Jonathan Colen
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View article: Training Set Augmentation and Harmonization Enables Radiomic Models to Detect Early Onset of Lung Cancer
Training Set Augmentation and Harmonization Enables Radiomic Models to Detect Early Onset of Lung Cancer Open
Radiomics-based machine learning models have the potential to detect lung cancer at inception from CT scans and transform patient outcomes. Low malignancy rates in early-development pulmonary nodules (PNs) and variable image acquisition hi…
View article: Sociohydrodynamics: Data-driven modeling of social behavior
Sociohydrodynamics: Data-driven modeling of social behavior Open
Living systems display complex behaviors driven by physical forces as well as decision-making. Hydrodynamic theories hold promise for simplified universal descriptions of socially generated collective behaviors. However, the construction o…
View article: Code and data accompanying "Sociohydrodynamics: data-driven modeling of social behavior"
Code and data accompanying "Sociohydrodynamics: data-driven modeling of social behavior" Open
Code and data accompanying "Sociohydrodynamics: data-driven modeling of social behavior". There are two files: sociohydro_code_v1.0-pnas.zip Contains code used to reproduce the paper, including scripts for inference, neural networks, and n…
View article: Harnessing the power of gradient-based simulations for multi-objective optimization in particle accelerators
Harnessing the power of gradient-based simulations for multi-objective optimization in particle accelerators Open
Particle accelerator operation requires simultaneous optimization of multiple objectives. Multi-objective optimization (MOO) is particularly challenging due to trade-offs between the objectives. Evolutionary algorithms, such as genetic alg…
View article: Explainable physics-based constraints on reinforcement learning for accelerator controls
Explainable physics-based constraints on reinforcement learning for accelerator controls Open
We present a reinforcement learning (RL) framework for controlling particle accelerator experiments that builds explainable physics-based constraints on agent behavior. The goal is to increase transparency and trust by letting users verify…
View article: Evaluation of radiomic feature harmonization techniques for benign and malignant pulmonary nodules.
Evaluation of radiomic feature harmonization techniques for benign and malignant pulmonary nodules. Open
Radiomic features of benign and malignant PNs require different corrective transformations to recover acquisition-independent distributions. This can be done using separate harmonization or harmonization with a covariate. Separate harmoniz…
View article: Harnessing the Power of Gradient-Based Simulations for Multi-Objective Optimization in Particle Accelerators
Harnessing the Power of Gradient-Based Simulations for Multi-Objective Optimization in Particle Accelerators Open
Particle accelerator operation requires simultaneous optimization of multiple objectives. Multi-Objective Optimization (MOO) is particularly challenging due to trade-offs between the objectives. Evolutionary algorithms, such as genetic alg…
View article: Predicting radiation‐induced immune suppression in lung cancer patients treated with stereotactic body radiation therapy
Predicting radiation‐induced immune suppression in lung cancer patients treated with stereotactic body radiation therapy Open
Background Stereotactic body radiation therapy (SBRT) is known to modulate the immune system and contribute to the generation of anti‐tumor T cells and stimulate T cell infiltration into tumors. Radiation‐induced immune suppression (RIIS) …
View article: Learning a conserved mechanism for early neuroectoderm morphogenesis
Learning a conserved mechanism for early neuroectoderm morphogenesis Open
Morphogenesis is the process whereby the body of an organism develops its target shape. The morphogen BMP is known to play a conserved role across bilaterian organisms in determining the dorsoventral (DV) axis. Yet, how BMP governs the spa…
View article: Interpreting neural operators: how nonlinear waves propagate in non-reciprocal solids
Interpreting neural operators: how nonlinear waves propagate in non-reciprocal solids Open
We present a data-driven pipeline for model building that combines interpretable machine learning, hydrodynamic theories, and microscopic models. The goal is to uncover the underlying processes governing nonlinear dynamics experiments. We …
View article: Motor crosslinking augments elasticity in active nematics
Motor crosslinking augments elasticity in active nematics Open
In active materials, motor proteins produce activity while also modulating elasticity.
View article: Learning a conserved mechanism for early neuroectoderm morphogenesis
Learning a conserved mechanism for early neuroectoderm morphogenesis Open
Morphogenesis is the process whereby the body of an organism develops its target shape. The morphogen BMP is known to play a conserved role across bilaterian organisms in determining the dorsoventral (DV) axis. Yet, how BMP governs the spa…
View article: Motor crosslinking augments elasticity in active nematics
Motor crosslinking augments elasticity in active nematics Open
In active materials, uncoordinated internal stresses lead to emergent long-range flows. An understanding of how the behavior of active materials depends on mesoscopic (hydrodynamic) parameters is developing, but there remains a gap in know…
View article: Zyxin is all you need: machine learning adherent cell mechanics.
Zyxin is all you need: machine learning adherent cell mechanics. Open
Cellular form and function emerge from complex mechanochemical systems within the cytoplasm. No systematic strategy currently exists to infer large-scale physical properties of a cell from its many molecular components. This is a significa…
View article: Zyxin is all you need: machine learning adherent cell mechanics
Zyxin is all you need: machine learning adherent cell mechanics Open
Cellular form and function emerge from complex mechanochemical systems within the cytoplasm. No systematic strategy currently exists to infer large-scale physical properties of a cell from its many molecular components. This is a significa…
View article: Negative group velocity and Kelvin-like wake pattern
Negative group velocity and Kelvin-like wake pattern Open
Wake patterns due to a uniformly traveling source are a result of the resonant emission of the medium's collective excitations. When there exists a frequency range where such excitations possess a negative group velocity, their interferenc…
View article: Negative group velocity and Kelvin-like wake in superfluid $^{4}He$
Negative group velocity and Kelvin-like wake in superfluid $^{4}He$ Open
The dispersion law $\Omega(k)$ of elementary excitations in superfluid $^{4}He$ is a non-monotonic function of the wave number $k$. After an initial increase, the function $\Omega(k)$ reaches a maximum followed by a roton minimum at finite…
View article: Machine learning active-nematic hydrodynamics
Machine learning active-nematic hydrodynamics Open
Hydrodynamic theories effectively describe many-body systems out of equilibrium in terms of a few macroscopic parameters. However, such parameters are difficult to determine from microscopic information. Seldom is this challenge more appar…
View article: Machine learning active-nematic hydrodynamics
Machine learning active-nematic hydrodynamics Open
Hydrodynamic theories effectively describe many-body systems out of equilibrium in terms of a few macroscopic parameters. However, such hydrodynamic parameters are difficult to derive from microscopics. Seldom is this challenge more appare…
View article: Elastic and electronic tuning of magnetoresistance in MoTe <sub>2</sub>
Elastic and electronic tuning of magnetoresistance in MoTe <sub>2</sub> Open
Uniaxial tensile strain changes the magnetoresistance according to the direction it is applied on in MoTe 2 .