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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.

MarkTechPostSep 16, 21:59 UTC · 14h agoAI research1

Affora: A Design System for Agent-Friendly Interfaces

Affora is a design system making interfaces legible to computer-use agents while preserving human workflows, with reusable components and executable checks.

Affora supports both human users and computer-use agents through a shared interface rather than a separate agent-only surface. Three controlled studies cover component implementations, visual variation, and interaction-design principles, producing guidance from individual components to complete sites with reusable implementations and executable checks. Evaluation on independently authored interfaces shows gains where agent-readability deficits exist, limited effects where they do not, and a workflow case gives preliminary evidence of reduced interaction cost.

arXiv cs.AI / cs.LG / cs.CLSep 16, 17:46 UTC · 19h agoAI research

PANORAMA: Panoptic Grounded Captioning via Mask Proposal Selection

Researchers introduce PANORAMA, a vision-language model grounding caption phrases in pixel masks, alongside the PanoCaps benchmark and gPQ metric.

The paper studies panoptic grounded captioning, requiring VLMs to describe foreground and background regions while grounding each phrase with pixel-level masks. The authors release PanoCaps, a human-annotated benchmark built from panoptic segmentation datasets, plus a phrase-mask matching protocol and a generalized Panoptic Quality (gPQ) metric. PANORAMA formulates grounding as selection from phrase-conditioned mask proposals generated by a pretrained segmenter, achieving the best overall grounding on PanoCaps and matching or exceeding specialized models. Code, data, and models are publicly available.

Hugging Face daily papersupdated Sep 16, 17:59 UTC · 18h agofirst Sep 15, 20:00 UTC · 1d agoAI research 2 sources

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

ScienceBuddy released: interactive scientific agent workspace coupling harness evolution with model reinforcement learning for continual self-improvement across four scientific task families.

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

Hugging Face daily papersupdated Sep 15, 17:55 UTC · 1d agofirst Sep 14, 20:00 UTC · 2d agoAI research 2 sources

A Chosen Future Can Still Be Rewritten: Causal Writability in Video Models

Study shows video models often learn correct physics but fail to use it; low-dimensional 'causal writability' edits can restore correct motion.

The paper demonstrates 'causal writability' in video generation models: physically correct motion remains available inside the model even when the model outputs incorrect motion. In a red/blue mass oscillation setup, a low-dimensional edit predicted from simple physical variables restores correct fast motion, with a sharp depth boundary marking commitment. Early causal writability predicts which training errors later get corrected, and both writability and closure reproduce in a pretrained 1.3B video model.

arXiv cs.AI / cs.LG / cs.CLSep 14, 17:58 UTC · 2d agoAI research

Disentangling Representation Evolution in Transformers through Directional Decomposition

Decomposes transformer representation updates into parallel and perpendicular components, linking geometry to editing robustness and better pretraining.

The paper decomposes learned transformer updates into parallel and perpendicular components relative to the hidden state, finding substantial parallel components beyond the residual identity path across pretrained models. Targeted edits reveal exclude-self value-space parallel manipulation is more robust than residual-space or perpendicular alternatives, and perpendicular error separates compression methods more clearly. Applying full-aggregate parallel suppression during from-scratch pretraining lowers validation loss and improves downstream averages, with the value-space variant strongest. Code is released on GitHub.

arXiv cs.AI / cs.LG / cs.CLSep 14, 17:56 UTC · 2d agoAI research 2 sources1

Learning Multimodal One-step Flow Policy via Value-weighted Optimal Transport

OptiFlow learns one-step multimodal flow policies for offline RL via state-wise entropic optimal transport, avoiding critic overestimation and mode collapse.

The paper introduces OptiFlow, a framework that frames one-step flow policy learning as a structured sample-allocation problem in offline reinforcement learning. It jointly trains a value-aware reference flow policy and a one-step policy, coupling action samples through state-wise entropic optimal transport where critic values set distillation priority and action-distance cost ensures geometrically compatible pairings. By avoiding direct critic maximization, it anchors the policy to high-value dataset-supported modes without out-of-distribution divergence. Code is released on GitHub and the method performs strongly across diverse offline RL benchmarks.

arXiv cs.AI / cs.LG / cs.CLSep 14, 17:10 UTC · 2d agoAI research1

When LLM judges agree, should we believe them?

Amazon ICML paper uses Ising models to correct correlated LLM-judge votes, beating accuracy-weighted panels by 9-14%.

Amazon Science describes an ICML paper, "Dependence-aware label aggregation for LLM-as-a-judge via Ising models," addressing how correlated judge outputs inflate majority-vote confidence. The unsupervised method models pairwise dependence between judges, learning both reliability and similarity without human reference labels. Tested on relevance, toxicity, and summarization tasks with 10 judge models at temperature zero, it outperformed accuracy-weighted voting by 9% to 14%.

Hacker News · AISep 14, 16:29 UTC · 2d agoAI research HN 41↑ · 23 comments