SVM and N-best algorithm classify microbial marker clades from genome sequences.
problem Classifying microbial clades from genome sequences, especially new species.
method Support vector machine (SVM) with N-best algorithm, time series feature extraction, random fragment generation, k-mer size selection.
result Recognition accuracy rates above 28% in top-1 candidate, above 91% in top-10 candidate.
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.
Generates new human genomic sequences for LAI training.
problem Lack of accessible reference data sets for LAI.
method Class-conditional VAE-GAN to generate realistic sequences.
result Generated sequences improve LAI method performance.
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…
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 …
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…
Paper proposes using LSTM for LSH-based sequence alignment.
problem Sequence alignment using deep learning models.
method Deep bidirectional LSTM for feature learning and LSH-based sequence alignment.
result Higher accuracy achieved with LSTM-based model.
TF-MoDISco finds transcription factor motifs from genomic data.
problem Identifying transcription factor motifs from genomic sequence data.
method Algorithm for motif discovery from basepair-level importance scores.
result Improved version v0.5.6.5 of TF-MoDISco.
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.
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.
New method combines personal and reference genomes for better machine learning in DNA sequencing.
problem Improving accuracy of genetic variant calls in sequencing data.
method Interlaces personal and reference genomes to generate images for machine learning.
result Significant improvement in germline variant calling and somatic variant calling across tumor/normal 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.
When analyzing the genome, researchers have discovered that proteins bind to DNA based on certain patterns of the DNA sequence known as "motifs". However, it is difficult to manually construct motifs due to their complexity. Recently, externally learned memory models have proven to be effective methods for reasoning ov…
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.
Study assesses linear classifiers for virus genotyping and subtyping.
problem Challenges in classifying viral sequences, especially in alignment-free methods.
method Comprehensive evaluation of linear classifiers on HCV genomes, varying parameters and sequence lengths.
result Several classifiers perform well under specific conditions, providing robust assessment.
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…
Method computes embeddings for RNA-seq data without genome alignment.
problem No need for genome alignment for RNA-seq data analysis.
method RNN transforms kmers into 2D latent space for transcriptomic analysis.
result Captures DNA sequence similarity and abundance in latent space.
Optimization approach for efficient sampling in optical mapping for structural variant detection.
problem Efficient sampling strategy for structural variant detection using optical mapping.
method Developed an optimization approach using a hyper-geometric distribution and probabilistic concentration inequalities.
result Optimal sampling strategy requires sampling most chromosomal fragments to detect variants at high confidence with little biological material.
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…
PromID predicts human promoter positions with high accuracy.
problem Difficulties in identifying human promoter sequences.
method Deep learning approach predicting exact TSS positions.
result Significantly reduces false positive predictions.
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.
Method corrects deep generative model likelihood scores for OOD detection.
problem Challenges in deploying neural networks on out-of-distribution data.
method Likelihood ratio method for deep generative models.
result Proposed method achieves state-of-the-art OOD detection performance.
Develops a faster soybean genome clustering method combining spectral and vector quantization.
problem Clustering soybean whole genome sequences efficiently.
method Combines Spectral Clustering and Vector Quantization for computational efficiency.
result Significantly outperforms existing methods in cluster quality and time complexity.
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…
A framework infers causal direction from symbolic sequences using compression measures.
problem Inferring causal direction from two observed discrete symbolic sequences.
method Lossless compressors for inferring context-free grammars (CFGs) and quantifying compression extent.
result Grammar inferred from one sequence better compresses the other sequence, indicating causal direction.
Robust machine learning models improve DNA regulatory sequence prediction under various shifts.
problem Real-world applications of DNA regulatory sequence prediction involve shifts not captured by standard i.i.d. assumptions.
method Introduces a robustness framework combining simulation benchmarks and real data analysis.
result Models remain accurate and calibrated under mild shifts but show higher error and miscalibration under strong shifts.
Semi-supervised deep learning detects problematic reads for genome assembly.
problem De novo genome assembly is hindered by specific types of reads.
method Analysis of coverage graphs converted to 1D-signals using semi-supervised deep learning models.
result Semi-supervised deep learning models can detect problematic reads with minimal labeled data.
