Selecting the right drugs for the right patients is a primary goal of precision medicine. In this manuscript, we consider the problem of cancer drug selection in a learning-to-rank framework. We have formulated the cancer drug selection problem as to accurately predicting 1). the ranking positions of sensitive drugs an…
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48 results for “cell lines”
Accurately predicting drug responses to cancer is an important problem hindering oncologists' efforts to find the most effective drugs to treat cancer, which is a core goal in precision medicine. The scientific community has focused on improving this prediction based on genomic, epigenomic, and proteomic datasets measu…
Dr.S recommends cancer drugs based on genomic data.
problem Personalizing cancer treatments using genomic information.
method Machine learning to identify optimal drug-gene associations.
result Developed a Drug Recommendation System (Dr.S) for cancer cell lines.
A Deep Autoencoder System for Differentiation of Cancer Types Based on DNA Methylation Stateq-bio.QM
A Deep Autoencoder based content retrieval algorithm is proposed for prediction and differentiation of cancer types based on the presence of epigenetic patterns of DNA methylation identified in genetic regions known as CpG islands. The developed deep learning system uses a CpG island state classification sub-system to …
The study compares different scRNA sequencing methods using a high-dimensional dataset.
problem To identify unique characteristics of different scRNA sequencing methods.
method Quantitative comparison through clustering analysis of a high-dimensional dataset.
result Identifies unique characteristics associated with different scRNA sequencing methods.
Model predicts anti-cancer drug responses using gene and molecular data.
problem Expensive and time-consuming cancer drug discovery and tailoring.
method Uses variational autoencoders and multi-layer perceptrons to encode gene expression and drug data.
result High average of 0.83 and 0.845 in predicting drug responses for breast and pan-cancer cell lines, respectively.
Predicting the response of cancer cells to drugs is an important problem in pharmacogenomics. Recent efforts in generation of large scale datasets profiling gene expression and drug sensitivity in cell lines have provided a unique opportunity to study this problem. However, one major challenge is the small number of sa…
Understanding the phenotypic drug response on cancer cell lines plays a vital rule in anti-cancer drug discovery and re-purposing. The Genomics of Drug Sensitivity in Cancer (GDSC) database provides open data for researchers in phenotypic screening to test their models and methods. Previously, most research in these ar…
Exploratory cancer drug studies test multiple tumor cell lines against multiple candidate drugs. The goal in each paired (cell line, drug) experiment is to map out the dose-response curve of the cell line as the dose level of the drug increases. We propose Bayesian Tensor Filtering (BTF), a hierarchical Bayesian model …
With the wealth of high-throughput sequencing data generated by recent large-scale consortia, predictive gene expression modelling has become an important tool for integrative analysis of transcriptomic and epigenetic data. However, sequencing data-sets are characteristically large, and previously modelling frameworks …
We introduce a tensor-based clustering method to extract sparse, low-dimensional structure from high-dimensional, multi-indexed datasets. This framework is designed to enable detection of clusters of data in the presence of structural requirements which we encode as algebraic constraints in a linear program. Our cluste…
The study of high-throughput genomic profiles from a pharmacogenomics viewpoint has provided unprecedented insights into the oncogenic features modulating drug response. A recent screening of ~1,000 cancer cell lines to a collection of anti-cancer drugs illuminated the link between genotypes and vulnerability. However,…
Motivation: Analysis of relationships of drug structure to biological response is key to understanding off-target and unexpected drug effects, and for developing hypotheses on how to tailor drug thera-pies. New methods are required for integrated analyses of a large number of chemical features of drugs against the corr…
Synergistic Drug Combination Prediction by Integrating Multi-omics Data in Deep Learning Modelsq-bio.GN
Drug resistance is still a major challenge in cancer therapy. Drug combination is expected to overcome drug resistance. However, the number of possible drug combinations is enormous, and thus it is infeasible to experimentally screen all effective drug combinations considering the limited resources. Therefore, computat…
Extends NAS to learn both intra-cell and inter-cell architectures for language modeling.
problem Limited NAS systems restrict search to recurrent or convolutional cells.
method Designs a joint learning method to perform intra-cell and inter-cell NAS simultaneously.
result Significantly outperforms a strong baseline on PTB and WikiText data.
