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新论文 · v1arXiv:2611.14844

AutoAssumption: Searching over Assumptions Discovers ML-Systems Algorithms

Igor Sadalski, Minghao Guo, Benjamin Jones, Wojciech Matusik

原文摘要

Many advances in ML systems came from breaking an assumption that earlier methods took for granted: speculative decoding dropped the assumption that a model needs one forward pass per token. Yet algorithms rarely state their assumptions, so experts and discovery harnesses search over programs, where one edit changes several design choices and gains are difficult to attribute. Searching over the assumptions themselves remains largely unexplored. Writing algorithms as proofs makes their assumptions explicit and turns algorithm design into a search over a small, structured space that an LLM can explore and a proof checker can audit. We formalize 89 algorithms from KV-cache eviction, weight pruning and speculative decoding as proof graphs with explicit assumptions, checked in Lean. Our harness, AutoAssumption, relaxes one assumption of a published method, re-derives and re-proves it, and generates its code. In KV-cache eviction and weight pruning, this search improved on every published algorithm we ran and produced state-of-the-art algorithms. The eviction algorithm has the highest RULER-4K score of the published methods we ran, and the pruning algorithm the lowest perplexity of thirteen on four LLaMA models. At equal budget, the harness scores within a point of OpenEvolve, an open-source implementation of AlphaEvolve, with a lower standard deviation across repeats. Future work will formalize more fields and combine them through the principal assumptions they share.

cs.AI · cs.LG

新论文 · v1arXiv:2611.13348

ProTEUS: A mutation-resolved world model for closed-loop protein evolution

Yikun Zhang, Minghao Guo, Guangxue Xu, Peter Yichen Chen, Wojciech Matusik, Wengong Jin, Jingjing Chai, Kaiyi Jiang

原文摘要

Protein engineering requires navigating rugged fitness landscapes, where small sequence changes can produce large functional differences, but experimental screening can only sample a small fraction of sequence space. Thus, a central challenge is to efficiently traverse the large combinatorial space of mutations in silico. We introduce ProTEUS, a mutation-resolved world model for closed-loop protein evolution. Pretrained on deep mutational scanning assays, ProTEUS learns a joint representation of sequence, evolutionary, and structural information using MutationFormer, a mutation-biased attention architecture. Variants are represented as states in this joint latent space, and mutations define actions whose functional consequences are predicted. To support exploration of many mutants, we developed a fast, physics-constrained all-atom predictor that utilizes explicit geometric constraint enforcement to achieve >10 fold increase in speed than AlphaFold3 with guaranteed physical validity. Lastly, ProTEUS refines its prediction and understanding of protein activity through closed loop experimental feedback to guide evolution toward a desired phenotype. ProTEUS surpasses established models in both zero-shot and supervised fine-tuning mutation prediction tasks. We experimentally demonstrate its utility in two closed-loop multi-objective engineering campaigns on aldehyde dehydrogenase and levansucrase, yielding variants with >10 fold higher activity than wild type. ProTEUS provides a world-model framework that connects virtual evaluation of mutational outcomes with experimental learning for efficient protein evolution.

q-bio.BM · cs.AI

版本更新 · v2arXiv:2605.09196

RigidFormer: Learning Rigid Dynamics using Transformers

Zhiyang Dou, Minghao Guo, Haixu Wu, Doug Roble, Tuur Stuyck, Wojciech Matusik

原文摘要

Learning-based simulation of multi-object rigid-body dynamics remains difficult because contact is discontinuous and errors compound over long horizons. Most existing methods remain tied to mesh connectivity and vertex-level message passing, which limits their applicability to mesh-free inputs such as point clouds and leads to high computational cost. Efficiently modeling high-fidelity rigid-body dynamics from mesh-free representations therefore remains challenging. We introduce RigidFormer, an object-centric Transformer-based model that learns mesh-free rigid-body dynamics with controllable integration step sizes. RigidFormer reasons at the object level and advances each object through compact anchors; Anchor-Vertex Pooling enriches these anchors with local vertex features, retaining contact-relevant geometry without dense vertex-level interaction. We propose Anchor-based RoPE to make attention aware of the objects' spatial layout while respecting the unordered nature of objects and anchors: object-token processing is permutation-equivariant, and the mean-pooled anchor descriptor is invariant to anchor reindexing. RigidFormer further enforces rigidity by projecting updates onto the rigid-body manifold using differentiable Kabsch alignment. On standard benchmarks, RigidFormer outperforms or matches mesh-based baselines using point inputs, runs faster, generalizes to unseen point resolutions and across datasets, and scales to 200+ objects; we also show a preliminary extension to command-conditioned articulated bodies by treating body parts as interacting object-level components. Project page: https://frank-zy-dou.github.io/projects/RigidFormer/

cs.CV · cs.AI · cs.GR · cs.LG · cs.RO