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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 · 15h agoAI research1

A Zeroth-Order Paradigm for LLM Preference Alignment

ComPO is a zeroth-order preference alignment method using comparison oracles to mitigate likelihood displacement across Mistral, Llama, Gemma, and Qwen3 models.

The paper proposes Comparison-based Preference Optimization (ComPO), a zeroth-order alignment method that extracts directional information from preference pairs with small likelihood margins without directly optimizing a differentiable preference loss. The authors prove convergence guarantees for the offline scheme and performance guarantees for a constrained online variant with reverse-KL control. Experiments on Mistral, Llama, Gemma-2, Qwen3, and Gemma-3 show improvements over existing direct alignment methods, including length-controlled win rates, with pair-level diagnostics consistent with mitigating likelihood displacement.

Hugging Face daily papersupdated Sep 16, 17:59 UTC · 19h agofirst Sep 15, 20:00 UTC · 1d agoAI research 2 sources

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

Task-Directed Residual AddUNet:Perfect-Reconstruction Routing for Full-Rate Representations

Paper recasts additive U-Net skip structure as a perfect-reconstruction filter bank and adds full-rate residual routing for task-directed representations.

The work proves a constrained additive U-Net's survivor-skip structure is exactly equivalent to a critically sampled perfect-reconstruction filter bank, and removes complementary-subband restrictions via a full-rate formulation. A Residual Full-Rate PR architecture routes task-irrelevant or redundant structure away from the task pathway while guaranteeing exact reconstruction without invertible operators, a matched synthesis bank, or a learned decoder. On TIMIT, the front-end improves test PER from 28.60±2.09% to 25.76±0.41% with recognizer and training held fixed.

arXiv cs.AI / cs.LG / cs.CLSep 14, 16:50 UTC · 2d agoAI research

A Princeton Researcher Proposes Recurrent Looped Transformer (RLT) that Carries Decoder State across Every Token, Fixing 96 Blocks per Token with Unbounded Temporal Depth

Princeton researcher Yifan Zhang proposes Recurrent Looped Transformer, carrying full decoder state across every token for unbounded temporal depth.

Yifan Zhang's technical report defines the Recurrent Looped Transformer (RLT), pairing a causal encoder with a recurrent decoder whose final output and layerwise sliding-window attention cache carry into every subsequent token with no prompt-response boundary reset. The reference configuration ties 48 encoder and 48 decoder layers, executing 96 logical blocks per token while the state path grows to 48t blocks after t tokens at fixed per-token compute. The report details RL replay contracts that rebuild all states under current parameters and exact prefix snapshots for multi-turn serving, but explicitly reports no measured efficiency, reasoning quality, or scaling results.

MarkTechPostSep 13, 17:02 UTC · 3d agoAI research1

SNAP3D: Physically Grounded 3D Parts for Assembly from a Single Image

SNAP3D uses physics simulation feedback to make single-image 3D part generation produce valid, stable assemblies, validated through 3D printing.

The framework improves part-aware 3D generation by resolving inter-part penetration, recovering contact graphs between neighboring parts, and placing parameterized connectors at contact surfaces. Physical simulation feedback refines connector placement, orientation, and dimensions to improve assembly stability while preserving geometry. A physics-based evaluation protocol tests assembly validity and stability under gravity, and results are validated through 3D printing and real-world assembly.

Hugging Face daily papersSep 10, 20:00 UTC · 6d agoAI research

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.CLSep 10, 17:30 UTC · 6d agoAI research