Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design architectures to suit it. As such, architectures that fit the structure of genomics should …
On-device research index
arXiv research
A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
168,657 papers · 148 categories
Trend · papers per month
48 results for “genomic data”
Application of Markov Structure of Genomes to Outlier Identification and Read Classificationq-bio.GN
Paper uses genome Markov structure for outlier detection and read classification.
problem Identifying outliers and classifying reads in genome databases.
method Applying second-order Markov models to triplet base distributions.
result Improved accuracy in outlier identification and read classification.
Elastic co-clustering improves clustering of single-cell genomic data.
problem Improving clustering performance of single-cell genomic datasets.
method Elastic coupled co-clustering in an unsupervised transfer learning framework.
result Our algorithm significantly improves clustering performance over traditional methods.
New method combines ensembling and regularization for genomic disease prediction.
problem Genomic diseases require accurate prediction and biomarker identification.
method Integrates regularization with ensembling techniques for high-dimensional binary classification.
result Identifies critical biomarkers overlooked by competing methods.
The paper predicts diseases using both clinical and genomics data.
problem Clinical predictions using genomics data are not common.
method Integrated clinical and genomics datasets, machine learning, Principal Component Analysis for feature selection.
result 73% accuracy in predicting 75 disease classes.
Private cancer prediction model trained on federated genomic data.
problem Train a private cancer prediction model on federated genomic data.
method Differentially private federated learning (FL) for genomic cancer prediction.
result Ranked 3rd in a competition for private cancer prediction.
The analysis of cancer genomic data has long suffered "the curse of dimensionality". Sample sizes for most cancer genomic studies are a few hundreds at most while there are tens of thousands of genomic features studied. Various methods have been proposed to leverage prior biological knowledge, such as pathways, to more…
Paper proposes scalable method for analyzing multi-omic data.
problem Integrating high-dimensional multi-omic data for cancer subtyping.
method Mixed graphical model approach using Birth-Death MCMC algorithm.
result Our method outperforms LASSO and standard BDMCMC in computational efficiency and model selection accuracy.
Measures DNA quality degradation effects.
problem Identifying degraded DNA sequence data.
method Novel quality quantification based on intentional degradation effects.
result Quantified measures of degradation can be used for multiple purposes.
Random Fragments Classification of Microbial Marker Clades with Multi-class SVM and N-Best Algorithmq-bio.QM
Microbial clades modeling is a challenging problem in biology based on microarray genome sequences, especially in new species gene isolates discovery and category. Marker family genome sequences play important roles in describing specific microbial clades within species, a framework of support vector machine (SVM) base…
fiBAG integrates multiplatform genomic data to identify disease markers.
problem Understanding complex mechanisms underlying human diseases from multiplatform genomic data.
method fiBAG uses Gaussian process models and Bayes factors to identify functional evidence and guide variable selection.
result fiBAG improves detection of disease-related markers compared to non-integrative methods.
With different genomes available, unsupervised learning algorithms are essential in learning genome-wide biological insights. Especially, the functional characterization of different genomes is essential for us to understand lives. In this book chapter, we review the state-of-the-art unsupervised learning algorithms fo…
Personalizing drug prescriptions in cancer care based on genomic information requires associating genomic markers with treatment effects. This is an unsolved challenge requiring genomic patient data in yet unavailable volumes as well as appropriate quantitative methods. We attempt to solve this challenge for an experim…
Local ancestry inference (LAI) allows identification of the ancestry of all chromosomal segments in admixed individuals, and it is a critical step in the analysis of human genomes with applications from pharmacogenomics and precision medicine to genome-wide association studies. In recent years, many LAI techniques have…
PKB framework boosts genomic data analysis by integrating pathway knowledge.
problem Boosting discovery power and connecting new findings with biological mechanisms in genomic data.
method Pathway-based Kernel Boosting (PKB) framework integrating clinical and pathway information for prediction of various outcomes.
result PKB substantially outperforms other methods in predicting drug response and cancer survival.
Matrix completion has attracted significant recent attention in many fields including statistics, applied mathematics and electrical engineering. Current literature on matrix completion focuses primarily on independent sampling models under which the individual observed entries are sampled independently. Motivated by a…
Guiding adaptive shrinkage by co-data to improve regression-based prediction and feature selectionstat.ME
Guided adaptive shrinkage uses co-data to improve feature selection in genomic studies.
problem Feature selection challenges in high-dimensional genomics data, especially in clinical settings.
method Guided adaptive shrinkage methods that use co-data to adapt shrinkage parameters.
result Improves feature selection in genomic studies, demonstrated through comparisons and examples.
