Agents reconstruct molecular workflows approximately right and exactly right far less often
AspireAI community · arXiv
LibStructBench is a document-grounded benchmark for whether agents can reconstruct sequencing-library structures and molecular workflows from protocol documents. The results are useful for anyone building a scientific agent: frontier agents often produce approximately correct reconstructions but stay unreliable at exact reconstruction, particularly in molecular-state representation and workflow connectivity. Swapping the underlying language model produced larger average performance differences than swapping the agent harness, with a statistically significant difference only for molecular-state reconstruction. Additional knowledge improved oligo-family recovery in a small pilot without improving mean molecular-workflow scores, and autonomous accumulation of procedural rules and cross-protocol examples showed non-monotonic validation performance and no mean held-out improvement on the trajectory tested. The authors use it to argue for more controlled and verifiable approaches to scientific reasoning about molecular processes rather than more autonomy.
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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.