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.
Memory Matching Networks classify DNA sequences for protein binding sites.
problem Manual construction of DNA motifs is difficult due to their complexity.
method Memory Matching Networks (MMN) learn a dynamic memory bank of encoded motifs and match them to new sequences.
result MMN effectively classifies DNA sequences as protein binding or nonbinding sites.
Prototype Matching Network (PMN) improves genomic TFBS prediction.
problem Predicting Transcription Factor Binding Sites (TFBSs) with hundreds of TFs as labels.
method Prototype Matching Network (PMN) that learns motif-like features and TF-TF interactions.
result PMN significantly outperforms baselines on a large TFBS dataset.
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.
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 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.
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.
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.
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.
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.
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 …
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.
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.
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.
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.
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 investigates how preprocessing, feature selection, and model selection affect performance on imbalanced genetic data.
problem Challenges in using machine learning on imbalanced genetic datasets.
method Comparative analysis of data preprocessing, feature selection techniques, and machine learning models on imbalanced genetic data.
result Class-imbalanced target variables and skewed predictors have little to no impact on classification performance.
PKB method uses pathway information for cancer sample classification.
problem Cancer genomic data's high dimensionality and limited sample sizes.
method Pathway-based Kernel Boosting (PKB) method integrating gene pathway information for sample classification.
result PKB method outperforms other methods and identifies relevant pathways.
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 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.
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…
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.
Deep learning models improve cancer detection and typing classification from gene expression data.
problem Challenges in establishing specificity for cancer diagnosis using gene expression data.
method Developed deep learning models using mRNA datasets for cancer detection and typing classification.
result Achieved 98% accuracy in cancer detection and 18 out of 32 cancer-typing classifications over 90% accuracy.
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.
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.
Deep neural network improves cancer mutation calls with confidence.
problem Improving accuracy and confidence in somatic variant calls from cancer sequencing.
method Deep Bayesian Recurrent Neural Network (RNN) with flexible priors.
result Enhanced confidence in mutation calls without performance degradation.
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.
TFiLM expands convolutional models' receptive field with minimal overhead.
problem Capturing long-range dependencies in sequential data.
method A novel architectural component using a recurrent neural network to modulate convolutional model activations.
result TFiLM significantly improves learning speed and accuracy on various tasks.
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.
Paper solves NP-hard haplotyping problem using matrix completion.
problem Reconstructing inherited genetic variations from DNA sequencing data.
method Binary matrix factorization and alternating minimization.
result The proposed technique achieves lower haplotype reconstruction error.
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.
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 …
New method learns low-dimensional representations of nonlinear time series without supervision.
problem Learning low-dimensional representations of nonlinear time series without supervision.
method Based on monotone variational inequality, the method learns representations by assuming sequences arise from a common domain.
result The method can learn the geometry for the entire domain and faithful representations for the dynamics of each individual sequence.
GSU tests association between complex genotypes and phenotypes.
problem Testing association between complex genotypes and phenotypes.
method GSU is a similarity-based test using Laplacian kernel for complex objects.
result GSU identified three genes associated with Alzheimer's Disease.
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 …
Graphs represent gene segment organization, revealing complex interrelationships in a scrambled genome.
problem Understanding gene segment organization and interrelationships in a scrambled genome.
method Directed graphs representing gene segments and their relationships, with graph properties mapped to higher-dimensional space for analysis.
result Emerging star-like structures indicate complex interrelationships, including segments from multiple genes interleaving or overlapping.
Symbolic dynamics applied to share prices reveals complex, non-Markovian patterns.
problem Analyzing complex systems like share prices using symbolic dynamics.
method Symbolic dynamics applied to time series of share price returns.
result Nontrivial spectrum of Renyi entropies found, indicating non-Markovian behavior.
Researchers use interpretable classifiers to predict antibiotic resistance.
problem Predicting antibiotic resistance from genome sequences.
method Set Covering Machines for highly interpretable models.
result Highly interpretable models for antibiotic resistance prediction.
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.