We applied machine learning to predict whether a gene is involved in axon regeneration. We extracted 31 features from different databases and trained five machine learning models. Our optimal model, a Random Forest Classifier with 50 submodels, yielded a test score of 85.71%, which is 4.1% higher than the baseline scor…
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48 results for “Gene Ontology”
Deep learning method improves gene ontology classification of neural images.
problem Classifying gene expression in neural in situ hybridization images.
method End-to-end deep learning using convolutional denoising autoencoders (CDAE).
result Significant improvement in classification accuracy (96% reduction in error rate).
The problem of multilabel classification when the labels are related through a hierarchical categorization scheme occurs in many application domains such as computational biology. For example, this problem arises naturally when trying to automatically assign gene function using a controlled vocabularies like Gene Ontol…
SL2MF predicts synthetic lethality using logistic matrix factorization.
problem Predicting synthetic lethality in human cancers from limited experimental data.
method Logistic matrix factorization incorporating biological knowledge.
result SL2MF effectively predicts known and unknown SL interactions.
Improved predictions for rare labels using neural networks and ontologies.
problem Long-tailed frequency distribution in multi-label prediction problems.
method Modified neural network output layer with a Bayesian network of sigmoids leveraging ontology relationships.
result Significant improvements in per-label AUROC and average precision for less common labels.
This paper presents a novel deep learning-based method for learning a functional representation of mammalian neural images. The method uses a deep convolutional denoising autoencoder (CDAE) for generating an invariant, compact representation of in situ hybridization (ISH) images. While most existing methods for bio-ima…
New method expands seed genes to functionally related clusters.
problem Discovering functionally related genes lacking GO terms.
method Semi-supervised learning with positive and unlabeled examples.
result LPU approaches significantly outperform existing methods.
Gene-Gene association for Imaging Genetics Data using Robust Kernel Canonical Correlation Analysisstat.ML
In genome-wide interaction studies, to detect gene-gene interactions, most methods are divided into two folds: single nucleotide polymorphisms (SNP) based and gene-based methods. Basically, the methods based on the gene are more effective than the methods based on a single SNP. Recent years, while the kernel canonical …
Artificial neural networks (ANNs) have gained a well-deserved popularity among machine learning tools upon their recent successful applications in image- and sound processing and classification problems. ANNs have also been applied for predicting the family or function of a protein, knowing its residue sequence. Here w…
We propose a novel hierarchical model for multitask bipartite ranking. The proposed approach combines a matrix-variate Gaussian process with a generative model for task-wise bipartite ranking. In addition, we employ a novel trace constrained variational inference approach to impose low rank structure on the posterior m…
Convolutional Neural Networks (CNNs) are a popular deep learning architecture widely applied in different domains, in particular in classifying over images, for which the concept of convolution with a filter comes naturally. Unfortunately, the requirement of a distance (or, at least, of a neighbourhood function) in the…
The FAIRnets Ontology makes neural networks findable, accessible, interoperable, and reusable.
problem The resource-intensive training of neural networks and the lack of training data availability.
method Development of FAIRnets Ontology to model neural networks on a meta-level and creation of a knowledge graph (FAIRnets) of over 18,400 neural networks.
result The FAIRnets Ontology and knowledge graph enable the reuse and recommendation of neural networks to data scientists.
Prototype learns automotive industry ontology from unstructured data.
problem Automatic learning of domain-specific ontologies from unstructured text data.
method Two-stage classification system: first classifier for concepts and irrelevant collocates, second classifier for concept types.
result Prototype validated with automotive industry complaint and repair data.
Estimates sub-Gaussian parameter with consistent and optimal rates.
problem Estimating sub-Gaussian parameter from random variables.
method Constrained maximization of empirical weighted cumulant generating function.
result Root-n rate estimator is consistent and optimal under certain conditions.
OMTL uses ontology to learn from imbalanced EHR data.
problem Imbalanced and small usable data for phenotypes in EHRs.
method Ontology-driven multi-task learning framework.
result Improved learning performance on phenotypes.
Enhanced ontology learning from text improves question-answering systems.
problem Improving ontology learning from unstructured text for better question-answering systems.
method Heuristically modified FP-Tree with DFA for concept extraction and frequent pattern mining for ontology learning.
result Our approach significantly improves question-answering system performance, answering 80% of questions compared to 28.4% with Text2Onto.
