Search: “molecular-design”

Smart search ranks by meaning as well as keywords (one row per story, last 45 days).

ScienceBuddy: Recursive-in-Recursive Self-Improvement for Interactive Scientific Agents

ScienceBuddy couples harness evolution with model reinforcement learning so scientific agents continually self-improve from researcher feedback in an interactive workspace.

The authors release ScienceBuddy, an interactive scientific research workspace that transforms researcher requests, feedback, and execution evidence into tasks and evaluation rubrics for continual learning. Its recursive-in-recursive self-improvement paradigm couples harness evolution (inner recursion, model fixed) with model reinforcement learning under the improved harness (outer recursion). Case studies span four scientific task families, and the system is released to the scientific community as a research product.

arXiv cs.AI / cs.LG / cs.CL·Sep 15, 17:55 UTC · 1d agoAI research 2 sources

35

DianShi-RxnDB: A Large-Scale, Fine-Grained Organic Reaction Data Platform Built via a Fully Automated Pipeline for Researchers and AI Agents

Researchers release DianShi-RxnDB, a database of roughly 24 million organic reaction instances extracted automatically from USPTO and EPO patents since 1976.

DianShi-RxnDB is built by a fully automated pipeline integrating patent text, images, and reaction schemes, yielding about 24 million reaction instances, of which 14.8 million (61.7%) pass automated qualification checks. Manual evaluation of 1,300 sampled instances showed 92.95% field-level accuracy, and comparisons with Pistachio found advantages in deduplicated record counts and granularity. The platform offers a web research workbench and a Model Context Protocol (MCP) service enabling AI agents to perform composable structured retrieval.

Hugging Face daily papers·Sep 5, 20:00 UTC · 11d agoAI research

28

HypoEvolve: Genetic Algorithms Enable Multi-Agent LLMs to Discover Scientific Hypotheses

HypoEvolve couples a generational genetic algorithm with specialized LLM agents to generate drug-repurposing hypotheses, beating six baselines on DepMap selectivity (0.171 vs 0.115).

HypoEvolve coordinates specialized LLM agents through a generational genetic algorithm in which scientific judgments and new proposals reshape a hypothesis population. Evaluation centers on drug repurposing, linking mechanistic explanations to target-level biological claims assessed via external measures adapted from DepMap and Open Targets. Across 34 cancer types, HypoEvolve scores highest against six baselines on both measures, with DepMap selectivity of 0.171 versus 0.115 for the strongest baseline, and gains generalize to held-out cancer types.

arXiv cs.AI / cs.LG / cs.CL·Sep 14, 17:44 UTC · 2d agoAI research1

28

LLM-Driven Algorithm Design for Quantum Circuit Synthesis based on Binary Decision Diagrams

QuantumEvo uses an LLM to evolve BDD variable-ordering heuristics, achieving a 70.9% tie-or-win rate on quantum circuit cost versus baseline methods.

The QuantumEvo framework uses an LLM as a heuristic generator for quantum-cost-aware BDD variable ordering in reversible circuit synthesis, searching over heuristics initialized from multiple families and selecting them by downstream quantum circuit cost. The discovered heuristic HGA-QE modifies the sifting step inside a genetic algorithm and achieves a 70.9% tie-or-win rate against the per-function best baseline, with strict wins on 13.5% of functions. Advantages are clearer on benchmark suites not used for heuristic discovery.

arXiv cs.AI / cs.LG / cs.CL·Sep 4, 16:25 UTC · 12d agoAI research1

20

How a researcher uses Codex and ChatGPT to search for new antimicrobial molecules

OpenAI profiles César de la Fuente's lab using ChatGPT and Codex alongside deep-learning models to accelerate antimicrobial molecule discovery.

OpenAI published a case study on bioengineer César de la Fuente's lab, which uses ChatGPT and Codex for hypothesis brainstorming, code writing, dataset processing, and bridging knowledge gaps across biology, chemistry, and computer science. The lab's deep-learning models scan genome and protein databases for antimicrobial peptide candidates, potentially cutting initial searches from years to hours. Bacterial antimicrobial resistance was associated with about five million deaths in 2021, a toll projected to roughly double by 2050.

OpenAI News·Sep 10, 16:00 UTC · 6d agoAI industry1

25

AI Is Learning to Write Genetic Code

AI models generated viable bacteriophage genomes, with 16 designs successfully replicating and some outperforming the original virus at attacking E. coli.

Two AI models generated complete genome designs for bacteriophages modeled on ΦX174, a virus known to infect E. coli. Researchers produced about 700,000 candidate designs, selected 285 promising ones, and synthesized DNA inserted into E. coli, yielding 16 viable viruses. Some of the newly generated viruses proved more effective at attacking E. coli than the original bacteriophage.

