Deep learning captures semantic structure of large documents.
problem Understanding complex, structured documents like scholarly articles and business reports.
method Deep learning-based document ontology to capture semantic structure and domain-specific concepts.
result The ontology enhances semantic indexing for better understanding by humans and machines.
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.
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.
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.
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.
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.
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.
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.
A new model embeds word and label hierarchies in hyperbolic space for HMLC.
problem Learning mappings from word hierarchies to label hierarchies in hierarchical multi-label classification.
method Proposes a Hyperbolic Interaction Model (HyperIM) to learn label-aware document representations in hyperbolic space.
result Demonstrates improved performance for HMLC compared to state-of-the-art methods.
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.
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.
ML-Schema offers a standardized format for machine learning components.
problem Lack of interoperability and interpretability in machine learning experiments.
method Developed a top-level ontology with classes, properties, and restrictions.
result ML-Schema enables better interoperability and interpretability of machine learning experiments.
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.
Convolutional neural networks (CNNs) have recently emerged as a popular building block for natural language processing (NLP). Despite their success, most existing CNN models employed in NLP share the same learned (and static) set of filters for all input sentences. In this paper, we consider an approach of using a smal…
PEHRT harmonizes EHR data for translational research.
problem Barriers in using EHR data for translational research.
method Common pipeline including open-source code, visualization tools, and detailed documentation.
result PEHRT harmonizes EHR data to standardized ontologies and generates robust embeddings.
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.
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 …
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…
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…
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.
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.
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).
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.
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…
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.
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…
Machine learning's data-centric philosophy conflicts with natural sciences' standards.
problem Conflict between machine learning's ontology and epistemology and natural sciences' practices.
method Identifying and analyzing contexts where ML can be beneficial or harmful in natural sciences.
result ML can enhance trustworthiness in causal inference but introduces biases in emulation and labeling.
Research creates a taxonomy to bridge AI security and regulatory gaps.
problem Disciplinary disconnect between technical and legal teams in AI risk assessment.
method Developed an AI System Threat Vector Taxonomy with 9 domains and 53 sub-threats.
result Empirically validated and aligned with ISO/IEC 42001 controls and NIST AI RMF functions.
Enhanced neural network framework improves constraint satisfaction with topological conditioning.
problem Maintaining semantic coherence while satisfying physical and logical constraints in neuro-symbolic reasoning.
method Integrates topological conditioning with gradient stabilization mechanisms using Forman-Ricci curvature, Deep Delta Learning, and Covariance Matrix Adaptation Evolution Strategy.
result Achieves mean energy reduction to 1.15 compared to baseline values of 11.68, with 95 percent success rate.
Paper proposes a graph network for EHR data that learns robust representations.
problem Learning robust representations for EHR data with implicit connections.
method Variationally regularized encoder-decoder graph network.
result Model outperforms existing methods in various EHR predictive tasks.
MuLan links music audio to natural language tags.
problem Traditional music tagging systems use rigid attributes; MuLan aims to link audio directly to natural language.
method Joint audio-text embedding model trained on 44 million music recordings and text annotations.
result MuLan's embeddings enable zero-shot functionalities and transfer learning.
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…
Framework uses deep learning to analyze large documents and identify their logical structure.
problem Analyzing large, multi-themed documents with diverse topics.
method Deep learning techniques to model and extract logical and semantic structure.
result Framework effectively identifies and classifies different sections of documents.
Imaging neuroscience links brain activation maps to behavior and cognition via correlational studies. Due to the nature of the individual experiments, based on eliciting neural response from a small number of stimuli, this link is incomplete, and unidirectional from the causal point of view. To come to conclusions on t…
Entity-GCN model answers multi-document questions by reasoning across documents.
problem Answering questions based on multiple documents and cross-document relations.
method Graph Convolutional Networks (GCNs) applied to a graph of mentions and their relations.
result Achieves state-of-the-art results on WikiHop dataset.
A new method for document network embedding interprets and generalizes well.
problem Lack of interpretability and generalization to new documents in existing methods.
method Introduces Topic-Word Attention (TWA) and Inductive Document Network Embedding (IDNE) to generate document representations.
result Achieves state-of-the-art performance on various networks and produces meaningful representations.
A new model CDTM improves text classification by concentrating document topics.
problem Unsupervised text classification with diverse topic distributions.
method Imposes an exponential entropy penalty on document topic distribution to encourage concentration.
result More coherent topics and concentrated, sparse document-topic distributions.
New document embedding method finds more relevant tech docs.
problem Computing document similarities for technical content.
method Hybrid approach using graph techniques to extract keyphrases and score sentences.
result Proposed methods outperform baselines up to 27% in NDCG.
We show that, under mild assumptions, some unimaginable events - which we refer to as Black Swan events - must necessarily occur. It follows as a corollary of our theorem that any computational model of decision-making under uncertainty is incomplete in the sense that not all events that occur can be taken into account…
Improved self-supervised learning for document images.
problem Performance of self-supervised pre-training on document images is poor.
method Proposed context-aware alternatives and a novel multi-modal method.
result Novel method outperforms other self-supervised methods on document image classification.
MarlRank uses multi-agent reinforcement learning to improve document ranking.
problem Neglecting mutual information among documents in ranking models.
method Formulated as a multi-agent Markov Decision Process (MDP), each document predicts relevance considering its own and similar documents features and actions.
result Significant performance gains over state-of-the-art baselines on LETOR benchmark datasets.
DocParser parses document structures from renderings like PDFs and scans.
problem Parsing complete hierarchical document structures from renderings.
method End-to-end system with novel weak supervision approach.
result Significant improvement in document structure parsing performance.
CCAligned creates a massive web document dataset for cross-lingual research.
problem Identifying comparable documents across different languages.
method Using URL signals to label web documents and mining Common Crawl corpus.
result Release of a dataset with over 392 million URL pairs from 8144 language pairs.
Study develops a diagnostic tool for rare diseases using reinforcement learning.
problem Minimize medical tests while reducing diagnostic uncertainty for rare diseases.
method Investigated reinforcement learning algorithms, combined expert knowledge with clinical data, integrated ontological information.
result Demonstrated a feasible decision support tool for rare diseases.
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.
Paper develops a new unsupervised scoring function for cross-lingual document alignment.
problem Aligning documents across different languages for NLP tasks.
method Uses cross-lingual sentence embeddings to compute semantic distances and guides document alignment.
result The proposed scoring function outperforms current methods by 7-22% on various language pairs.