Machine learning accurately diagnoses cancer from whole genome sequencing data.
problem Accurate cancer diagnosis at all stages.
method Novel MLAC (Machine Learning Against Cancer) method using next-gen RNA sequencing.
result Perfect precision, sensitivity, and specificity achieved for most tumor types.
Locally epistatic genomic relationship matrices for genomic association, prediction and selectionstat.AP
As the amount and complexity of genetic information increases it is necessary that we explore some efficient ways of handling these data. This study takes the "divide and conquer" approach for analyzing high dimensional genomic data. Our aims include reducing the dimensionality of the problem that has to be dealt one a…
SEISM tests neural network features for regulatory genomics.
problem Testing neural network features for regulatory genomics.
method Selective inference procedure for sequence motifs.
result Sampling under specific parameters characterizes composite null hypothesis.
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient sharing of research material through community databases have opened up new view…
In this paper we propose network methodology to infer prognostic cancer biomarkers based on the epigenetic pattern DNA methylation. Epigenetic processes such as DNA methylation reflect environmental risk factors, and are increasingly recognised for their fundamental role in diseases such as cancer. DNA methylation is a…
Genomic models learn DNA sequences to predict functions.
problem Understanding complex genetic interactions.
method Training LLMs on DNA sequences to predict functions.
result gLMs can predict functions of DNA elements.
Cluster Quilting clusters fragmented data sets for neuroscience and genomics.
problem Clustering fragmented data sets in neuroscience and genomics.
method Cluster Quilting method using patch ordering, patchwise SVD, sequential linear mapping, and k-means.
result Cluster Quilting discovers more accurate clusters than other methods.
Extracting Epistatic Interactions in Type 2 Diabetes Genome-Wide Data Using Stacked Autoencodercs.LG
2 Diabetes is a leading worldwide public health concern, and its increasing prevalence has significant health and economic importance in all nations. The condition is a multifactorial disorder with a complex aetiology. The genetic determinants remain largely elusive, with only a handful of identified candidate genes. G…
We consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA's 3-dimensional conformation. In order to study long-distance dependencies, we develop and release …
Reducing the number of false discoveries is presently one of the most pressing issues in the life sciences. It is of especially great importance for many applications in neuroimaging and genomics, where datasets are typically high-dimensional, which means that the number of explanatory variables exceeds the sample size…
We present a novel method for extracting cancer signatures by applying statistical risk models (http://ssrn.com/abstract=2732453) from quantitative finance to cancer genome data. Using 1389 whole genome sequenced samples from 14 cancers, we identify an "overall" mode of somatic mutational noise. We give a prescription …
Fast and cheaper next generation sequencing technologies will generate unprecedentedly massive and highly-dimensional genomic and epigenomic variation data. In the near future, a routine part of medical record will include the sequenced genomes. A fundamental question is how to efficiently extract genomic and epigenomi…
The increased affordability of whole genome sequencing has motivated its use for phenotypic studies. We address the problem of learning interpretable models for discrete phenotypes from whole genomes. We propose a general approach that relies on the Set Covering Machine and a k-mer representation of the genomes. We sho…
A Neural Network Model to Classify Liver Cancer Patients Using Data Expansion and Compressionstat.ML
We develop a neural network model to classify liver cancer patients into high-risk and low-risk groups using genomic data. Our approach provides a novel technique to classify big data sets using neural network models. We preprocess the data before training the neural network models. We first expand the data using wavel…
New algorithm clusters sparse data effectively.
problem Challenges in clustering sparse data.
method Deterministic Information Bottleneck framework for joint feature weighting and clustering.
result Demonstrated effectiveness on real-world genomics data.
New algorithm classifies and generates genomic sequences using RG-flow categorifier.
problem Classifying and generating genomic sequences for disease prediction.
method RG-flow based categorifier combining quantum field theory, holographic duality, and neural ODEs.
result RG categorifier can classify and generate new sequences from genomic data.
