Work · Research Data Mining & Information Accessibility

Rethinking search in science.

Manual curation of available information is a time-consuming task and puts a heavy burden on researchers, and while databases have been created to provide machine-readable data, they capture only a small fraction of what the literature holds. The bulk of data is still composed in running text — published in articles and supplementary material — and since this is an established praxis unlikely to change soon, effective search methods that work directly on that text matter more than producing yet more papers. To this end, this project aims to turn the running text of diabetes articles into a machine-readable graph, which we then use for literature-based discovery.

Ultimately, my work is on the knowledge graph itself. If you already accept that conventional search falls short and just want to know why it must be a graph, you can skip the rest of this page and jump straight to the text-to-graph project. Otherwise, read on for why popularity scores, keyword search, and semantic search each fall short.

PDF Text2Graph — Information Retrieval Project Project deck · 11 slides · 2.9 MB Download Open
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1. Popularity scores: a hindrance to new discoveries

Groundbreaking science is often hindered by popularity bias. Search engines prioritize content by general appeal and prior interactions — colliding with the scientific goal of surfacing new discoveries. Useful-but-unpopular information includes:

2. Keyword searches

Scientific concepts and their interrelations can rarely be reduced to simple keywords without losing essential context. Researchers sift through overloads of loosely related documents in a tedious, iterative process of refining terms. This yields a high rate of false positives and may also increase the likelihood of missing critical information (false negatives).

3. Semantic searches

Semantic search is a step forward — but not flawless. Today’s vectorization tools cannot losslessly convert running text into vector representations. Scientific articles, which discuss observations bordering on off-topic, are particularly affected: during vectorization, details get lost, so querying for that detail can’t surface the document.

4. A novel solution: graph-based document representation

Each scientific document can be conceptualized as a network of interconnected pieces of information rather than a linear block of text. Each observation, result, and concept becomes a node; the relationships become edges. This allows nuanced indexing based on the strength and nature of connections, not mere occurrence.

Advantages:

Although implementing graph-based representations can be resource-intensive, the potential for transforming scientific research is profound.

Conclusion

The adoption of graph-based document representations challenges the status quo of document search and opens a pathway to more effective scientific inquiry — ensuring crucial information is no longer obscured by the limitations of conventional search. This leap could well be a pivotal moment in accelerating scientific progress.

See the solution Literature review