Suzanne Sindi

A. Ali Heydari, Oscar A. Davalos, Katrina K. Hoyer et al.

Single-cell RNA sequencing (scRNAseq) is rapidly advancing our understanding of cellular composition within complex tissues and organisms. A major limitation in most scRNAseq analysis pipelines is the reliance on manual annotations to determine cell identities, which are time consuming, subjective, and require expertise. Given the surge in cell sequencing, supervised methods-especially deep learning models-have been developed for automatic cell type identification (ACTI), which achieve high accuracy and scalability. However, all existing deep learning frameworks for ACTI lack interpretability and are used as "black-box" models. We present N-ACT (Neural-Attention for Cell Type identification): the first-of-its-kind interpretable deep neural network for ACTI utilizing neural-attention to detect salient genes for use in cell-type identification. We compare N-ACT to conventional annotation methods on two previously manually annotated data sets, demonstrating that N-ACT accurately identifies marker genes and cell types in an unsupervised manner, while performing comparably on multiple data sets to current state-of-the-art model in traditional supervised ACTI.

Maria-Veronica Ciocanel, John T. Nardini, Kevin B. Flores et al.

Agent-based modeling (ABM) is a powerful tool for understanding self-organizing biological systems, but it is computationally intensive and often not analytically tractable. Equation learning (EQL) methods can derive continuum models from ABM data, but they typically require extensive simulations for each parameter set, raising concerns about generalizability. In this work, we extend EQL to Multi-experiment equation learning (ME-EQL) by introducing two methods: one-at-a-time ME-EQL (OAT ME-EQL), which learns individual models for each parameter set and connects them via interpolation, and embedded structure ME-EQL (ES ME-EQL), which builds a unified model library across parameters. We demonstrate these methods using a birth--death mean-field model and an on-lattice agent-based model of birth, death, and migration with spatial structure. Our results show that both methods significantly reduce the relative error in recovering parameters from agent-based simulations, with OAT ME-EQL offering better generalizability across parameter space. Our findings highlight the potential of equation learning from multiple experiments to enhance the generalizability and interpretability of learned models for complex biological systems.

Alex John Quijano, Rick Dale, Suzanne Sindi

The availability of large linguistic data sets enables data-driven approaches to study linguistic change. The Google Books corpus unigram frequency data set is used to investigate the word rank dynamics in eight languages. We observed the rank changes of the unigrams from 1900 to 2008 and compared it to a Wright-Fisher inspired model that we developed for our analysis. The model simulates a neutral evolutionary process with the restriction of having no disappearing and added words. This work explains the mathematical framework of the model - written as a Markov Chain with multinomial transition probabilities - to show how frequencies of words change in time. From our observations in the data and our model, word rank stability shows two types of characteristics: (1) the increase/decrease in ranks are monotonic, or (2) the rank stays the same. Based on our model, high-ranked words tend to be more stable while low-ranked words tend to be more volatile. Some words change in ranks in two ways: (a) by an accumulation of small increasing/decreasing rank changes in time and (b) by shocks of increase/decrease in ranks. Most words in all of the languages we have looked at are rank stable, but not as stable as a neutral model would predict. The stopwords and Swadesh words are observed to be rank stable across eight languages indicating linguistic conformity in established languages. These signatures suggest unigram frequencies in all languages have changed in a manner inconsistent with a purely neutral evolutionary process.