Novel framework explains machine learning models using ontology-based sampling.
problem Generating precise and insightful explanations for machine learning models.
method Ontology-based sampling technique and learnable anchor algorithm.
result Our approach generates more precise and insightful explanations.
Transposable data represents interactions among two sets of entities, and are typically represented as a matrix containing the known interaction values. Additional side information may consist of feature vectors specific to entities corresponding to the rows and/or columns of such a matrix. Further information may also…
Parallel Protein Community Detection in Large-scale PPI Networks Based on Multi-source Learningcs.SI
Paper proposes MLPCD for protein community detection in large PPI networks.
problem Identifying reliable protein communities from large-scale PPI networks.
method Integrates Gene Expression Data and uses Multi-source Learning with cloud computing.
result Demonstrates superior performance compared to existing methods.
O-GANs improve fashion image generation by conditioning on a hierarchical ontology.
problem Challenges in training GANs to generate images from text descriptions.
method Ontology Generative Adversarial Networks (O-GANs) that condition on a hierarchical fashion ontology.
result O-GANs achieve better image quality and conditioning results compared to standard GANs.
We explain the meaning of local symmetries in physics.
problem Understanding the meaning of local symmetries in physics.
method We argue that general covariance and gauge principles are principles of epistemic access to physical laws, leading to ontological insights.
result Relationality is a core notion in gauge field theory, encoded by local symmetries.
We developed OmicsMapNet approach to take advantage of existing deep leaning frameworks to analyze high-dimensional omics data as 2-dimensional images. The omics data of individual samples were first rearranged into 2D images in which molecular features related in functions, ontologies, or other relationships were orga…
ODVICE augments EHR cohorts using ontology to improve analysis robustness.
problem Limited records in cohorts for rare diseases hamper robust analysis.
method Ontology-driven Monte-Carlo graph spanning algorithm for data augmentation.
result ODVICE augmented cohorts show ~30% improvement in AUC over non-augmented datasets.
For most problems in science and engineering we can obtain data sets that describe the observed system from various perspectives and record the behavior of its individual components. Heterogeneous data sets can be collectively mined by data fusion. Fusion can focus on a specific target relation and exploit directly ass…
Deep generative models have achieved remarkable success in various data domains, including images, time series, and natural languages. There remain, however, substantial challenges for combinatorial structures, including graphs. One of the key challenges lies in the difficulty of ensuring semantic validity in context. …
Model tags biomedical texts with tree-structured tags.
problem Tagging unstructured texts with an arbitrary number of terms from an ontology.
method Neural tree decoding approach starting from the root node of an ontology.
result Outperforms state-of-the-art approaches on MeSH term assignment.
The worldwide surge of multiresistant microbial strains has propelled the search for alternative treatment options. The study of Protein-Protein Interactions (PPIs) has been a cornerstone in the clarification of complex physiological and pathogenic processes, thus being a priority for the identification of vital compon…
System exposes study population descriptions in clinical guidelines.
problem Challenges in understanding applicability of clinical guidelines.
method Developed an ontology-enabled prototype system using SIO.
result Allows medical practitioners to better understand study populations.
ANNETT-O: An Ontology for Describing Artificial Neural Network Evaluation, Topology and Trainingcs.AI
Deep learning models, while effective and versatile, are becoming increasingly complex, often including multiple overlapping networks of arbitrary depths, multiple objectives and non-intuitive training methodologies. This makes it increasingly difficult for researchers and practitioners to design, train and understand …
Deep learning methods exhibit promising performance for predictive modeling in healthcare, but two important challenges remain: -Data insufficiency:Often in healthcare predictive modeling, the sample size is insufficient for deep learning methods to achieve satisfactory results. -Interpretation:The representations lear…
The ML-Schema, proposed by the W3C Machine Learning Schema Community Group, is a top-level ontology that provides a set of classes, properties, and restrictions for representing and interchanging information on machine learning algorithms, datasets, and experiments. It can be easily extended and specialized and it is a…
Neural networks enhance relation extraction from biomedical literature.
problem Automated extraction of relations between biomedical concepts.
method Use of multichannel architectures in deep neural networks with biomedical ontologies.
result State-of-the-art results in relation extraction tasks.