Schneier on Security·Aug 21, 16:52 UTC · 26d agoAI research

35

Enabling Creative Exploration for Vibe Design Agents

Separating design-direction exploration from code generation via structured specifications broadens UI alternatives without destabilizing output.

The paper proposes an inference architecture for vibe design agents that makes design direction an explicit intermediate decision: a Verbalized Sampling-inspired pre-pass proposes structured design specifications with typicality scores, an external selector samples one, and a downstream generator realizes it under fixed settings. Across 168 prompts with 1,255 paired comparisons per temperature, theme sampling broadens selection coverage and screenshot variation, with LLM-judge preferences varying across interventions and prompt complexity. An online experiment with over 300,000 tasks found the code-export increase statistically uncertain, though negative feedback events decreased alongside modest operational costs.

Hugging Face daily papers·Sep 13, 20:00 UTC · 3d agoAI research

28

Molecular Déjà Vu: Digit-Level Retrieval of Published Values in Frontier Language Models

Audit of 22 frontier models finds widespread verbatim retrieval of published molecular property values, with higher reasoning increasing recall of memorized numbers.

An arXiv audit tests 22 frontier LLMs across 12 molecular regression benchmarks for verbatim retrieval of published values. More than 50% of the LLMs show verbatim retrieval on five datasets, and identical experiments are flagged 89% more often at a high reasoning level than at the lowest one. Suppressing retrieval moves model prediction errors closer together in relative terms, suggesting predictive capability is not determined solely by memorized values.

arXiv cs.AI / cs.LG / cs.CL·Sep 4, 17:32 UTC · 12d agoAI research1

42

Stanford Researchers Release Paper2Agent: Turning Research Papers Into AI Agents That Reproduce Results and Run on New Data

Stanford researchers released Paper2Agent, a Nature-published pipeline that turns research papers into MCP servers agents can execute.

A Stanford team led by Jiacheng Miao and James Zou published Paper2Agent in Nature on 16 September 2026. Built on Claude Code's agent SDK, it converts a paper and its codebase into a Model Context Protocol server with validated tools, resources, and prompts. In benchmarks, the AlphaGenome agent built 22 tools in about 45 minutes for US$14, scored 100% on 15 novel queries versus 78.7% for Claude Code with repository access, and cut median runtime 1.9x. In scale tests, 74 of 100 bioRxiv papers were converted and 593 of 599 proposed tools passed validation.

MarkTechPost·Sep 16, 21:59 UTC · 5h agoAI research

58

Reduced-Space Multi-Fidelity Bayesian Optimization of Process Simulation Models

RS-MFBO couples global sensitivity analysis with fidelity-augmented Gaussian processes to slash costly high-fidelity simulation runs in industrial flowsheet optimization.

The paper presents RS-MFBO, a reduced-space multi-fidelity Bayesian optimization framework for high-dimensional, expensive black-box functions. It integrates Global Sensitivity Analysis for dimensionality reduction with a fidelity-augmented Gaussian process and a cost-aware acquisition strategy featuring cooldown and promotion mechanisms. Validation on a plasmid DNA bioprocess (SuperPro Designer) and a green fuel synthesis plant (Aspen HYSYS) shows substantial reductions in high-fidelity evaluations while remaining competitive with single-fidelity baselines.

arXiv cs.AI / cs.LG / cs.CL·Sep 15, 16:46 UTC · 1d agoAI research

15

Dr. Claw: An AI Scientist Workspace for Vibe Research

Researchers release Dr. Claw, an open-source auditable workspace that wraps coding agents like Claude Code for end-to-end AI-assisted research workflows.

Paper 2609.00365 presents Dr. Claw, an open-source workspace that wraps existing coding-agent executors such as Claude Code and Gemini CLI in a controllable, human-in-the-loop research workflow. It uses persistent state objects, a reusable skill library, and multi-executor coordination to make research decisions auditable and recoverable, rather than adding another autonomous agent. Holding the executor fixed, Dr. Claw scores higher on research completeness than a bare command-line agent while preserving an auditable process trail. The code is released under AGPL-3.0 on GitHub (OpenLAIR/dr-claw).

Hugging Face daily papers·Aug 30, 20:00 UTC · 17d agoAI research1

45

Design Docs Are All You Need: An AI-native Machine-Learning Performance Tool

Researchers present SMART, an ML performance-modeling library regenerated by AI coding agents from natural-language design docs instead of code.

