arXiv research

Despite great advances, molecular cancer pathology is often limited to the use of a small number of biomarkers rather than the whole transcriptome, partly due to computational challenges. Here, we introduce a novel architecture of Deep Neural Networks (DNNs) that is capable of simultaneous inference of various properti…

Paper develops a method to predict cancer patient survival using molecular profiles.

Study identifies biomarkers for lung cancer in female non-smokers.

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,…

With the advent of deep generative models in computational chemistry, in silico anticancer drug design has undergone an unprecedented transformation. While state-of-the-art deep learning approaches have shown potential in generating compounds with desired chemical properties, they disregard the genetic profile and prop…

Improved accuracy in machine learning with Cross-Cluster Weighted Forests.

Omics-GAN uses GANs to generate synthetic multi-omics data for improved disease prediction.

Modeling correlated mutations in cancer for personalized treatment.

Model predicts anti-cancer drug responses using gene and molecular data.

Study compares single vs ensemble feature selection for cancer diagnosis.

Paper tackles cancer mutation data challenges by creating useful low-dimensional representations.

Kernel testing compares cell states in single-cell data.

Deep neural network for cancer classification using autoencoders.

Cancer survival prediction is an active area of research that can help prevent unnecessary therapies and improve patient's quality of life. Gene expression profiling is being widely used in cancer studies to discover informative biomarkers that aid predict different clinical endpoint prediction. We use multiple modalit…

Bayesian model clusters diverse 'omics data for disease subtyping.

New task aligns molecular structure with gene expression changes.

Deep Bayesian neural networks improve somatic variant calling accuracy.

The medical research facilitates to acquire a diverse type of data from the same individual for particular cancer. Recent studies show that utilizing such diverse data results in more accurate predictions. The major challenge faced is how to utilize such diverse data sets in an effective way. In this paper, we introduc…

Study uses LLMs to create personalized treatment plans for rare gynecological tumors.

Flatsomatic compresses cancer mutation data with VAEs, maintaining predictive power.

Method predicts ODX scores for breast cancer patients based on clinical data.

Deep learning improves tumor type classification accuracy.

The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of phenotypes makes high-throughput phenotype profiling a very difficult and labor…

Different aspects of a clinical sample can be revealed by multiple types of omics data. Integrated analysis of multi-omics data provides a comprehensive view of patients, which has the potential to facilitate more accurate clinical decision making. However, omics data are normally high dimensional with large number of …

BIDIFAC+ factorizes linked matrices for cancer studies.

Identifying altered pathways that are associated with specific cancer types can potentially bring a significant impact on cancer patient treatment. Accurate identification of such key altered pathways information can be used to develop novel therapeutic agents as well as to understand the molecular mechanisms of variou…

Motivation: Driver (epi)genomic alterations underlie the positive selection of cancer subpopulations, which promotes drug resistance and relapse. Even though substantial heterogeneity is witnessed in most cancer types, mutation accumulation patterns can be regularly found and can be exploited to reconstruct predictive …

Gene expression profiles have been widely used to characterize patterns of cellular responses to diseases. As data becomes available, scalable learning toolkits become essential to processing large datasets using deep learning models to model complex biological processes. We present an autoencoder to capture nonlinear …

DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in the context of CpG (cytosine and guanine bases linked by phosphate backbone) dinu…

Precision medicine aims for personalized prognosis and therapeutics by utilizing recent genome-scale high-throughput profiling techniques, including next-generation sequencing (NGS). However, translating NGS data faces several challenges. First, NGS count data are often overdispersed, requiring appropriate modeling. Se…

BayReL learns molecular interactions across multi-omics data.

Stem uses diffusion models to infer gene expression from H&E images.

Machine learning accurately diagnoses cancer from whole genome sequencing data.

Due to the complexity of cancer, clustering algorithms have been used to disentangle the observed heterogeneity and identify cancer subtypes that can be treated specifically. While kernel based clustering approaches allow the use of more than one input matrix, which is an important factor when considering a multidimens…

We review some statistical many-agent models of economic and social systems inspired by microscopic molecular models and discuss their stochastic interpretation. We apply these models to wealth exchange in economics and study how the relaxation process depends on the parameters of the system, in particular on the savin…

Enhances diffusion-based sampling for molecular systems.

Paper presents a machine learning method to predict cancer sub-clones.

MolHF generates complex molecules with hierarchical flow-based model.

Deep neural network improves cancer mutation calls with confidence.

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 introduce the anti-profile Support Vector Machine (apSVM) as a novel algorithm to address the anomaly classification problem, an extension of anomaly detection where the goal is to distinguish data samples from a number of anomalous and heterogeneous classes based on their pattern of deviation from a normal stable c…

Paper proposes inference method for high-dimensional censored quantile regression.

fiBAG integrates multiplatform genomic data to identify disease markers.

TransST improves spatial transcriptomics data analysis by identifying cell clusters and biomarkers.

A key goal of computational personalized medicine is to systematically utilize genomic and other molecular features of samples to predict drug responses for a previously unseen sample. Such predictions are valuable for developing hypotheses for selecting therapies tailored for individual patients. This is especially va…

Boolean tensor decomposition approximates data of multi-way binary relationships as product of interpretable low-rank binary factors, following the rules of Boolean algebra. Here, we present its first probabilistic treatment. We facilitate scalable sampling-based posterior inference by exploitation of the combinatorial…

Bayesian Cox model identifies biomarkers from multi-omics data.

This review explores the use of machine learning in discovering collective variables for biomolecular dynamics.