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.
The paper predicts diseases using both clinical and genomics data.
Dr.S recommends cancer drugs based on genomic data.
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…
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…
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…
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…
PKB framework boosts genomic data analysis by integrating pathway knowledge.
Elastic co-clustering improves clustering of single-cell genomic data.
New algorithm clusters sparse data effectively.
Paper proposes scalable method for analyzing multi-omic data.
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…
BioBO optimizes gene perturbation design using Bayesian optimization with biological priors.
IEN speeds up T-Rex+GVS for fast, efficient GWAS.
Proposes a new clustering algorithm for high-dimensional data.
Optimizes personalized medicine prediction by individual tuning.
In plant and animal breeding studies a distinction is made between the genetic value (additive + epistatic genetic effects) and the breeding value (additive genetic effects) of an individual since it is expected that some of the epistatic genetic effects will be lost due to recombination. In this paper, we argue that t…
Motivation: Human genomic datasets often contain sensitive information that limits use and sharing of the data. In particular, simple anonymisation strategies fail to provide sufficient level of protection for genomic data, because the data are inherently identifiable. Differentially private machine learning can help b…
Paper uses genome Markov structure for outlier detection and read classification.
Proposes a copula-based model for multi-view clustering with directional dependency.
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 …
In this work we propose a method to compute continuous embeddings for kmers from raw RNA-seq data, without the need for alignment to a reference genome. The approach uses an RNN to transform kmers of the RNA-seq reads into a 2 dimensional representation that is used to predict abundance of each kmer. We report that our…
New algorithm classifies and generates genomic sequences using RG-flow categorifier.
Genomic models learn DNA sequences to predict functions.
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…
Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic assumptions on fluxes due to the convenience of formulating the problem as a linear prog…
New method combines ensembling and regularization for genomic disease prediction.
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…
We consider learning ancestral causal relationships in high dimensions. Our approach is driven by a supervised learning perspective, with discrete indicators of causal relationships treated as labels to be learned from available data. We focus on the setting in which some causal (ancestral) relationships are known (via…
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…
Tensor analysis tackles complex multidimensional data across fields.
Bayesian Cox model identifies biomarkers from multi-omics data.
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…
Generates new human genomic sequences for LAI training.
Federated learning improves bioinformatics by sharing data legally.
Copula-based fusion improves breast cancer risk stratification.
Private cancer prediction model trained on federated genomic data.
SEISM tests neural network features for regulatory genomics.
Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set based analyses improve the biologists' capability to discover functional relevance of their experiment design. While elucidating gene set individually, inter gene sets association is rarely taken into co…
New method reduces memory usage for high-dimensional variable selection.
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…
Measures DNA quality degradation effects.
Variable selection in high dimensional space has challenged many contemporary statistical problems from many frontiers of scientific disciplines. Recent technology advance has made it possible to collect a huge amount of covariate information such as microarray, proteomic and SNP data via bioimaging technology while ob…
We consider the problem of performing matrix completion with side information on row-by-row and column-by-column similarities. We build upon recent proposals for matrix estimation with smoothness constraints with respect to row and column graphs. We present a novel iterative procedure for directly minimizing an informa…
Paper uses machine learning to identify key pathways for c-di-GMP in bacterial genomes.
Users of a personalised recommendation system face a dilemma: recommendations can be improved by learning from data, but only if the other users are willing to share their private information. Good personalised predictions are vitally important in precision medicine, but genomic information on which the predictions are…
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…
fiBAG integrates multiplatform genomic data to identify disease markers.
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 …