolek injects Morgan fingerprint embeddings into an instruction-tuned text model, then fine-tunes on molecular alignment and synthetic chain-of-thought tasks to improve performance and grounding on 15 TDC binary classification endpoints while generalizing to unseen tasks.
A multi-agent LLM framework autonomously completes the full computational mechanics pipeline from a photograph to a code-compliant engineering report on a steel L-bracket example.
The paper proposes a four-role framework for LLMs in scientific innovation and reviews methods, benchmarks, and limitations across Assistant, Collaborator, Scientist, and Evaluator roles.
citing papers explorer
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Evaluating Large Language Models in Scientific Discovery
The SDE benchmark shows LLMs lag on scientific discovery tasks relative to general science tests, with diminishing scaling returns and shared weaknesses across models.
-
LAB-Bench: Measuring Capabilities of Language Models for Biology Research
LAB-Bench provides over 2,400 multiple-choice questions to measure LLM performance on real biology research tasks like literature recall, figure reading, database access, and sequence manipulation, with initial results compared against human expert biologists.
-
SCICONVBENCH: Benchmarking LLMs on Multi-Turn Clarification for Task Formulation in Computational Science
SCICONVBENCH is a new benchmark evaluating LLMs on multi-turn disambiguation and inconsistency resolution for task formulation in computational science, with frontier models reaching only 52.7% success on fluid mechanics disambiguation cases.
-
Margin-calibrated Classifier Guidance for Property-driven Synthesis Planning
Margin-calibrated classifier guidance via Sequence Completion Ranking raises multi-step retrosynthesis solve rates from 16.8% to 95.3% on USPTO-190 and unlocks previously unsolvable targets.
-
The Moltbook Files: A Harmless Slopocalypse or Humanity's Last Experiment
An AI-agent social platform generated mostly neutral content whose use in fine-tuning reduced model truthfulness comparably to human Reddit data, suggesting limited unique harm but flagging tail risks like secret leaks.
-
Scaffold-Conditioned Preference Triplets for Controllable Molecular Optimization with Large Language Models
SCPT creates similarity-constrained preference triplets from scaffolds to train LLMs as conditional molecular editors that improve properties while keeping scaffolds intact.
-
MatClaw: An Autonomous Code-First LLM Agent for End-to-End Materials Exploration
MatClaw shows a code-first LLM agent autonomously generating and executing workflows for ML force field training, Curie temperature prediction, and parameter search on CuInP2S6, succeeding on code but requiring interventions for tacit domain knowledge.
-
Integrating Domain-Specialized Language Models with AI Measurement Tools for Deterministic Atomic-Resolution Experimentation
Domain-specialized small language models enable deterministic atomic-resolution scanning probe microscopy control with 99.3% command accuracy, lower computational cost, and better domain performance than larger general models.
-
AlphaEvolve: A coding agent for scientific and algorithmic discovery
AlphaEvolve is an LLM-orchestrated evolutionary coding agent that discovered a 4x4 complex matrix multiplication algorithm using 48 scalar multiplications, the first improvement over Strassen's algorithm in 56 years, plus optimizations for Google data centers and hardware.
-
ColPackAgent: Agent-Skill-Guided Hard-Particle Monte Carlo Workflows for Colloidal Packing
ColPackAgent integrates a custom colpack Python package wrapping HOOMD-blue with MCP tools and an agent skill to enable reliable autonomous workflows for colloidal packing simulations across interactive, prompt-driven, and autoresearch modes.
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Self-Driving Datasets: From 20 Million Papers to Nuanced Biomedical Knowledge at Scale
An LLM entity-tagging pipeline plus multi-agent system extracts ~6.3M nuanced records from 22.5M PubMed papers across six tasks with lower measured error than existing curated databases.
-
BioTool: A Comprehensive Tool-Calling Dataset for Enhancing Biomedical Capabilities of Large Language Models
BioTool dataset enables fine-tuning a 4B-parameter LLM to outperform GPT-5.1 in biomedical tool calling while improving downstream answer quality per human experts.
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In-situ process monitoring for defect detection in wire-arc additive manufacturing: an agentic AI approach
A multi-agent AI framework using processing and acoustic agents achieves 91.6% accuracy and 0.821 F1 score for in-situ porosity defect detection in wire-arc additive manufacturing.
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Large Language Model Agent for User-friendly Chemical Process Simulations
An LLM agent integrated with AVEVA Process Simulation via MCP enables natural language driven flowsheet analysis, optimization, and construction for chemical separation processes.
-
CodeDistiller: Automatically Generating Code Libraries for Scientific Coding Agents
CodeDistiller distills 250 materials-science GitHub repositories into vetted code libraries that improve the accuracy and scientific soundness of experiments generated by ASD agents.
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DynaMate2: Democratization of Agentic AI for Expert-Designed Custom Workflows
DynaMate2 is an open-source hierarchical agentic framework that converts expert-defined Python functions into AI-callable tools for supervised multi-agent scientific workflows.
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Evidence-Grounded Frontier Mapping and Agentic Hypothesis Generation in Nanomedicine
pArticleMap combines article embeddings, graph-based frontier extraction, and agentic LLMs to map nanomedicine literature and generate hypotheses, achieving 10.8% gold recovery and 61% future-neighborhood rate in retrospective benchmarks.
-
Bolek: A Multimodal Language Model for Molecular Reasoning
Bolek injects Morgan fingerprint embeddings into an instruction-tuned text model, then fine-tunes on molecular alignment and synthetic chain-of-thought tasks to improve performance and grounding on 15 TDC binary classification endpoints while generalizing to unseen tasks.
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From Perception to Autonomous Computational Modeling: A Multi-Agent Approach
A multi-agent LLM framework autonomously completes the full computational mechanics pipeline from a photograph to a code-compliant engineering report on a steel L-bracket example.
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Evolving Roles of LLMs in Scientific Innovation: Assistant, Collaborator, Scientist, and Evaluator
The paper proposes a four-role framework for LLMs in scientific innovation and reviews methods, benchmarks, and limitations across Assistant, Collaborator, Scientist, and Evaluator roles.
- ToolRosella: Translating Code Repositories into Standardized Tools for Scientific Agents