Author

Alexander Anufriev

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#small language model Open access Sep 2026

Deterministic Finite-Scale Geometry of RNA Language Model Embeddings Predicts siRNA Efficacy: Gϵ(r) Outperforms LID as a Functional Complexity Measure

Motivation. BLAST-based screening of small interfering RNAs (siRNAs) frequently produces false positives in the “grey zone”, where alignment statistics are marginally significant but functional affinity is low. Existing approaches based on local intrinsic dimensionality (LID) of language model embeddings are unstable o...

Andrey V. Timofeev, Alexander Anufriev · Preprints.org · 0 citations

#graph neural networks Open access Sep 2026

Fast and Interpretable Estimation of Amino Acid Residue Surface Accessibility Based on Protein Contact Graph

Three empirical functions for estimating relative SASA—approx_sasa, surface_score, and exp_sasa—using node degree as the sole argument are proposed and validated and shown to be suitable for large-scale pipelines requiring both speed and interpretability.

A. Timofeev, Alexander Bratchikov, Alexander Anufriev · Physchem · 0 citations