BioMatrix unifies sequences, structures, and language for molecules and proteins inside one decoder-only foundation model via shared discrete tokens and achieves SOTA or competitive results on 77 of 80 downstream tasks.
Zhangchen Xu, Yang Liu, Yueqin Yin, Mingyuan Zhou, and Radha Poovendran
6 Pith papers cite this work. Polarity classification is still indexing.
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VibeProteinBench is a new benchmark evaluating LLMs on open-ended language-interfaced protein design across recognition, engineering, and generation, with no model showing strong performance in all areas.
RosettaSearch applies LLM-driven multi-objective search at inference time to improve backbone-conditioned protein sequences, recovering designs with 18-68% better structural fidelity and 2.5x higher success rates than single-pass models like LigandMPNN.
AlphaEvolve is an LLM-orchestrated evolutionary coding agent that discovered a 4x4 complex matrix multiplication algorithm using 48 scalar multiplications, the first improvement over Strassen's algorithm in 56 years, plus optimizations for Google data centers and hardware.
AMix-2 unifies protein sequences and text in one LLM via shared tokens and block-wise diffusion modeling, introduces the ProteinArena benchmark, and reports competitive performance against task-specific protein models and frontier LLMs.
SciCustom constructs application-specific benchmarks for LLM scientific capabilities from large-scale data using ontology-grounded units, automated tagging, consensus retrieval, and proxy selection.
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VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design
VibeProteinBench is a new benchmark evaluating LLMs on open-ended language-interfaced protein design across recognition, engineering, and generation, with no model showing strong performance in all areas.