The paper describes SMART, a symbolic performance-modeling library whose main branch contains almost no code: the repository is a DAG of self-contained design documents, and coding sub-agents regenerate implementations from only the docs on version updates. Reliability rests on a worked-example doc style used as in-context demonstrations and a minimal operator IR with SymPy cost expressions, offering both fast analytical roll-up and fine-grained modulo-scheduling modes. Regenerated implementations reproduce hand-audited reference models, including DeepSeek-V3 serving on a TPU pod slice, to round-off precision.

arXiv cs.AI / cs.LG / cs.CL·Sep 4, 17:08 UTC · 12d agoAI research1

30

Observational Indistinguishability and Integrity Blind Regions in Hybrid Quantum-Classical Workflows

Framework formalizes integrity blind regions in hybrid quantum-classical workflows, validated across 3,600 label interventions with conformal detection rules.

The paper presents a claim-relative evidence and reference framework for integrity of hybrid quantum-classical workflows, distinguishing structural blind regions caused by observational indistinguishability from finite-batch statistical misses. Experiments over 3,600 label interventions show exact label-path invariance for feature and prediction views. The geometry-aligned construction detects 343 of 2,700 conclusion-changing interventions using the conformal rule and 1,183 of 2,700 with the uncorrected union, with executed conformal clean false-action rates of 0.048-0.059.

arXiv cs.CR·Sep 15, 13:16 UTC · 1d agoResearch

12

Embedded Graph Flows for Categorical Graph Generation

Researchers propose Embedded Graph Flows, a generative model with learned categorical embeddings that beats DiGress and GruM on molecular graph benchmarks.

Embedded Graph Flows (EGF) learns continuous embeddings for node and unordered-edge categories and transports Gaussian noise toward these endpoints using a permutation-equivariant graph transformer. On QM9 it achieves the best result on all four reported metrics, with a Fréchet ChemNet Distance of 0.150 versus 0.717 for DiGress and 0.812 for GruM. On ZINC250k it retains the lowest NSPDK MMD, indicating close agreement with local substructures of reference molecules. Code is released on GitHub.

arXiv cs.AI / cs.LG / cs.CL·Sep 4, 16:26 UTC · 12d agoAI research1

22

MIT creates method to force AI to comply with safety rules

MIT researchers published HardFlow, a method enforcing hard safety constraints on flow-matching generative models' final outputs without retraining.

MIT researchers led by Zeyang Li and Navid Azizan developed HardFlow, a trajectory-optimization method that enforces strict, non-negotiable constraints on flow-matching generative models by checking rule satisfaction only at the final generation step. Published in IEEE TPAMI, it outperformed six rival projection and guidance methods on four simulated benchmarks including D3IL robotic manipulation, Maze2D, physical process control, and image editing. All results are simulation-only, with no independent reproduction yet reported.

Hacker News · security·Sep 14, 16:18 UTC · 2d agoAI researchHN 24↑ · 25 comments

25

EvoSafeHarness: Evolving Model- and Domain-Specific Harnesses for Securing Agents

EvoSafeHarness auto-synthesizes per-model, per-domain safety harnesses, cutting prompt-injection attack success on AgentDojo to 0.0% at 82.8% utility.

EvoSafeHarness is an optimization framework that synthesizes deployable safety harnesses for frozen LLM agents in a target domain, jointly searching natural-language policies and executable code logic guided by model behavior, domain specifications, and adversarial review. On DecodingTrust-Agent it reduces average attack success rate from 45.6% to 10.0% at a 3.3-point utility cost, and on AgentDojo reaches 82.8% utility at 0.0% ASR, twice CaMeL's utility at that operating point. It keeps mean ASR below 20% under adaptive PAIR attacks and transfers unchanged to unseen AgentDyn suites. The analysis finds domain semantics determine required safety relations while model and runtime behavior determine enforcement points.

Hugging Face daily papers·Sep 4, 20:00 UTC · 12d agoAI safety & security

48

Building the materials foundation for AI

Syensqo's CTO says AI pushes semiconductors and data centers to physical limits, driving advanced materials demand and AI-accelerated materials discovery.

MIT Technology Review's Business Lab podcast, produced in partnership with Syensqo, features CTO Mike Finelli discussing how AI workloads push semiconductors and data centers to physical limits in performance, thermal management, and reliability. Syensqo develops high-voltage data center materials, semiconductor sealing materials, and immersion cooling fluids, while using AI agents to digitally synthesize millions of molecular combinations and predict performance before lab testing. Finelli describes a reinforcing cycle where AI improves materials that in turn enable better AI infrastructure.

