On-device research index

arXiv research

A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.

168,695 papers · 148 categories

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3 results for “proteinMPNN”

Fast non-autoregressive inverse folding with discrete diffusionq-bio.BM

Non-autoregressive method speeds up protein folding prediction 23 times.

problem Generating protein sequences with higher order interactions.

method Discrete diffusion conditioned on 3D structure using ProteinMPNN.

result 23 times speed up in inference without performance loss.

protein design 3D structure discrete diffusion proteinMPNN inference speed

2023-12-05abs ↗pdf ↗

Kernel-Based Evaluation of Conditional Biological Sequence Modelsstat.ML

New tools evaluate and optimize conditional sequence models in bioinformatics.

problem Evaluating and optimizing conditional sequence models in bioinformatics.

method Kernel-based discrepancy measure (ACMMD) to estimate model fit and tune hyperparameters.

result Rejects the hypothesis that ProteinMPNN fits its data for various protein families and optimizes model temperature.

kernel-based evaluation conditional sequence models bioinformatics maximum mean discrepancy protein design

2025-10-17abs ↗pdf ↗

Controllable protein design with particle-based Feynman-Kac steeringcs.LG

New method steers protein design towards desired properties.

problem Challenges in designing proteins with specific structures and properties.

method Feynman-Kac framework applied to RFdiffusion models with guiding potentials.

result Significant improvement in predicted interface energetics and binder designability.

protein design Feynman-Kac diffusion models structural relaxation user-defined rewards

2025-11-12abs ↗pdf ↗