An approximate search engine for structural databases
Bibliographic record
Abstract
When a person interested in a topic enters a keyword into a Web search engine, the response is nearly instantaneous (and sometimes overwhelming). The impressive speed is due to clever inverted index structures, caching, and a domain-independent knowledge of strings. Our project seeks to construct algorithms, data structures, and software that approach the speed of keyword-based search engines for queries on structural databases. A structural database is one whose data objects include trees, graphs, or a set of interrelated labeled points in two, three, or higher dimensional space. Examples include databases holding (i) protein secondary and tertiary structure, (ii) phylogenetic trees, (iii) neuroanatomical networks, (iv) parse trees, (v) molecular diagrams, and (vi) XML documents. Comparison queries on such databases require solving variants of the graph isomorphism or subisomorphism problems (for which all known algorithms are exponential), so we have explored a large heuristic space.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.017 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.005 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.003 | 0.010 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.007 | 0.004 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".