We propose a linear-time, single-pass, top-down algorithm for multiple testing on directed acyclic graphs (DAGs), where nodes represent hypotheses and edges specify a partial ordering in which hypotheses must be tested. The procedure is guaranteed to reject a sub-DAG with bounded false discovery rate (FDR) while satisf…
Paper proposes a novel method for aligning hierarchical data using optimal transport in hyperbolic spaces.
problem Aligning hierarchical data like ontologies without external supervision.
method Optimal transport over hyperbolic spaces.
result The method outperforms standard embedding alignment techniques.
A new method uses gene interaction networks to predict gene functions.
problem Predicting gene functions from gene interactions.
method Context graph kernel approach in a machine learning framework.
result The proposed method outperforms linkage-assumption-based methods.
IterefinE combines KG refinement with embeddings to improve KG quality.
problem Noisy Knowledge Graphs lead to poor performance in downstream tasks.
method Iterative KG refinement using embeddings and inference rules.
result Improved KG refinement leading to higher F1 scores.
New model enables AI to learn autonomously.
problem Enabling AI to acquire domain knowledge.
method Hybrid model combining ontology, knowledge graph, and Logic Neural Network.
result System can enrich and extend its knowledge.
VEGN uses graph neural networks to predict disease-causing mutations from genetic variants.
problem Identifying disease-causing mutations from millions of genetic variants.
method VEGN employs a graph neural network on a heterogeneous graph of genes and variants, learning gene-gene interactions.
result VEGN outperforms existing state-of-the-art models in variant effect prediction.
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…
System identifies health risks using semantic and machine learning.
problem Identifying risk factors associated with health conditions in subpopulations.
method Developed a combined semantic and machine learning system using a health risk ontology and knowledge graph.
result Dynamic discovery of risk factors and their subpopulations.
Bayesian model learns cell types and gene networks from two data views.
problem Estimating cell types and their regulatory networks from single-cell gene expression and epigenetic data.
method Symphony Bayesian hierarchical multi-view mixture model with Variational EM inference.
result Symphony outperforms other methods in learning cell types and regulatory networks.
Identifying significant subsets of the genes, gene shaving is an essential and challenging issue for biomedical research for a huge number of genes and the complex nature of biological networks,. Since positive definite kernel based methods on genomic information can improve the prediction of diseases, in this paper we…
Recent work in learning ontologies (hierarchical and partially-ordered structures) has leveraged the intrinsic geometry of spaces of learned representations to make predictions that automatically obey complex structural constraints. We explore two extensions of one such model, the order-embedding model for hierarchical…
GLasso: Regularized Multi-task Graphical Lasso for Joint Estimation of eQTL Mapping and Gene Networkstat.ML
A new method for joint eQTL mapping and gene network estimation.
problem Discovering SNP-gene relationships and gene-gene relationships in gene expression regulation.
method L1-2 regularized multi-task graphical lasso (L1-2 GLasso).
result Competitive performance on capturing true sparse structures of eQTL mapping and gene network.
New method handles correlated genes for better genomic prediction.
problem Technical issues with highly correlated genes in prediction models.
method Grouping algorithm that treats correlated genes as a group and uses their common patterns.
result Significantly outperforms standard models in prediction and feature selection.
Popular online enrichment analysis tools from the field of molecular systems biology provide users with the ability to submit their experimental results as gene sets for individual analysis. Such queries are kept private, and have never before been considered as a resource for integrative analysis. By harnessing gene s…
Proposes a new neural head for asymmetric representation learning.
problem Asymmetric representation learning in directed relations.
method Role-aware neural convex divergence head.
result Role-aware projections improve directional accuracy over plain ICNN-Bregman heads.
Towards Probabilistic Generative Models Harnessing Graph Neural Networks for Disease-Gene Predictioncs.LG
VGAE learns gene-disease associations from networks, predicting disease-genes.
problem Predicting gene-disease associations from disease-gene networks.
method Introducing VGAE, a variational graph auto-encoder for disease-gene prediction.
result VGAE and C-VGAE outperform baseline methods in disease-gene prediction.