MIT Technology Review · AI·Sep 16, 12:47 UTC · 14h agoAI industry

25

Register Tokens for Bounded-State Reasoning in Diffusion Language Models

Register tokens let diffusion language models like LLaDA and Dream carry reasoning state across cleared chunks, gaining up to 19.5 points on code.

Researchers propose register tokens: dedicated fixed-position tokens whose continuous hidden states are trained to carry reasoning progress across generation chunks in masked diffusion language models. After decoding and clearing a chunk, the model continues from the prompt and the carried register state instead of retaining earlier text. On LLaDA and Dream, registers outperform discrete-text carry on every benchmark, with gains up to 8.5 points on math and 19.5 points on code. Registers are especially effective for bounded code generation and can be further refined with reinforcement learning on long-horizon reasoning tasks.

Hugging Face daily papers·Sep 13, 20:00 UTC · 3d agoAI research

38

Evaluating Verified Autonomy in Quantum Engineering

Quantum-Harbor lab and QIQCBench (49 tasks) expose wide performance gaps across 17 frontier agentic systems in verified quantum engineering.

Researchers built Quantum-Harbor, a virtual laboratory providing a controlled execution environment where scientific AI agents interacting with quantum systems can have both actions and conclusions directly verified. QIQCBench contributes 49 expert-authored tasks spanning calibration and control, error correction and compilation, and sensing and networking. Across 17 frontier agentic systems, verified performance varied widely, exposing a substantial gap between demonstrated capability and reliable autonomous operation.

arXiv cs.AI / cs.LG / cs.CL·Sep 15, 16:46 UTC · 1d agoAI research1

30

Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens

Researchers release AssayBench-Loop, a 1,389-screen CRISPR benchmark, and AssayLoop, a framework that learns adaptive hit discovery policies.

The paper introduces AssayBench-Loop, a large-scale benchmark of 1,389 CRISPR screens across five phenotype categories for adaptive hit discovery under budget constraints. It also introduces AssayLoop, which combines AssayFormer, a transformer-based amortized acquisition policy trained across historical screens, with LLM-derived biological priors via an adaptive handoff. On temporally held-out screens, AssayLoop achieves 5.67-fold enrichment over random selection and recovers 27.7% of hits after assaying roughly 5% of the candidate library, outperforming existing adaptive-design methods and standalone LLMs.

arXiv cs.AI / cs.LG / cs.CL·Sep 10, 17:45 UTC · 6d agoAI research1

30

ExecCritic: Learn to Test, Test to Improve for Coding Agents

ExecCritic separates test generation from patching for coding agents, lifting SWE-bench Verified resolution to 72.6%.

ExecCritic pairs a test-verify-revise scaffold with role-specific reinforcement learning: a Test agent writes repository-native tests and a Repair agent fixes code from execution feedback, both using Qwen-3.5-35B-A3B backbones. Post-trained Qwen agents compose to 72.6% on SWE-bench Verified, an 11.4-point gain over the 61.2% no-test baseline, without stronger-model or oracle feedback at evaluation time. The work shows test quality is the key variable: base-agent tests lowered resolution to 57.3% while GPT-5.6-sol tests raised it to 65.3%.

arXiv cs.AI / cs.LG / cs.CL·Sep 8, 17:53 UTC · 8d agoAI research1

36

LongAgent: History-Guided Agentic Search for Longitudinal Outcome Prediction

LongAgent autonomously searches variable sets and temporal windows to predict longitudinal medical outcomes, beating the strongest non-agent baseline on synthetic data.

The paper proposes LongAgent, an agent-based method that searches over combinations of variable sets, temporal windows and aggregation functions for outcome prediction on heterogeneous medical longitudinal data. It uses a history memory of previous searches and numerical evidence to guide exploration. On synthetic data it achieves mean RMSE 1.7376, improving over the best non-agent baseline by 0.0151 (95% CI [0.0045, 0.0260]; p=0.0273), and performs comparably to the best baseline on a real clinical dataset.

arXiv cs.AI / cs.LG / cs.CL·Sep 14, 16:51 UTC · 2d agoAI research

16

From Concept to Context Engine: How Wiz Built AI-Powered Data Discovery

Wiz details the multi-agent pipeline and feedback loops that evolved its bucket scanner into AI-powered data discovery.

Wiz published an engineering write-up on building its AI-powered data discovery capability, tracing the evolution from a bucket scanner to a context engine. The post explains the multi-agent pipeline and feedback loops behind the system. The article is a vendor engineering deep-dive with no disclosed vulnerabilities, incidents, or exploitation activity.

Wiz Blog·Aug 27, 15:52 UTC · 20d agoTools1

22

StudyBench: Can Self-Evolution Squeeze Textbooks for Olympiad Capability?