Organic Solar Cells are a promising technology for solving the clean energy crisis in the world. However, generating candidate chemical compounds for solar cells is a time-consuming process requiring thousands of hours of laboratory analysis. For a solar cell, the most important property is the power conversion efficie…
A line field on a manifold is a smooth map which assigns a tangent line to all but a finite number of points of the manifold. As such, it can be seen as a generalization of vector fields. They model a number of geometric and physical properties, e.g. the principal curvature directions dynamics on surfaces or the stress…
Free energy of the edge of an open lipid bilayer based on the interactions of its constituent moleculescond-mat.soft
Lipid-bilayers are the fundamental constituents of the walls of most living cells and lipid vesicles, giving them shape and compartment. The formation and growing of pores in a lipid bilayer have attracted considerable attention from an energetic point of view in recent years. Such pores permit targeted delivery of dru…
Recently V. Krushkal and D. Renardy generalized the Tutte polynomial from graphs to cell complexes. We show that evaluating this polynomial at the origin gives the number of cellular spanning trees in the sense of A. Duval, C. Klivans, and J. Martin. Moreover, after a slight modification, the Tutte-Krushkal-Renardy pol…
Chemotherapeutic response of cancer cells to a given compound is one of the most fundamental information one requires to design anti-cancer drugs. Recent advances in producing large drug screens against cancer cell lines provided an opportunity to apply machine learning methods for this purpose. In addition to cytotoxi…
We give a new algorithm computing local system cohomology groups for complexified real line arrangements. Using it, we obtain several conditions for the first local system cohomology to vanish and to be at most one-dimensional, which generalize a result by Cohen-Dimca-Orlik. The conditions are described in terms of dis…
Most of the banks' operational risk internal models are based on loss pooling in risk and business line categories. The parameters and outputs of operational risk models are sensitive to the pooling of the data and the choice of the risk classification. In a simple model, we establish the link between the number of ris…
A Distributed Approach for Networked Flying Platform Association with Small Cells in 5G+ Networkscs.NI
The densification of small-cell base stations in a 5G architecture is a promising approach to enhance the coverage area and facilitate the ever increasing capacity demand of end users. However, the bottleneck is an intelligent management of a backhaul/fronthaul network for these small-cell base stations. This involves …
New task aligns molecular structure with gene expression changes.
problem Modeling the relationship between chemical structure and gene expression changes.
method Developed a cross-modal small molecule retrieval task and a coordinated deep learning approach to align chemical structure and gene expression profiles.
result Demonstrated the feasibility of the new task and highlighted the limitations of current data and systems.
Proposes using entity embedding vectors to improve Gaussian Process models for knowledge transfer across cell lines.
problem Lack of reuse of experimental data for predicting novel processes.
method Hybrid Gaussian Process models with entity embedding vectors to represent product identity.
result Improved performance in predicting novel processes compared to traditional methods.
Contrastive Mixture of Posteriors for Counterfactual Inference, Data Integration and Fairnessstat.ML
A new method improves data representation for diverse tasks.
problem Learning meaningful representations for tasks like batch correction and counterfactual inference.
method Contrastive Mixture of Posteriors (CoMP) method using misalignment penalties.
result CoMP achieves state-of-the-art performance on challenging tasks.
Paper quantifies uncertainties in EIS spectra of SOFCs, proposing VB method for online monitoring.
problem Distortions in EIS spectra due to disturbances, drifts, and sensor noise.
method Proposes variational Bayes (VB) method for quantifying spectral uncertainty in EIS of SOFCs.
result VB method provides approximate distributions of ECM parameters with low computational load.
Motivated by applications to perverse sheaves, we study combinatorics of two cell decompositions of the symmetric product of the complex line, refining the complex stratification by multiplicities. Contingency matrices, appearing in classical statistics, parametrize the cells of one such decomposition, which has the pr…
In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder. Our model is based on the three key pillars of drug sensitivity: compounds' structure i…
Meta-learning consists in learning learning algorithms. We use a Long Short Term Memory (LSTM) based network to learn to compute on-line updates of the parameters of another neural network. These parameters are stored in the cell state of the LSTM. Our framework allows to compare learned algorithms to hand-made algorit…
Kernel testing compares cell states in single-cell data.
problem Comparing non-linear cell states in single-cell data.
method Kernel-based testing framework for non-linear distribution comparison.
result Identifies subtle population variations in cell states.
Review of Single-cell RNA-seq Data Clustering for Cell Type Identification and Characterizationq-bio.GN
This study reviews and evaluates clustering methods for single-cell RNA-seq data.
problem Identifying and characterizing novel cell types from single-cell RNA-seq data.
method Review and performance comparison of clustering methods.
result Performance comparison experiments on two datasets.
