arXiv subjects

Chaitra Agrahar

Publications and source records attributed to Chaitra Agrahar.

3 recordsLinked to original sources

arXiv2026

PRiMeFlow: Capturing Complex Expression Heterogeneity in Perturbation Response Modelling

Predicting the effects of perturbations in-silico on cell state can identify drivers of cell behavior at scale and accelerate drug discovery. However, modeling challenges remain due to the inherent heterogeneity of single cell gene expression and the complex, latent gene dependencies. Here, we present PRiMeFlow, an end-to-end flow matching based approach to directly model the effects of genetic and small molecule perturbations in the gene expression space. The distribution-fitting approach taken by PRiMeFlow enables it to accurately approximate the empirical distribution of single-cell gene expression, which we demonstrate through extensive benchmarking inside PerturBench. Through ablation studies, we also validate important model design choices such as operating in gene expression space and parameterizing the velocity field with a U-Net architecture. Finally, by scaling PRiMeFlow to a broad perturbation data atlas spanning multiple datasets and employing a carefully designed pretraining-finetuning strategy, we demonstrate its outstanding performance on the H1 human embryonic stem cells from the ARC Virtual Cell Challenge benchmark.

cs.LG↗

arXiv2024

Pathspace Kalman Filters with Dynamic Process Uncertainty for Analyzing Time-course Data

Kalman Filter (KF) is an optimal linear state prediction algorithm, with applications in fields as diverse as engineering, economics, robotics, and space exploration. Here, we develop an extension of the KF, called a Pathspace Kalman Filter (PKF) which allows us to a) dynamically track the uncertainties associated with the underlying data and prior knowledge, and b) take as input an entire trajectory and an underlying mechanistic model, and using a Bayesian methodology quantify the different sources of uncertainty. An application of this algorithm is to automatically detect temporal windows where the internal mechanistic model deviates from the data in a time-dependent manner. First, we provide theorems characterizing the convergence of the PKF algorithm. Then, we numerically demonstrate that the PKF outperforms conventional KF methods on a synthetic dataset lowering the mean-squared-error by several orders of magnitude. Finally, we apply this method to biological time-course dataset involving over 1.8 million gene expression measurements.

stat.ML↗

arXiv2019

Stability of Disordered Topological Superconducting Phases in Magnet--Superconductor Hybrid Systems

Magnet-superconductor hybrid heterostructures constitute a promising candidate system for the quantum engineering of chiral topological superconductivity. Here, we investigate the stability of their topological phases in the presence of various types of potential and magnetic disorder. In particular we consider magnetic disorder in the coupling strength and spin-orientation, as well as percolation type disorder representing missing magnetic moments. We show that potential disorder leads to the weakest suppression of topological phases, while percolation disorder leads to their strongest suppression. In addition, we demonstrate that in the case of correlated potential disorder, the spatial structure of the disorder potential is correlated not only with the particle number density, but also the Chern number density. Finally, we demonstrate how the disorder-induced destruction of topological superconductivity is reflected in the spatial structure and distribution of the Chern number density.

cond-mat.supr-con↗