Tom Chou
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View article: Martingale Properties of Entropy Production and a Generalized Work Theorem with Decoupled Forward and Backward Processes
Martingale Properties of Entropy Production and a Generalized Work Theorem with Decoupled Forward and Backward Processes Open
By decoupling forward and backward stochastic trajectories, we construct a family of martingales and work theorems for both overdamped and underdamped Langevin dynamics. Our results are made possible by an alternative derivation of work th…
View article: Mechanical activity enables patterning and discrimination at the immune synapse
Mechanical activity enables patterning and discrimination at the immune synapse Open
Immune cells recognize and discriminate antigens through immunological synapses - dynamic intercellular junctions exhibiting highly organized receptor-ligand patterns. While much work has focused on molecular kinetics and passive mechanism…
View article: Efficient portfolio selection through preference aggregation with Quicksort and the Bradley–Terry model
Efficient portfolio selection through preference aggregation with Quicksort and the Bradley–Terry model Open
How to allocate limited resources to projects that will yield the greatest long-term benefits is a problem that often arises in decision-making under uncertainty. For example, organizations may need to evaluate and select innovation projec…
View article: Reconstructing noisy gene regulation dynamics using extrinsic-noise-driven neural stochastic differential equations
Reconstructing noisy gene regulation dynamics using extrinsic-noise-driven neural stochastic differential equations Open
Proper regulation of cell signaling and gene expression is crucial for maintaining cellular function, development, and adaptation to environmental changes. Reaction dynamics in cell populations is often noisy because of (i) inherent stocha…
View article: Alcohol-induced deaths in the United States across age, race, gender, geography, and the COVID-19 pandemic
Alcohol-induced deaths in the United States across age, race, gender, geography, and the COVID-19 pandemic Open
We analyze alcohol-induced deaths by race, gender, age and geography on a yearly (1999–2024) and monthly (2018–2024) basis, using data from the National Vital Statistics System. Crude rates for alcohol-induced deaths increased by 89% from …
View article: Correction: Aggregating multiple test results to improve medical decision-making
Correction: Aggregating multiple test results to improve medical decision-making Open
[This corrects the article DOI: 10.1371/journal.pcbi.1012749.].
View article: Braid Group Representations and Defect Operators in AdS/CFT Correspondence
Braid Group Representations and Defect Operators in AdS/CFT Correspondence Open
This paper investigates the connection between braid group representations, defect operators, and holography within the AdS/CFT framework. It focuses on the correspondence between bulk Wilson loops and boundary defect operators, emphasizin…
View article: Reconstructing Noisy Gene Regulation Dynamics Using Extrinsic-Noise-Driven Neural Stochastic Differential Equations
Reconstructing Noisy Gene Regulation Dynamics Using Extrinsic-Noise-Driven Neural Stochastic Differential Equations Open
Proper regulation of cell signaling and gene expression is crucial for maintaining cellular function, development, and adaptation to environmental changes. Reaction dynamics in cell populations is often noisy because of (i) inherent stocha…
View article: Reconstructing Noisy Gene Regulation Dynamics Using Extrinsic-Noise-Driven Neural Stochastic Differential Equations
Reconstructing Noisy Gene Regulation Dynamics Using Extrinsic-Noise-Driven Neural Stochastic Differential Equations Open
Proper regulation of cell signaling and gene expression is crucial for maintaining cellular function, development, and adaptation to environmental changes. Reaction dynamics in cell populations is often noisy because of (i) inherent stocha…
View article: Incorporating stochastic gene expression, signaling-mediated intercellular interactions, and regulated cell proliferation in models of coordinated tissue development
Incorporating stochastic gene expression, signaling-mediated intercellular interactions, and regulated cell proliferation in models of coordinated tissue development Open
Formulating quantitative and predictive models for tissue development requires consideration of the complex, stochastic gene expression dynamics, its regulation via cell-to-cell interactions, and cell proliferation. Including all of these …
View article: Aggregating multiple test results to improve medical decision-making
Aggregating multiple test results to improve medical decision-making Open
Gathering observational data for medical decision-making often involves uncertainties arising from both type I (false positive) and type II (false negative) errors. In this work, we develop a statistical model to study how medical decision…
View article: Fusion Categories Arising from Generalized Module Functors
Fusion Categories Arising from Generalized Module Functors Open
View article: Sharp rises in alcohol-induced deaths in the United States (1999-2022) across genders, ages, races
Sharp rises in alcohol-induced deaths in the United States (1999-2022) across genders, ages, races Open
Importance Alcohol-induced deaths rose by 163% in the United States between 1999 and 2022, with sharp increases across most gender, age, and race groups in Spring 2020, concurrent with the onset of COVID-19. This study analyzes monthly mor…
View article: An efficient Wasserstein-distance approach for reconstructing jump-diffusion processes using parameterized neural networks
An efficient Wasserstein-distance approach for reconstructing jump-diffusion processes using parameterized neural networks Open
We analyze the Wasserstein distance ( W -distance) between two probability distributions associated with two multidimensional jump-diffusion processes. Specifically, we analyze a temporally decoupled squared W 2 -distance, which provides b…
View article: Martingale properties of entropy production and a generalized work theorem with decoupled forward and backward processes
Martingale properties of entropy production and a generalized work theorem with decoupled forward and backward processes Open