Cell detection and cell type classification from biomedical images play an important role for high-throughput imaging and various clinical application. While classification of single cell sample can be performed with standard computer vision and machine learning methods, analysis of multi-label samples (region containi…
Forest Fire Clustering discovers cell types from single-cell data.
problem Discovering cell types from large-scale single-cell sequencing data.
method Iterative label propagation and parallelized Monte Carlo simulation.
result Forest Fire Clustering outperforms state-of-the-art methods on diverse benchmarks.
Proposes CCCVAE for better single-cell clustering with cell-cell communication.
problem Improving single-cell RNA sequencing clustering by incorporating cell-cell communication.
method Integrates cell-cell communication into a variational autoencoder framework.
result Empirical results show CCCVAE outperforms standard VAEs in clustering performance.
Matching cells over time has long been the most difficult step in cell tracking. In this paper, we approach this problem by recasting it as a classification problem. We construct a feature set for each cell, and compute a feature difference vector between a cell in the current frame and a cell in a previous frame. Then…
Improved GPLVM model for single-cell RNA-seq data.
problem Lack of effective scalable models for clustering cell types in large-scale single-cell RNA-seq data.
method Introduces amortized stochastic variational Bayesian GPLVM (BGPLVM) tailored for single-cell RNA-seq.
result Matches the performance of scVI on synthetic and real-world datasets and reveals more interpretable latent structures.
Structures of optimal discrete gradient vector fields on surface with one or two critical cellsmath.DS
The study identifies all possible vector field structures on specific 2D shapes.
problem Optimal discrete gradient vector fields on surfaces with 1-2 critical cells.
method Analysis of discrete vector fields on 2D shapes with minimal critical cells.
result All possible structures of discrete Morse functions on specified shapes.
New model identifies cell-specific genes for cancer prognosis.
problem No statistical model to integrate multiscale cancer data.
method Bayesian generalized promotion time cure models (GPTCMs).
result Improves cancer prognosis by identifying cell-specific genes.
MarkerMap selects key genes for cell type analysis in single-cell RNA-seq.
problem Selecting informative genes from large single-cell RNA-seq datasets is challenging and computationally intensive.
method MarkerMap is a generative model that identifies minimal gene sets explaining cell type variability.
result MarkerMap outperforms existing methods in both supervised and unsupervised marker selection.
Proposes CXNs for neural network computations on cell complexes.
problem Performing neural network computations on complex topological spaces.
method Introduces a message passing scheme and a unified encoder-decoder framework for cell complexes.
result Generalizes message passing to cell complexes and provides a cell2vec representation.
New metric scores perturbations across populations, not cells, improving model comparison.
problem Single-cell perturbation data overlaps, making per-cell accuracy unreliable.
method Average per-cell probability vectors over all cells of a perturbation to form a population profile and rank candidate perturbations.
result Classifier Discrimination Score (CDS) identifies true perturbation more reliably than pseudobulk-based scores.
Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative. Single-cell RNA sequencing can now be used to measure the gene expression profiles of individual neurons and to categorize neurons based on their gene expression profil…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the precise geometry of an organism and its parts in space. Here, we suggest a set of …
Hippocampal dentate granule cells are among the few neuronal cell types generated throughout adult life in mammals. In the normal brain, new granule cells are generated from progenitors in the subgranular zone and integrate in a typical fashion. During the development of epilepsy, granule cell integration is profoundly…
Learning-based link scheduling improves network performance in millimeter-wave multi-connectivity.
problem Efficient link scheduling is crucial for maximizing network performance in millimeter-wave multi-connectivity.
method A learning-based approach to predict optimal link scheduling.
result The learning-based solution outperforms base line methods and approaches the optimal solution.
NESS improves neighbor embedding for smooth cell-state transitions in single-cell data.
problem Challenges in extracting smooth, low-dimensional representations from noisy single-cell data.
method Builds on PCS framework to develop NESS, a stable machine learning approach.
result NESS consistently yields useful biological insights across diverse single-cell datasets.
We extend cell decomposition to moduli space of convex projective structures.
problem Cell decomposition of moduli space of convex projective structures.
method Use Fock and Goncharov's -coordinates and edge-flipping algorithm.
result Holonomy groups are semi-arithmetic in many cases.