The paper develops a scalable method to infer GRNs from sparse data.
problem Inferring complex gene regulatory networks from limited and temporally sparse data.
method Bayesian optimization and kernel-based methods to construct a Gaussian Process (GP) model.
result The method efficiently searches for the topology with the highest likelihood value.
Discriminative neural networks offer little or no performance guarantees when deployed on data not generated by the same process as the training distribution. On such out-of-distribution (OOD) inputs, the prediction may not only be erroneous, but confidently so, limiting the safe deployment of classifiers in real-world…
A Bayesian Boolean Matrix Factorization for cancer genomics
problem Identifying coordinated feature changes in cancer
method Bayesian Boolean Matrix Factorization
result Captures widespread, near-simultaneous chromosome-number changes
Proposes a copula-based model for multi-view clustering with directional dependency.
problem Challenges in integrating multi-source datasets with directional dependency.
method Copula-based multi-view clustering model accounting for directional dependence.
result Ignoring directional dependence negatively impacts clustering performance.
Joint and individual variation explained (JIVE) for integrated analysis of multiple data typesstat.ML
Research in several fields now requires the analysis of data sets in which multiple high-dimensional types of data are available for a common set of objects. In particular, The Cancer Genome Atlas (TCGA) includes data from several diverse genomic technologies on the same cancerous tumor samples. In this paper we introd…
One of the fundamental tasks in understanding genomics is the problem of predicting Transcription Factor Binding Sites (TFBSs). With more than hundreds of Transcription Factors (TFs) as labels, genomic-sequence based TFBS prediction is a challenging multi-label classification task. There are two major biological mechan…
Unlocking Noisy Real-World Corpora for Foundation Model Pre-Training via Quality-Aware Tokenizationcs.AI
QA-Token improves tokenization for noisy data, boosting model performance.
problem Tokenization ignores data quality, limiting model effectiveness on noisy corpora.
method QA-Token combines signal quality with vocabulary construction through bilevel optimization and reinforcement learning.
result QA-Token achieves state-of-the-art performance on genomic and financial datasets.
SynthBH uses synthetic data to control FDR in multiple testing.
problem Controlling false discovery rate in multiple hypothesis testing.
method SynthBH, a synthetic-powered multiple testing procedure.
result SynthBH guarantees FDR control with synthetic data.
Recent advances in high-throughput cDNA sequencing (RNA-Seq) technology have revolutionized transcriptome studies. A major motivation for RNA-Seq is to map the structure of expressed transcripts at nucleotide resolution. With accurate computational tools for transcript reconstruction, this technology may also become us…
The paper develops methods for causal inference from single-cell RNA sequencing data with multiple outcomes.
problem Causal inference from single-cell RNA sequencing data with multiple heterogeneous outcomes.
method Generic semiparametric inference framework for doubly robust estimation with multiple derived outcomes.
result Demonstrates the use of semiparametric inferential results for estimating causal effects in genomics.
We develop a Vector Quantized Spectral Clustering (VQSC) algorithm that is a combination of Spectral Clustering (SC) and Vector Quantization (VQ) sampling for grouping Soybean genomes. The inspiration here is to use SC for its accuracy and VQ to make the algorithm computationally cheap (the complexity of SC is cubic in…
Copula-based fusion improves breast cancer risk stratification.
problem Combining clinical and genomic risk scores using simple rules fails to capture their joint relationship.
method Used copulas to model the joint relationship between clinical and genomic risk scores.
result Copula-based fusion improves risk stratification, identifying subgroups with the worst prognosis.
The combination of multiple classifiers using ensemble methods is increasingly important for making progress in a variety of difficult prediction problems. We present a comparative analysis of several ensemble methods through two case studies in genomics, namely the prediction of genetic interactions and protein functi…
ParKCa combines multiple causal inference methods to infer new causes from known and unknown factors.
problem Causal inference from observational data when randomized experiments are not feasible.
method ParKCa uses a stacking approach to combine results from multiple causal inference methods.
result ParKCa infers more causes than existing methods in real-world and simulated datasets.
New methods improve genetic studies of complex diseases.
problem Improving genetic studies of complex diseases using high-dimensional clinical data.
method Evaluation of unsupervised disentangled representation learning methods (autoencoders, VAE, beta-VAE, FactorVAE) for genetic association studies.
result FactorVAEs and beta-VAEs outperform standard VAEs and non-variational autoencoders in genetic studies of asthma and COPD.