By decoupling forward and backward stochastic trajectories, we construct a family of martingales and work theorems for both overdamped and underdamped Langevin dynamics. Our results are made possible by an alternative derivation of work th…
View article: 7948 Integration of Epigenomics and Metabolomics Reveals New Signaling in Aggressive Thyroid Cancer
7948 Integration of Epigenomics and Metabolomics Reveals New Signaling in Aggressive Thyroid Cancer Open
Disclosure: A. Sanghi: None. S. Wu: None. T. Chou: None. L.A. Orloff: None. M. Kasowski: None. M. Snyder: None. Although genetic mutations are causal in human cancers, the contribution of chromatin changes to cancer onset and progression r…
View article: 7948 Integration Of Epigenomics And Metabolomics Reveals New Signaling In Aggressive Thyroid Cancer
7948 Integration Of Epigenomics And Metabolomics Reveals New Signaling In Aggressive Thyroid Cancer Open
Disclosure: A. Sanghi: None. S. Wu: None. T. Chou: None. L.A. Orloff: None. M. Kasowski: None. M. Snyder: None. Although genetic mutations are causal in human cancers, the contribution of chromatin changes to cancer onset and progression r…
View article: Aggregating multiple test results to improve medical decision-making
Aggregating multiple test results to improve medical decision-making Open
Gathering observational data for medical decision-making often involves uncertainties arising from both type I (false positive)and type II (false negative) errors. In this work, we develop a statistical model to study how medical decision-…
View article: A knapsack for collective decision-making
A knapsack for collective decision-making Open
Collective decision-making is the process through which diverse stakeholders reach a joint decision. Within societal settings, one example is participatory budgeting, where constituents decide on the funding of public projects. How to most…
View article: Overcompensation of transient and permanent death rate increases in age-structured models with cannibalistic interactions
Overcompensation of transient and permanent death rate increases in age-structured models with cannibalistic interactions Open
View article: Reliable ligand discrimination in stochastic multistep kinetic proofreading: First passage time vs. product counting strategies
Reliable ligand discrimination in stochastic multistep kinetic proofreading: First passage time vs. product counting strategies Open
Cellular signaling, crucial for biological processes like immune response and homeostasis, relies on specificity and fidelity in signal transduction to accurately respond to stimuli amidst biological noise. Kinetic proofreading (KPR) is a …
View article: Learning unbounded-domain spatiotemporal differential equations using adaptive spectral methods
Learning unbounded-domain spatiotemporal differential equations using adaptive spectral methods Open
Rapidly developing machine learning methods have stimulated research interest in computationally reconstructing differential equations (DEs) from observational data, providing insight into the underlying mechanistic models. In this paper, …
View article: An efficient Wasserstein-distance approach for reconstructing jump-diffusion processes using parameterized neural networks
An efficient Wasserstein-distance approach for reconstructing jump-diffusion processes using parameterized neural networks Open
We analyze the Wasserstein distance ($W$-distance) between two probability distributions associated with two multidimensional jump-diffusion processes. Specifically, we analyze a temporally decoupled squared $W_2$-distance, which provides …
View article: A probabilistic model of relapse in drug addiction
A probabilistic model of relapse in drug addiction Open
More than 60% of individuals recovering from substance use disorder relapse within one year. Some will resume drug consumption even after decades of abstinence. The cognitive and psychological mechanisms that lead to relapse are not comple…
View article: A probabilistic model of relapse in drug addiction
A probabilistic model of relapse in drug addiction Open
More than 60% of individuals recovering from substance use disorder relapse within one year. Some will resume drug consumption even after decades of abstinence. The cognitive and psychological mechanisms that lead to relapse are not comple…
View article: Kinetic theories of state- and generation-dependent cell populations
Kinetic theories of state- and generation-dependent cell populations Open
We formulate a general, high-dimensional kinetic theory describing the internal state (such as gene expression or protein levels) of cells in a stochastically evolving population. The resolution of our kinetic theory also allows one to tra…
View article: Order-of-Mutation Effects on Cancer Progression: Models for Myeloproliferative Neoplasm
Order-of-Mutation Effects on Cancer Progression: Models for Myeloproliferative Neoplasm Open
View article: Reliable ligand discrimination in stochastic multistep kinetic proofreading: First passage time vs. product counting strategies
Reliable ligand discrimination in stochastic multistep kinetic proofreading: First passage time vs. product counting strategies Open
Cellular signaling, crucial for biological processes like immune response and homeostasis, relies on specificity and fidelity in signal transduction to accurately respond to stimuli amidst biological noise. Kinetic proofreading (KPR) is a …
View article: Reliable ligand discrimination in stochastic multistep kinetic proofreading: First passage time vs. product counting strategies
Reliable ligand discrimination in stochastic multistep kinetic proofreading: First passage time vs. product counting strategies Open
Cellular signaling, crucial for biological processes like immune response and homeostasis, relies on specificity and fidelity in signal transduction to accurately respond to stimuli amidst biological noise. Kinetic proofreading (KPR) is a …
View article: Forecasting drug-overdose mortality by age in the United States at the national and county levels
Forecasting drug-overdose mortality by age in the United States at the national and county levels Open
The drug-overdose crisis in the United States continues to intensify. Fatalities have increased 5-fold since 1999 reaching a record high of 108,000 deaths in 2021. The epidemic has unfolded through distinct waves of different drug types, u…