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 …
Second generation sequencing technologies are being increasingly used for genetic association studies, where the main research interest is to identify sets of genetic variants that contribute to various phenotype. The phenotype can be univariate disease status, multivariate responses and even high-dimensional outcomes.…
New method for valid and exact statistical inference of multi-dimensional change-points.
problem Statistical inference of change-points in multi-dimensional sequences.
method Proposes a method to guarantee the statistical reliability of both location and components of detected changes.
result Demonstrates the effectiveness of the method in genomic abnormality identification and human behavior analysis.
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…
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 …
Proposes using MLP for predicting optimal penalty in changepoint detection.
problem Predicting optimal penalty for changepoints in sequences.
method Uses a multilayer perceptron (MLP) with ReLU activation function to predict penalty.
result Improves accuracy and F1 score compared to existing models.
A novel conLSH algorithm improves alignment of noisy SMRT reads.
problem High error probability in SMRT sequencing data.
method Context-based Locality Sensitive Hashing (conLSH) for efficient alignment.
result Comprehensive improvement in speed and memory requirements compared to rHAT.
New method infers centromere locations in yeast using Hi-C data.
problem Difficulty in inferring centromere locations in yeast.
method Simulation-based inference using Hi-C data and simulated contact maps.
result Infers stochastic locations of all centromeres in budding yeast.
Bayesian model learns cancer subtypes from diverse NGS data.
problem Overdispersed NGS count data and limited samples for specific cancer types.
method Bayesian Multi-Domain Learning (BMDL) model using hierarchical negative binomial factorization.
result BMDL achieves reproducible cancer subtyping without negative transfer effects.
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of the activation maximization ("deep dream") design method; and a joint procedure wh…
Advances of modern sensing and sequencing technologies generate a deluge of high dimensional space-temporal physiological and next-generation sequencing (NGS) data. Physiological traits are observed either as continuous random functions, or on a dense grid and referred to as function-valued traits. Both physiological a…
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this rev…
Study proposes a more accurate method for classifying transposable elements.
problem Classifying transposable elements for understanding their genetic and evolutionary effects.
method Utilized Support Vector Machines (SVM) for hierarchical classification of transposable elements.
result Proposed a robust approach for hierarchical classification of transposable elements with higher accuracy.
Study on the structure of classifier boundaries in DNA sequencing.
problem Understanding the structure of boundaries in a Bayes classifier for DNA sequencing.
method Examined the structure of the boundary in a Bayes classifier applied to DNA sequencing data. Introduced a new measure of uncertainty, Neighbor Similarity.
result The boundary is large and complex, and Neighbor Similarity effectively measures classifier uncertainty.
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.
High throughput sequencing techniques have highly impactedon modern biology, widening the gap between sequenced andannotated data. Automatic annotation tools are thereforeof the foremost importance to guide biologists' experiments. However, most of the state-of-the-art methods rely on annotation transfer, offering reli…
When learning a hidden Markov model (HMM), sequen- tial observations can often be complemented by real-valued summary response variables generated from the path of hid- den states. Such settings arise in numerous domains, includ- ing many applications in biology, like motif discovery and genome annotation. In this pape…
Double descent observed in tree-based models for genomic prediction.
problem Understanding the generalization behavior of tree-based models in machine learning.
method Systematic variation of model complexity in a genomic prediction task using whole-genome sequencing data.
result Double descent emerges only when complexity is scaled jointly across learner capacity and ensemble size.
Framework uses machine learning to distinguish major COVID-19 variants.
problem Discriminate and visualize associations between major COVID-19 variants based on genome sequences.
method Unsupervised machine learning methods, including k-mer analysis, PCA, t-SNE, UMAP, and agglomerative hierarchical clustering.
result Framework effectively distinguishes between major variants and identifies emerging variants.
New algorithm reconstructs genealogies from genetic data.
problem Reconstructing genealogies from genetic data.
method Iterative algorithm {\sc Rec-Gen} for pedigrees from a generative model.
result Accurate reconstruction of a large fraction of pedigrees with low sample complexity.
This study evaluates and compares novelty detection algorithms for discrete sequences.
problem Identifying anomalies in temporal data.
method Experimental comparison of state-of-the-art novelty detection methods on various public and industrial datasets.
result Recommendations for efficient and appropriate methods based on extensive experiments and scalability tests.