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Marc Jacobs

Publications and source records attributed to Marc Jacobs.

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Quantitative Evidence Mining for Plausibility-Aware Biomedical AI

Biomedical artificial intelligence (AI) systems increasingly extract, organize, and reuse scientific claims from literature, clinical trials, and regulatory documents. But automatic extraction alone does not make a claim reliable evidence: a claim becomes useful only when it can be traced to its source, linked to the quantitative details that support it, and read within its biomedical context and uncertainty. This matters as large language models (LLMs) and increasingly autonomous systems drive evidence synthesis, knowledge graph (KG) construction, and decision support. Many text-mining and LLM pipelines remain relation-centric: they capture entities and relations such as Drug--TREATS--Disease, but drop the dose, effect size, population, comparator, uncertainty, and conditions under which a claim holds. Such relations can look actionable yet remain hard to verify, compare, or reuse. In this perspective, we argue for a shift toward quantitative evidence mining---extracting values, units, measured entities and properties, context, uncertainty, provenance, and plausibility as structured evidence units that populate evidence-aware KGs and can be checked for source grounding, unit consistency, completeness, and biological plausibility. We outline a framework for plausibility-aware AI that treats extracted claims not as final answers but as auditable evidence objects, making clear what was measured, how much it changed, in which setting, with what uncertainty, and from which source. The central risk is not only incorrect extraction, but claims that look like evidence while lacking the structure needed to trust them.

cs.CL

Towards context in large scale biomedical knowledge graphs

Contextual information is widely considered for NLP and knowledge discovery in life sciences since it highly influences the exact meaning of natural language. The scientific challenge is not only to extract such context data, but also to store this data for further query and discovery approaches. Here, we propose a multiple step knowledge graph approach using labeled property graphs based on polyglot persistence systems to utilize context data for context mining, graph queries, knowledge discovery and extraction. We introduce the graph-theoretic foundation for a general context concept within semantic networks and show a proof-of-concept based on biomedical literature and text mining. Our test system contains a knowledge graph derived from the entirety of PubMed and SCAIView data and is enriched with text mining data and domain specific language data using BEL. Here, context is a more general concept than annotations. This dense graph has more than 71M nodes and 850M relationships. We discuss the impact of this novel approach with 27 real world use cases represented by graph queries.

cs.DB