Modelling digital health data: The ExaMode ontology for computational pathology.

Computational pathology can significantly benefit from ontologies to standardize the employed nomenclature and help with knowledge extraction processes for high-quality annotated image datasets. The end goal is to reach a shared model for digital pathology to overcome data variability and integration problems. Indeed, data annotation in such a specific domain is still an unsolved challenge and datasets cannot be steadily reused in diverse contexts due to heterogeneity issues of the adopted labels, multilingualism, and different clinical practices. Material and methods: This paper presents the ExaMode ontology, modeling the histopathology process by considering 3 key cancer diseases (colon, cervical, and lung tumors) and celiac disease. The ExaMode ontology has been designed bottom-up in an iterative fashion with continuous feedback and validation from pathologists and clinicians. The ontology is organized into 5 semantic areas that defines an ontological template to model any disease of interest in histopathology. Results: The ExaMode ontology is currently being used as a common semantic layer in: (i) an entity linking tool for the automatic annotation of medical records; (ii) a web-based collaborative annotation tool for histopathology text reports; and (iii) a software platform for building holistic solutions integrating multimodal histopathology data. Discussion: The ontology ExaMode is a key means to store data in a graph database according to the RDF data model. The creation of an RDF dataset can help develop more accurate algorithms for image analysis, especially in the field of digital pathology. This approach allows for seamless data integration and a unified query access point, from which we can extract relevant clinical insights about the considered diseases using SPARQL queries.

Empowering digital pathology applications through explainable knowledge extraction tools.

Exa-scale volumes of medical data have been produced for decades. In most cases, the diagnosis is reported in free text, encoding medical knowledge that is still largely unexploited. In order to allow decoding medical knowledge included in reports, we propose an unsupervised knowledge extraction system combining a rule-based expert system with pre-trained Machine Learning (ML) models, namely the Semantic Knowledge Extractor Tool (SKET). Combining rule-based techniques and pre-trained ML models provides high accuracy results for knowledge extraction. This work demonstrates the viability of unsupervised Natural Language Processing (NLP) techniques to extract critical information from cancer reports, opening opportunities such as data mining for knowledge extraction purposes, precision medicine applications, structured report creation, and multimodal learning. SKET is a practical and unsupervised approach to extracting knowledge from pathology reports, which opens up unprecedented opportunities to exploit textual and multimodal medical information in clinical practice. We also propose SKET eXplained (SKET X), a web-based system providing visual explanations about the algorithmic decisions taken by SKET. SKET X is designed/developed to support pathologists and domain experts in understanding SKET predictions, possibly driving further improvements to the system.

Diabetes and Prediabetes Classification Using Glycemic Variability Indices From Continuous Glucose Monitoring Data.

BACKGROUND: Tens of glycemic variability (GV) indices are available in the literature to characterize the dynamic properties of glucose concentration profiles from continuous glucose monitoring (CGM) sensors. However, how to exploit the plethora of GV indices for classifying subjects is still controversial. For instance, the basic problem of using GV indices to automatically determine if the subject is healthy rather than affected by impaired glucose tolerance (IGT) or type 2 diabetes (T2D), is still unaddressed. Here, we analyzed the feasibility of using CGM-based GV indices to distinguish healthy from IGT&T2D and IGT from T2D subjects by means of a machine-learning approach. METHODS: The data set consists of 102 subjects belonging to three different classes: 34 healthy, 39 IGT, and 29 T2D subjects. Each subject was monitored for a few days by a CGM sensor that produced a glucose profile from which we extracted 25 GV indices. We used a two-step binary logistic regression model to classify subjects. The first step distinguishes healthy subjects from IGT&T2D, the second step classifies subjects into either IGT or T2D. RESULTS: Healthy subjects are distinguished from subjects with diabetes (IGT&T2D) with 91.4% accuracy. Subjects are further subdivided into IGT or T2D classes with 79.5% accuracy. Globally, the classification into the three classes shows 86.6% accuracy. CONCLUSIONS: Even with a basic classification strategy, CGM-based GV indices show good accuracy in classifying healthy and subjects with diabetes. The classification into IGT or T2D seems, not surprisingly, more critical, but results encourage further investigation of the present research.