optimal transport

Designing diverse and high-performance proteins with a large language model in the loop

This paper introduces BADASS, an optimization algorithm for protein design that improves fitness prediction and sequence diversity compared to existing methods.

Forward Engineering Organ Development and Cancer Therapeutics with Optogenetics

This study uses optogenetics to control organ growth in Drosophila by manipulating calcium signaling, revealing how light intensity and timing affect organ size and tumor morphology.

FISHnet: Detecting chromatin domains in single-cell sequential Oligopaints imaging data

FISHnet detects chromatin domains in single-cell sequential Oligopaints imaging data using graph theory and network modularity optimization.

Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation

OTVelo estimates gene velocities using optimal transport to infer dynamic gene regulatory networks from time-stamped single-cell gene expression data.

Multi-objective computational optimization of human 5' UTR sequences

This study develops a computational pipeline to optimize human 5' UTR sequences using a multi-objective framework, addressing up to four conflicting objectives.

scACCorDiON: A clustering approach for explainable patient level cell cell communication graph analysis

scACCorDiON clusters patient-specific cell-cell communication graphs using optimal transport, improving disease status prediction in scRNA-seq data.

Red Light-Activated Reversible Inhibition of Protein Functions by Assembled Trap

The paper introduces R-LARIAT, a red light-induced protein clustering system that inhibits protein functions in HeLa cells by trapping GFP-tagged proteins, demonstrating high efficiency and stability.

Inferring macroscopic intrinsic neural timescales using optimal control theory

The paper develops a framework using optimal control theory to estimate brain structure-function interactions from MRI data, showing correlations between self-inhibition parameters and neural timescales across species.

Programmatic design and editing of cis-regulatory elements

The paper introduces Ledidi, a computational method for designing cis-regulatory elements by optimizing continuous sequences guided by deep learning models, validated experimentally for controlling transcriptional outcomes.

Unsupervised alignment reveals structural commonalities and differences in neural representations of natural scenes across individuals and brain areas

This paper introduces an unsupervised alignment method using Gromov-Wasserstein Optimal Transport to compare neural representations of natural scenes across individuals and brain areas, finding alignment within visual cortical areas but not across different areas.

Uncovering critical transitions and molecule mechanisms in disease progressions using Gaussian graphical optimal transport

This paper introduces GGOT to detect critical transitions and identify trigger molecules in disease progression by analyzing data distributions and transport maps across disease stages.

Data Imbalance in Drug Response Prediction - Multi-Objective Optimization Approach in Deep Learning Setting

This paper addresses data imbalance in drug response prediction by introducing a multi-objective optimization approach using a custom loss function to improve model performance.

biscot: an Optimal Transport framework for multimodal bacterial single-cell data analysis

biscot uses optimal transport to integrate and analyze multimodal bacterial single-cell data, showing improved speed and accuracy in disentangling communities and aligning gene expression with cytometry data.

Evaluating Evolutionary and Gradient-Based Algorithms for Optimal Pathfinding

This study compares Genetic Algorithm, Particle Swarm Optimization, and Sequential Quadratic Programming for pathfinding in nonlinear terrains, finding SQP to be more efficient and reliable.

Optimal Transport Model for Gas Migration in Pneumatosis Intestinalis

This paper develops an optimal transport model to quantify gas migration in pneumatosis intestinalis, showing how gas spreads from the lumen to deeper gut layers through diffusion and trapping mechanisms.

Computational Methods for Optimal Coil Placement and Maximization of Lobule-Focused Cortical Activation in Cerebellar TMS

This paper develops a computational pipeline to optimize TMS coil placement for targeted cerebellar lobule activation, showing improved electric field intensity and reduced spillover.

Minimum biomechanical energy expenditure predicts upper-limb motor strategies in individuals with limb loss

This study proposes an optimal path planning framework for upper-limb motion that outperforms existing models in accuracy and computational efficiency for individuals with and without limb loss.

Optimal Control Prevents Itself from Eradicating Stochastic Disease Epidemics

This paper shows that deterministic optimal control strategies are insufficient for eradicating stochastic disease epidemics and proposes heuristics that outperform Model Predictive Control in such scenarios.

Hexagons all the way down: Grid cells as a conformal isometric map of space

This paper investigates grid cells as a conformal isometric map of space, showing that a module of at least seven grid cells can achieve a distance-preserving representation with regular hexagonal phase patterns.

Dynamic and Biphasic Regulation of Cell Migration by Ras

This study shows that Ras activity has a biphasic effect on cell migration, with both high and low activity impairing movement, and reveals that Ras regulates migration through rapid, non-transcriptional mechanisms.

Optimal marker genes for c-separated cell types

The paper proposes a method to identify a small set of marker genes that optimally separate cell types in single-cell RNA-seq data by considering expression variation within cell types.

TOPOLOW: A MAPPING ALGORITHM FOR ANTIGENIC CROSS-REACTIVITY AND BINDING AFFINITY ASSAY RESULTS

TOPOLOW maps antigenic relationships from incomplete cross-reactivity data, improving prediction accuracy over MDS for influenza and HIV viruses.

Inferring cell trajectories of spatial transcriptomics via optimal transport analysis

spaTrack infers spatial cell trajectories using optimal transport, revealing spatiotemporal dynamics in regeneration and tumor development.

Strange effects of activation dynamics on musculoskeletal trajectory optimization

The paper shows that using activation instead of excitation in optimization objectives for human movement avoids issues with rapid switching strategies in musculoskeletal trajectory optimization.

DeST-OT: Alignment of Spatiotemporal Transcriptomics Data

DeST-OT aligns spatiotemporal transcriptomics data from developmental timepoints using optimal transport to model cell growth, death, and differentiation.

Zmap: an intelligent region-allocation method to map single-cell into spatial data

Zmap maps single-cell data to spatial coordinates efficiently, uncovering hidden gene expression patterns in brain sections with high accuracy.

Mapping cells through time and space with moscot

moscot unifies optimal transport for temporal, spatial and spatiotemporal single-cell mapping, using multimodal cost spaces and low-rank solvers to scale to 1.7 million mouse embryo cells.

Mechanical efficiency during sub-maximal cycling is underestimated because negative muscular power is ignored

The paper shows that mechanical efficiency during sub-maximal cycling is underestimated because negative muscular power is not accounted for, leading to significant corrections in efficiency estimates.

Debiasing Sinkhorn divergence in optimal transport of cellular dynamics

This paper evaluates how Sinkhorn divergence affects optimal transport in single-cell RNA-seq analysis of cellular dynamics, showing its effectiveness depends on temporal sparsity.

Optogenetic control of a horizontally acquired region in yeast prevent stuck fermentations

This study uses optogenetics to show that region A genes in wine yeast are essential for completing fermentation under low nitrogen conditions.