AIMC Topic: Semantics

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DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis.

Bioinformatics (Oxford, England)
SUMMARY: Disease ontology (DO) annotates human genes in the context of disease. DO is important annotation in translating molecular findings from high-throughput data to clinical relevance. DOSE is an R package providing semantic similarity computati...

RGFinder: a system for determining semantically related genes using GO graph minimum spanning tree.

IEEE transactions on nanobioscience
Biologists often need to know the set S' of genes that are the most functionally and semantically related to a given set S of genes. For determining the set S', most current gene similarity measures overlook the structural dependencies among the Gene...

Towards semantic-driven high-content image analysis: an operational instantiation for mitosis detection in digital histopathology.

Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society
This study concerns a novel symbolic cognitive vision framework emerged from the Cognitive Microscopy (MICO(1)) initiative. MICO aims at supporting the evolution towards digital pathology, by studying cognitive clinical-compliant protocols involving ...

Literature-based biomedical image classification and retrieval.

Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society
Literature-based image informatics techniques are essential for managing the rapidly increasing volume of information in the biomedical domain. Compound figure separation, modality classification, and image retrieval are three related tasks useful fo...

Toward a view-oriented approach for aligning RDF-based biomedical repositories.

Methods of information in medicine
INTRODUCTION: This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems".

PromptAid: Visual Prompt Exploration, Perturbation, Testing and Iteration for Large Language Models.

IEEE transactions on visualization and computer graphics
Large language models (LLMs) have gained widespread popularity due to their ability to perform ad-hoc natural language processing (NLP) tasks with simple natural language prompts. Part of the appeal for LLMs is their approachability to the general pu...

Retrieval-Augmented Generation for ICD-10 Coding in German Clinical Texts - A Technical Case Report.

Studies in health technology and informatics
INTRODUCTION: Manual ICD-10 coding of German clinical texts is time-consuming and error-prone. This project aims to develop a semi-automated pipeline for efficient coding of unstructured medical documentation.

Enhancing cancer diagnostics through a novel deep learning-based semantic segmentation algorithm: A low-cost, high-speed, and accurate approach.

Computers in biology and medicine
Deep learning-based semantic segmentation approaches provide an efficient and automated means for cancer diagnosis and monitoring, which is important in clinical applications. However, implementing these approaches outside the experimental environmen...

Semantic discrete decoder based on adaptive pixel clustering for monocular depth estimation.

Neural networks : the official journal of the International Neural Network Society
Monocular depth estimation (MDE) has long been a popular and challenging task. Currently, mainstream methods mainly include regression methods based on geometric constraints and ordinal regression methods based on discretized depth intervals. However...

Knowledge graph information bottleneck enhanced molecular representation learning.

Neural networks : the official journal of the International Neural Network Society
Effective molecular representation learning (MRL) is essential for advancing molecular property prediction. In recent years, graph-based MRL methods have made significant progress by effectively utilizing the topology structure of molecules. Research...