Anisha Parsan

Yu Li, Anisha Parsan, Bill Wang et al.

Audio commands are a preferred communication medium to keep inspectors in the loop of civil infrastructure inspection performed by a semi-autonomous drone. To understand job-specific commands from a group of heterogeneous and dynamic inspectors, a model must be developed cost-effectively for the group and easily adapted when the group changes. This paper is motivated to build a multi-tasking deep learning model that possesses a Share-Split-Collaborate architecture. This architecture allows the two classification tasks to share the feature extractor and then split subject-specific and keyword-specific features intertwined in the extracted features through feature projection and collaborative training. A base model for a group of five authorized subjects is trained and tested on the inspection keyword dataset collected by this study. The model achieved a 95.3% or higher mean accuracy in classifying the keywords of any authorized inspectors. Its mean accuracy in speaker classification is 99.2%. Due to the richer keyword representations that the model learns from the pooled training data, adapting the base model to a new inspector requires only a little training data from that inspector, like five utterances per keyword. Using the speaker classification scores for inspector verification can achieve a success rate of at least 93.9% in verifying authorized inspectors and 76.1% in detecting unauthorized ones. Further, the paper demonstrates the applicability of the proposed model to larger-size groups on a public dataset. This paper provides a solution to addressing challenges facing AI-assisted human-robot interaction, including worker heterogeneity, worker dynamics, and job heterogeneity.

Divya Nori, Anisha Parsan, Caroline Uhler et al.

Protein binder design has been transformed by hallucination-based methods that optimize structure prediction confidence metrics, such as the interface predicted TM-score (ipTM), via backpropagation. However, these metrics do not reflect the statistical likelihood of a binder-target complex under the learned distribution and yield sparse gradients for optimization. In this work, we propose a method to extract such likelihoods from structure predictors by reinterpreting their confidence outputs as an energy-based model (EBM). By leveraging the Joint Energy-based Modeling (JEM) framework, we introduce pTMEnergy, a statistical energy function derived from predicted inter-residue error distributions. We incorporate pTMEnergy into BindEnergyCraft (BECraft), a design pipeline that maintains the same optimization framework as BindCraft but replaces ipTM with our energy-based objective. BECraft outperforms BindCraft, RFDiffusion, and ESM3 across multiple challenging targets, achieving higher in silico binder success rates while reducing structural clashes. Furthermore, pTMEnergy establishes a new state-of-the-art in structure-based virtual screening tasks for miniprotein and RNA aptamer binders.

Rebonto Haque, Oliver M. Turnbull, Anisha Parsan et al.

Sparse autoencoders (SAEs) are a mechanistic interpretability technique that have been used to provide insight into learned concepts within large protein language models. Here, we employ TopK and Ordered SAEs to investigate an autoregressive antibody language model, p-IgGen, and steer its generation. We show that TopK SAEs can reveal biologically meaningful latent features, but high feature concept correlation does not guarantee causal control over generation. In contrast, Ordered SAEs impose an hierarchical structure that reliably identifies steerable features, but at the expense of more complex and less interpretable activation patterns. These findings advance the mechanistic interpretability of domain-specific protein language models and suggest that, while TopK SAEs are sufficient for mapping latent features to concepts, Ordered SAEs are preferable when precise generative steering is required.