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 …
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169,051 papers · 148 categories
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48 results for “Visual Genome”
Context-aware ZSL improves object recognition by considering object context.
problem Previous ZSL approaches ignore object context, limiting their effectiveness.
method Proposes a new approach that models the conditional likelihood of objects appearing in specific contexts.
result Contextual information significantly improves ZSL performance and is robust to class imbalance.
Discriminative Bimodal Networks for Visual Localization and Detection with Natural Language Queriescs.CV
Associating image regions with text queries has been recently explored as a new way to bridge visual and linguistic representations. A few pioneering approaches have been proposed based on recurrent neural language models trained generatively (e.g., generating captions), but achieving somewhat limited localization accu…
Unsupervised machine learning framework for discriminating major variants of concern during COVID-19q-bio.OT
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.
Study improves recognition of long-tail visual relationships.
problem Improving recognition of structured visual relationships from long-tail classes.
method Developed two benchmarks, introduced VilHub loss, and applied RelMix augmentation.
result Simple techniques significantly improved performance on tail classes.
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…
Towards the Latent Transcriptomeq-bio.GN
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…
Machine understanding of complex images is a key goal of artificial intelligence. One challenge underlying this task is that visual scenes contain multiple inter-related objects, and that global context plays an important role in interpreting the scene. A natural modeling framework for capturing such effects is structu…
Dynamic Visualization and Fast Computation for Convex Clustering via Algorithmic Regularizationstat.ML
Convex clustering is a promising new approach to the classical problem of clustering, combining strong performance in empirical studies with rigorous theoretical foundations. Despite these advantages, convex clustering has not been widely adopted, due to its computationally intensive nature and its lack of compelling v…
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.
Random Fragments Classification of Microbial Marker Clades with Multi-class SVM and N-Best Algorithmq-bio.QM
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.
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.
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.
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.
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 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…
Dr.S recommends cancer drugs based on genomic data.
problem Personalizing cancer treatments using genomic information.
method Machine learning to identify optimal drug-gene associations.
result Developed a Drug Recommendation System (Dr.S) for cancer cell lines.
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…
Generative model improves scene graph prediction for rare compositions.
problem Challenges in inferring unseen or rare scene graph compositions.
method Synthesizing rare scene graphs by perturbing real ones, using conditional GANs.
result Marginal but consistent improvements in zero- and few-shot metrics.
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.
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.
Antimicrobial resistance is an important public health concern that has implications in the practice of medicine worldwide. Accurately predicting resistance phenotypes from genome sequences shows great promise in promoting better use of antimicrobial agents, by determining which antibiotics are likely to be effective i…
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…
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.
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.
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.
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…
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.
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…
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…
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…
Autoencoding Random Forestsstat.ML
Proposes autoencoding with random forests using spectral graph theory.
problem Learning low-dimensional embeddings of random forest models.
method Combines nonparametric statistics and spectral graph theory for optimization.
result Establishes a universal consistent decoder for random forest models.
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.
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.
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.
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 …
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.
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…
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.
An approach for learning ancestral causal relationships in high dimensions, validated on human genome-wide data.
problem Learning ancestral causal relationships in high-dimensional biological data.
method Supervised learning approach with discrete indicators treated as labels, scalable to large problems.
result The approach is highly effective and scalable to the human genome-wide setting, robust to perturbations of input information.
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…
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…
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.
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.
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…
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…
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…