Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix
Bibliographic record
Abstract
MOTIVATION: Phylogenetic reconstruction is a fundamental problem in computational biology. The Neighbor Joining (NJ) algorithm offers an efficient distance-based solution to this problem, which often serves as the foundation for more advanced statistical methods. Despite prior efforts to enhance the speed of NJ, the computation of the n2 entries of the distance matrix, where n is the number of phylogenetic tree leaves, continues to pose a limitation in scaling NJ to larger datasets. RESULTS: In this work, we propose a new algorithm which does not require computing a dense distance matrix. Instead, it dynamically determines a sparse set of at most O(n log n) distance matrix entries to be computed in its basic version, and up to O(n log 2n) entries in an enhanced version. We show by experiments that this approach reduces the execution time of NJ for large datasets, with a trade-off in accuracy. AVAILABILITY AND IMPLEMENTATION: Sparse Neighbor Joining is implemented in Python and freely available at https://github.com/kurtsemih/SNJ.
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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 | 0.004 | 0.021 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.004 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.003 | 0.004 |
| Open science | 0.004 | 0.004 |
| Research integrity | 0.002 | 0.003 |
| Insufficient payload (model declined to judge) | 0.008 | 0.007 |
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".