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Martin Hofmann-Apitius

Publications and source records attributed to Martin Hofmann-Apitius.

4 recordsLinked to original sources

Quantitative Evidence Mining for Plausibility-Aware Biomedical AI: A Narrative Review and Conceptual Framework

Biomedical artificial intelligence is moving from literature retrieval toward evidence synthesis for knowledge graphs, clinical decision support, and computational models. Yet most information-extraction systems still represent findings as simple relations, discarding the quantitative and contextual detail needed for interpretation and reuse. A claim that one entity affects another is insufficient when the magnitude, unit, population, comparator, experimental conditions, uncertainty, and provenance are missing. We define quantitative evidence mining as a framework for transforming biomedical findings into structured, context-rich, and auditable evidence units. We define the core elements of an evidence unit: the claim; measured entity and property; value, unit, or scale; comparator; population; biological or clinical conditions; temporal context; uncertainty; provenance; validation results; and expert-review status. We propose an eight-stage reference architecture spanning corpus selection, entity recognition, quantity extraction, context linking, normalization, evidence-unit assembly, multidimensional plausibility assessment, and export and governance. A central principle is that plausibility should not be collapsed into a single truth label; statistical, biological, methodological, contextual, and provenance-based support should remain explicit. The framework links information extraction to evidence synthesis and computational reuse, with applications in clinical-trial analysis, biomarker research, pharmacovigilance, knowledge-graph construction, and mechanistic modelling. It is a research agenda rather than a validated end-to-end system. Progress will require annotated multimodal benchmarks, rigorous component- and workflow-level evaluation, prospective testing, transparent provenance, and sustained expert oversight.

cs.CL↗

On the influence of several factors on pathway enrichment analysis

Pathway enrichment analysis has become a widely used knowledge-based approach for the interpretation of biomedical data. Its popularity has led to an explosion of both enrichment methods and pathway databases. While the elegance of pathway enrichment lies in its simplicity, multiple factors can impact the results of such an analysis which may not be accounted for. Researchers may fail to give influential aspects their due, resorting instead to popular methods and gene set collections, or default settings. Despite ongoing efforts to establish set guidelines, meaningful results are still hampered by a lack of consensus or gold standards around how enrichment analysis should be conducted. Nonetheless, such concerns have prompted a series of benchmark studies specifically focused on evaluating the influence of various factors on pathway enrichment results. In this review, we organize and summarize the findings of these benchmarks to provide a comprehensive overview on the influence of these factors. Our work covers a broad spectrum of factors, spanning from methodological assumptions to those related to prior biological knowledge, such as pathway definitions and database choice. In doing so, we aim to shed light on how these aspects can lead to insignificant, uninteresting, or even contradictory results. Finally, we conclude the review by proposing future benchmarks as well as solutions to overcome some of the challenges which originate from the outlined factors.

q-bio.GN↗

Integrative Data Semantics through a Model-enabled Data Stewardship

Motivation: The importance of clinical data in understanding the pathophysiology of complex disorders has prompted the launch of multiple initiatives designed to generate patient-level data from various modalities. While these studies can reveal important findings relevant to the disease, each study captures different yet complementary aspects and modalities which, when combined, generate a more comprehensive picture of disease aetiology. However, achieving this requires a global integration of data across studies, which proves to be challenging given the lack of interoperability of cohort datasets. Results: Here, we present the Data Steward Tool (DST), an application that allows for semi-automatic semantic integration of clinical data into ontologies and global data models and data standards. We demonstrate the applicability of the tool in the field of dementia research by establishing a Clinical Data Model (CDM) in this domain. The CDM currently consists of 277 common variables covering demographics (e.g. age and gender), diagnostics, neuropsychological tests, and biomarker measurements. The DST combined with this disease-specific data model shows how interoperability between multiple, heterogeneous dementia datasets can be achieved.

q-bio.QM↗

Converting Alzheimer s disease map into a heavyweight ontology: a formal network to integrate data

Alzheimer s disease (AD) pathophysiology is still imperfectly understood and current paradigms have not led to curative outcome. Omics technologies offer great promises for improving our understanding and generating new hypotheses. However, integration and interpretation of such data pose major challenges, calling for adequate knowledge models. AlzPathway is a disease map that gives a detailed and broad account of AD pathophysiology. However, AlzPathway lacks formalism, which can lead to ambiguity and misinterpretation. Ontologies are an adequate framework to overcome this limitation, through their axiomatic definitions and logical reasoning properties. We introduce the AD Map Ontology (ADMO) an ontological upper model based on systems biology terms. We then propose to convert AlzPathway into an ontology and to integrate it into ADMO. We demonstrate that it allows one to deal with issues related to redundancy, naming, consistency, process classification and pathway relationships. Further, it opens opportunities to expand the model using elements from other resources, such as generic pathways from Reactome or clinical features contained in the ADO (AD Ontology). A version of the ontology will be made freely available to the community on Bioportal at the time of the confer-ence.

q-bio.QM↗