arXiv subjects

Mihir Rao

Publications and source records attributed to Mihir Rao.

4 recordsLinked to original sources

arXiv2026

A thermodynamic metric quantitatively predicts disordered protein partitioning and multicomponent phase behavior

Intrinsically disordered regions (IDRs) of proteins mediate sequence-specific interactions underlying diverse cellular processes, including the formation of biomolecular condensates. Although IDRs strongly influence condensate compositions, quantitative frameworks that predict and explain their phase behavior in complex mixtures remain lacking. Here we introduce a thermodynamic model that quantitatively predicts the behavior of arbitrary combinations of IDRs across a wide range of concentrations, with accuracy comparable to state-of-the-art simulations. The model learns low-dimensional, context-independent representations of IDR sequences that combine to form mixture representations, producing context-dependent interactions. These representations define a thermodynamic metric space in which distances between IDRs correspond directly to differences in their thermodynamic properties. We show that the model predicts multicomponent phase diagrams in quantitative agreement with molecular simulations without being trained on free-energy or phase-coexistence data. The metric space provides geometrically intuitive predictions of IDR partitioning, multicomponent condensation, and context-dependent mutational effects, addressing several central problems in IDR biophysics within a single model. Systematic interrogation of the learned representations reveals how amino-acid composition and sequence patterning jointly determine mixture thermodynamics. Together, our results establish a unified and interpretable framework for predicting and understanding the behavior of complex mixtures of IDRs and other sequence-dependent biomolecules.

cond-mat.soft↗

arXiv2025

Information Efficiency of Scientific Automation

Scientific discovery can be framed as a thermodynamic process in which an agent invests physical work to acquire information about an environment under a finite work budget. Using established results about the thermodynamics of computing, we derive finite-budget bounds on information gain over rounds of sequential Bayesian learning. We also propose a metric of information-work efficiency, and compare unpartitioned and federated learning strategies under matched work budgets. The presented results offer guidance in the form of bounds and an information efficiency metric for efforts in scientific automation at large.

cs.IT↗

arXiv2021

Novel Local Radiomic Bayesian Classifiers for Non-Invasive Prediction of MGMT Methylation Status in Glioblastoma

Glioblastoma, an aggressive brain cancer, is amongst the most lethal of all cancers. Expression of the O6-methylguanine-DNA-methyltransferase (MGMT) gene in glioblastoma tumor tissue is of clinical importance as it has a significant effect on the efficacy of Temozolomide, the primary chemotherapy treatment administered to glioblastoma patients. Currently, MGMT methylation is determined through an invasive brain biopsy and subsequent genetic analysis of the extracted tumor tissue. In this work, we present novel Bayesian classifiers that make probabilistic predictions of MGMT methylation status based on radiomic features extracted from FLAIR-sequence magnetic resonance imagery (MRIs). We implement local radiomic techniques to produce radiomic activation maps and analyze MRIs for the MGMT biomarker based on statistical features of raw voxel-intensities. We demonstrate the ability for simple Bayesian classifiers to provide a boost in predictive performance when modelling local radiomic data rather than global features. The presented techniques provide a non-invasive MRI-based approach to determining MGMT methylation status in glioblastoma patients.

q-bio.QM↗

arXiv2020

Conversion and Implementation of State-of-the-Art Deep Learning Algorithms for the Classification of Diabetic Retinopathy

Diabetic retinopathy (DR) is a retinal microvascular condition that emerges in diabetic patients. DR will continue to be a leading cause of blindness worldwide, with a predicted 191.0 million globally diagnosed patients in 2030. Microaneurysms, hemorrhages, exudates, and cotton wool spots are common signs of DR. However, they can be small and hard for human eyes to detect. Early detection of DR is crucial for effective clinical treatment. Existing methods to classify images require much time for feature extraction and selection, and are limited in their performance. Convolutional Neural Networks (CNNs), as an emerging deep learning (DL) method, have proven their potential in image classification tasks. In this paper, comprehensive experimental studies of implementing state-of-the-art CNNs for the detection and classification of DR are conducted in order to determine the top performing classifiers for the task. Five CNN classifiers, namely Inception-V3, VGG19, VGG16, ResNet50, and InceptionResNetV2, are evaluated through experiments. They categorize medical images into five different classes based on DR severity. Data augmentation and transfer learning techniques are applied since annotated medical images are limited and imbalanced. Experimental results indicate that the ResNet50 classifier has top performance for binary classification and that the InceptionResNetV2 classifier has top performance for multi-class DR classification.

cs.CV↗