Researchers introduce StudyBench, a physics benchmark showing self-evolution gains on textbook problems rarely transfer to olympiad-level questions.

StudyBench is a controlled physics benchmark splitting test data into an Application Set of difficult textbook problems and a Transfer Set of olympiad-level problems. Across three base models, representative self-evolution methods improved on the Application Set but rarely transferred to the harder Transfer Set. A guidance ablation reveals a Guidance Gap, and every method hits a Compute Plateau, indicating the remaining limits are method problems rather than data or compute problems.

Hugging Face daily papers·Aug 31, 20:00 UTC · 16d agoAI research

28

Model-Aware Schedules Improve Generation via Fiberwise Optimal Transport

Researchers introduce model-aware diffusion schedules via fiberwise optimal transport, cutting flow-matching FID on CIFAR-10 by 38.6% at 16 function evaluations.

The paper proposes constructing diffusion and flow-matching sampling schedules from a fiberwise prediction risk defined via optimal transport, combined with coefficient-path kinetic action, yielding a closed-form time allocation. Across DDPM and flow-matching experiments spanning targets, datasets, and architectures, the schedules beat model-agnostic baselines, including a 38.6% relative FID reduction for flow matching on CIFAR-10 at 16 function evaluations. Normalized fiberwise-risk profiles from independently trained models align closely, suggesting empirical universality, and a frozen analytic allocation template retains most of the gains.

arXiv cs.AI / cs.LG / cs.CL·Sep 10, 17:30 UTC · 6d agoAI research

32

Bridging Control, Inference, Transport, and Thermodynamics: From Theory to Applications in Learning

Review connects control theory, optimal transport, probabilistic inference, thermodynamics, and machine learning via free-energy optimization under constraints.

The review unifies five fields: control theory, optimal transport, probabilistic inference, non-equilibrium thermodynamics, and machine learning. The common conceptual thread is optimization of free-energy-like functionals under dynamical or statistical constraints. Selected applications are presented in reinforcement learning, variational inference, and generative modeling. The tutorial-style text assumes no prior familiarity and begins from physics principles.

arXiv cs.AI / cs.LG / cs.CL·Sep 14, 17:16 UTC · 2d agoAI research

15

Procedural Graphs: Self-Evolving Execution Structures for LLM Agents

Researchers introduce Procedural Graphs, self-evolving (procedure, relation, procedure) structures guiding LLM agent tool use and planning.

Procedural Graphs organize procedural knowledge into (procedure, relation, procedure) triplets to guide LLM agent actions, addressing drift such as lost objectives, out-of-order tool calls, and repeated unproductive steps. At each decision step the framework localizes the active node and a guidance model translates the surrounding subgraph into step-level situational guidance. An LLM refiner edits graph topology by contrasting failed with successful trajectories, and across datasets, task types and LLMs the approach outperforms memory-based baselines and matches or surpasses hand-designed graphs.

arXiv cs.AI / cs.LG / cs.CL·Sep 8, 17:59 UTC · 8d agoAI research1

25

I wrote an AI textbook — how long until AI can do it better?

AI researcher Nathan Lambert argues LLMs remain weak at long-form technical writing, questioning whether models can autonomously organize scientific knowledge for breakthroughs.

Nathan Lambert describes writing a post-training textbook, Reinforcement Learning from Human Feedback, and finds today's LLMs weak at organizing long-form technical content despite becoming superhuman at coding and math. He notes GPT 5.5 Pro found deep typos across a 200-300 page manuscript while Claude models proved more useful as editors. He argues that compressing knowledge through writing is a prerequisite for autonomous scientific insight and tempers expectations for near-term AI-driven open science.

Interconnects·Aug 12, 13:01 UTC · Aug 12, 2026AI research

24

OmniHarness: Harnessing Generalizable Visual Generation via Symbolic Policy Learning

OmniHarness learns symbolic policies for visual generation agents, reaching a 95.0% resolve rate on ComfyBench Creative tasks, 27.5 points above the strongest baseline.

OmniHarness abstracts verified executions into symbolic policies for visual generation task families, which are instantiated, adapted, and composed for new tasks while model parameters remain fixed. Intermediate verification guides refinement and failure recovery during execution, and self-directed inquiry generates practice tasks near capability limits before downstream objectives are specified. Experiments across six benchmarks, three MLLM backbones, and three visual agent frameworks show strong performance; on ComfyBench Creative tasks it achieves a 95.0% resolve rate, exceeding the strongest baseline by 27.5 percentage points. Frozen policy snapshots improve existing visual agent systems through plug-and-play reuse.

Hugging Face daily papers·Sep 12, 20:00 UTC · 4d agoAI research

33