Daniel Gurevich | Searcharxiv

arXiv2023

Exploring the Interplay Between Colorectal Cancer Subtypes Genomic Variants and Cellular Morphology: A Deep-Learning Approach

Molecular subtypes of colorectal cancer (CRC) significantly influence treatment decisions. While convolutional neural networks (CNNs) have recently been introduced for automated CRC subtype identification using H&E stained histopathological images, the correlation between CRC subtype genomic variants and their corresponding cellular morphology expressed by their imaging phenotypes is yet to be fully explored. The goal of this study was to determine such correlations by incorporating genomic variants in CNN models for CRC subtype classification from H&E images. We utilized the publicly available TCGA-CRC-DX dataset, which comprises whole slide images from 360 CRC-diagnosed patients (260 for training and 100 for testing). This dataset also provides information on CRC subtype classifications and genomic variations. We trained CNN models for CRC subtype classification that account for potential correlation between genomic variations within CRC subtypes and their corresponding cellular morphology patterns. We assessed the interplay between CRC subtypes' genomic variations and cellular morphology patterns by evaluating the CRC subtype classification accuracy of the different models in a stratified 5-fold cross-validation experimental setup using the area under the ROC curve (AUROC) and average precision (AP) as the performance metrics. Combining the CNN models account for variations in CIMP and SNP further improved classification accuracy (AUROC: 0.847$\pm$0.01 vs. 0.787$\pm$0.03, p$=$0.01, AP: 0.68$\pm$0.02 vs. 0.64$\pm$0.05).

cs.CV↗

arXiv2022

Optimal Control with Learning on the Fly: System with Unknown Drift

This paper derives an optimal control strategy for a simple stochastic dynamical system with constant drift and an additive control input. Motivated by the example of a physical system with an unexpected change in its dynamics, we take the drift parameter to be unknown, so that it must be learned while controlling the system. The state of the system is observed through a linear observation model with Gaussian noise. In contrast to most previous work, which focuses on a controller's asymptotic performance over an infinite time horizon, we minimize a quadratic cost function over a finite time horizon. The performance of our control strategy is quantified by comparing its cost with the cost incurred by an optimal controller that has full knowledge of the parameters. This approach gives rise to several notions of "regret." We derive a set of control strategies that provably minimize the worst-case regret; these arise from Bayesian strategies that assume a specific fixed prior on the drift parameter. This work suggests that examining Bayesian strategies may lead to optimal or near-optimal control strategies for a much larger class of realistic dynamical models with unknown parameters.

math.OC↗