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An 8B protein tool agent hit 61.0 percent annotation coverage, beating DeepSeek-V3.2-Thinking 671B at 41.6, once tool calls got their own credit

AspireAI community · arXiv
ProtAgent asks whether a compact model can learn protein-annotation tool use through post-training against real bioinformatics tools, rather than by scaling up. The pipeline is a supervised fine-tune that teaches the tool interface, followed by plain on-policy REINFORCE that improves the interaction policy. Intermediate tool calls receive action rewards and the final answer receives a terminal reward; step-level returns assign those rewards to the responses and preceding actions that produced them, where the episode-level baseline gives every action the same single return. On a fixed closed-loop protocol with real tools, ProtAgent-8B reaches 61.00% success on the annotation-coverage metric, against 41.60% for DeepSeek-V3.2-Thinking 671B and 60.80% for the strongest evaluated frontier system. Across three seeds, mean success is 42.70% with episode-level returns and 61.40% with step-level returns under identity normalisation. The honest limit: the metric measures recovery of reference annotations under one protocol, which the authors state does not establish biological correctness or complete evidence grounding. https://arxiv.org/abs/2610.33746
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One distance function matched sparse-autoencoder features across layers and compressed feature circuits into supernodes
Two sparse-autoencoder analyses have resisted scaling: matching semantically similar features across layers, and compressing large feature circuits into interpretable supernodes. This paper argues both are the same underlying problem, estimating semantic distances between SAE features that sit on different activation manifolds. Its representation treats each feature not as a single decoder vector but as an activation-weighted distribution over the hidden states expressing it, projects those distributions into a shared reference space, and compares them with Wasserstein distance. The representation is proved invariant to activation rescaling and stable under perturbation, and recovers true matches under finite-sample margin conditions. Empirically it outperformed decoder-vector and LLM-based baselines and captured subtle functional distinctions between related features, and it compressed large feature circuits into interpretable supernodes automatically. The limitation is that this is interpretability tooling: the paper demonstrates better feature matching and circuit compression, not that downstream interpretability claims become more accurate.
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