learning Archives

Machine Learning and Optimal Control of Enzyme Activities to Preserve Solvent Capacity in the Cell

April 7, 2020

Experimental measurements or computational model predictions of the post-translational regulation of enzymes needed in a metabolic pathway is a difficult problem. Consequently, regulation is mostly known only for well-studied reactions of central metabolism in various model organisms. In this study, we utilize two approaches to predict enzyme regulation policies and investigate the hypothesis that regulation…
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Convergent selection in antibody repertoires is revealed by deep learning

February 26, 2020

Adaptive immunity is driven by the ability of lymphocytes to undergo V(D)J recombination and generate a highly diverse set of immune receptors (B cell receptors/secreted antibodies and T cell receptors) and their subsequent clonal selection and expansion upon molecular recognition of foreign antigens. These principles lead to remarkable, unique and dynamic immune receptor repertoires. Deep…
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Semi-supervised machine learning facilitates cell colocalization and tracking in intravital microscopy

November 4, 2019

2-photon intravital microscopy (2P-IVM) is a key technique to investigate cell migration and cell-to-cell interactions in organs and tissues of living organisms. Focusing on immunology, 2P-IVM allowed recording videos of leukocytes during the immune response, highlighting unprecedented mechanisms of the immune system. However, the automatic analysis of the acquired videos remains challenging and poorly reproducible.…
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Weakly-Supervised Prediction of Cell Migration Modes in Confocal Microscopy Images Using Bayesian Deep Learning

October 18, 2019

Cell migration is pivotal for their development, physiology and disease treatment. A single cell on a 2D surface can utilize continuous or discontinuous migration modes. To comprehend the cell migration, an adequate quantification for single cell-based analysis is crucial. An automatized approach could alleviate tedious manual analysis, facilitating large-scale drug screening. Supervised deep learning has…
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Accurate cell tracking and lineage construction in live-cell imaging experiments with deep learning

October 14, 2019

Live-cell imaging experiments have opened an exciting window into the behavior of living systems. While these experiments can produce rich data, the computational analysis of these datasets is challenging. Single-cell analysis requires that cells be accurately identified in each image and subsequently tracked over time. Increasingly, deep learning is being used to interpret microscopy image…
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Machine Learning Analysis of Motor Evoked Potential Time Series to Predict Disability Progression in Multiple Sclerosis

September 20, 2019

Background: Evoked potentials (EPs) are a measure of the conductivity of the central nervous system. They are used to monitor disease progression of multiple sclerosis patients. Previous studies only extracted a few variables from the EPs, which are often further condensed into a single variable: the EP score. We perform a machine learning analysis of…
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Connecting Histopathology Imaging and Proteomics in Kidney Cancer through Machine Learning

September 5, 2019

Proteomics data encode molecular features of diagnostic value and accurately reflect key underlying biological mechanisms in cancers. Histopathology imaging is a well-established clinical approach to cancer diagnosis. The predictive relationship between large-scale proteomics and H&E-stained histopathology images remains largely uncharacterized. Here we investigate such associations through the application of machine learning, including deep neural networks,…
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Interpretable Machine Learning for Perturbation Biology

August 28, 2019

Systematic perturbation of cells followed by comprehensive measurements of molecular and phenotypic responses provides an informative data resource for constructing computational models of cell biology. Models that generalize well beyond training data can be used to identify combinatorial perturbations of potential therapeutic interest. Major challenges for machine learning on large biological datasets are to find…
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DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning

August 1, 2019

Microscopy image analysis is a major bottleneck in quantification of single-cell microscopy data, typically requiring human supervision and curation, which limit both accuracy and throughput. To address this, we developed a deep learning-based image analysis pipeline that performs segmentation, tracking, and lineage reconstruction. Our analysis focuses on time-lapse movies of Escherichia coli cells trapped in…
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Antibody Complementarity Determining Region Design Using High-Capacity Machine Learning

June 26, 2019

The precise targeting of antibodies and other protein therapeutics is required for their proper function and the elimination of deleterious off-target effects. Often the molecular structure of a therapeutic target is unknown and randomized methods are used to design antibodies without a model that relates antibody sequence to desired properties. Here we present a machine…
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