optimal transport

Key-cutting machine: A novel optimization framework for tailored protein and peptide design

The paper introduces KCM, an optimization framework for protein and peptide design that outperforms generative models by enabling precise backbone geometry control with minimal computational resources.

Efficient Prospective Electric Field-Informed Localization of Motor Cortical Targets of Transcranial Magnetic Stimulation

This study introduces an optimization strategy for TMS-based motor mapping using farthest point sampling, showing it is more efficient and robust than random sampling.

Beyond Letters: Optimal Transport as a Model for Sub-Letter Orthographic Processing

This paper proposes optimal transport theory as a framework for modeling sub-letter orthographic processing, showing it aligns with early neural activity and captures geometric invariances better than existing methods.

Temporal Variability of Brain-Behavior Relationships in Fine-Scale Dynamics of Edge Time Series

The paper shows that selecting specific time points from fMRI data improves brain-behavior correlations compared to full scan data across multiple behaviors.

High-Resolution Time-Lapse Imaging of Droplet-Cell Dynamics via Optimal Transport and Contrastive Learning

This paper develops a method to track microfluidic droplets over time using optimal transport and contrastive learning, achieving high accuracy in tracking without labeled data.

Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal Transport

This paper introduces HM-OT to infer cell type differentiation maps from developmental transcriptomics time series by simultaneously clustering cells and learning transitions between cell types.

Personalized electric field simulations of deformable large TMS coils based on automatic position and shape optimization

This paper introduces a method for optimizing the position and shape of deformable TMS coils based on individual head anatomy, improving electric field simulations and enabling systematic dose-response comparisons.

Fast and exact gap-affine partial order alignment with POASTA

POASTA is an optimal algorithm for partial order alignment that improves speed and memory efficiency, enabling larger alignments in bacterial gene datasets.

Aggregating Residue-Level Protein Language Model Embeddings with Optimal Transport

This paper introduces an optimal transport-based method to aggregate residue-level protein language model embeddings into fixed-length representations, showing improved performance over average pooling for downstream tasks.

Functional Control of Network Dynamical Systems: An Information Theoretic Approach

The paper develops a framework for designing perturbation signals to achieve desired information routing patterns in complex networks, applying it to brain stimulation and gene regulatory networks.

CORTADO: Hill Climbing Optimization for Cell-Type SpecificMarker Gene Discovery

CORTADO identifies cell-type-specific marker genes using hill-climbing optimization, improving sensitivity and specificity over existing methods.

scEGOT: Single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport

scEGOT is a single-cell trajectory inference framework that identifies cell populations and segregation events in time-series scRNA-seq data, revealing key transcription factors involved in PGCLC differentiation.

Accurate RNA velocity estimation based on multibatch network reveals complex lineage in batch scRNA-seq data

This paper introduces VeloVGI, a method for accurate RNA velocity estimation in batch scRNA-seq data, outperforming existing methods in various datasets.

Optogenetic control of mechanotransduction based on light-induced homodimerization of talin

This paper introduces a single-construct optogenetic tool to control talin dimerization, enabling precise manipulation of mechanotransduction in integrin-based adhesions.

Automated Cell Type Annotation with Reference Cluster Mapping

This paper introduces RefCM, a method that improves cell type annotation in scRNA-seq data using optimal transport and integer programming, achieving accurate cross-technology, cross-tissue, and cross-species mappings.

Conserved moiety fluxomics

This paper introduces a new method for genome-scale metabolic flux inference using conserved moieties, demonstrating its computational efficiency and accuracy with isotopic labeling data.

Genomic prediction of heterosis, inbreeding control, and mate allocation in outbred diploid and tetraploid populations

The paper develops a convex optimization framework for mate allocation in polyploid populations to control inbreeding and predict heterosis, showing improved genetic gain with pedigree kinship.

Modeling CAR Response at the Single-Cell Level Using Conditional Optimal Transport

This paper uses conditional optimal transport to model CAR T cell responses at the single-cell level and predict gene expression for unseen CAR variants.

PangeBlocks: customized construction of pangenome graphs via maximal blocks

This paper introduces a method to construct pangenome graphs by solving an exact cover problem on blocks, showing how different objectives affect graph properties.

scMultiNODE: Recovering Developmental Dynamics in Weakly Resolved Modalities through Multi-Modal Integration

scMultiNODE integrates gene expression and chromatin accessibility data across timepoints to recover developmental dynamics and annotations for weak modalities.

Unified knowledge-driven network inference from omics data

The paper introduces CORNETO, a unified framework for knowledge-driven network inference from omics data, improving performance on biological tasks using simulated and real data.

Optogenetic dissection of transcriptional repression in a multicellular organism

This study uses optogenetics and mathematical modeling to show that the zinc-finger repressor Knirps rapidly and memorylessly represses gene expression by reducing transcriptional burst frequency.

Energy Aware Technology Mapping of Genetic Logic Circuits

This paper introduces Energy Aware Technology Mapping to design genetic logic circuits with energy efficiency and functionality, showing energy efficiency improves by 37.2% over functionally optimized variants.

Potent photoswitch for expression of biotherapeutics in mammalian cells by light

The paper introduces a photoswitch called DEL-VPR that enables strong, light-induced gene expression in mammalian cells, surpassing constitutive promoters and improving protein production.

Optimal control of spiking neural networks

This paper develops a mathematical framework for optimal control of spiking neural networks, using a feedback controller to steer network dynamics towards target states.

Vina-GPU 2.1: towards further optimizing docking speed and precision of AutoDock Vina and its derivatives

This paper introduces Vina-GPU 2.1, an optimized version of AutoDock Vina that improves docking speed and precision using new algorithms and optimizations.

Optimal control of combination immunotherapy for a virtual murine cohort in a glioblastoma-immune dynamics model

This paper optimizes combination immunotherapy regimens for glioblastoma using a virtual murine cohort and finds personalized treatment improves survival.

ImSpiRE: Image feature-aided spatial resolution enhancement method

ImSpiRE enhances spatial transcriptomic resolution using image features and optimal transport to improve subspot-level resolution and discover tissue domains and signaling patterns.

Understanding flux switching in metabolic networks through an analysis of synthetic lethals

The paper identifies alternate metabolic pathways rerouted during synthetic lethal reaction pairs using a constraint-based optimization approach and applies it to genome-scale models.

Optimal Performance Objectives in the Highly Conserved Bone Morphogenetic Protein Signaling Pathway

The paper examines how the BMP-Smad pathway balances trade-offs among response speed, noise amplification, and sensitivity to receptor input by tuning non-conserved parameters.