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Record W3041251855 · doi:10.1186/s12859-020-03595-2

Efficient implied alignment

2020· article· en· W3041251855 on OpenAlex
Alex Washburn, Ward C. Wheeler

Why this work is in the frame

A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.

fundA Canadian funder is recorded on the work.
no affNo Canadian affiliation: this work is invisible to an affiliation-only frame.
No Canadian affiliation. An affiliation-only frame, the usual design, would never have seen this work. It is one of the works that make the case for inverting the frame.

Bibliographic record

VenueBMC Bioinformatics · 2020
Typearticle
Languageen
FieldComputer Science
TopicTopological and Geometric Data Analysis
Canadian institutionsnot available
FundersRobert J. Kleberg, Jr. and Helen C. Kleberg FoundationDefense Sciences Office, DARPADefense Advanced Research Projects AgencyMcGill University
KeywordsAlgorithmTree traversalArtificial intelligenceComputer science

Abstract

fetched live from OpenAlex

BACKGROUND: Given a binary tree [Formula: see text] of n leaves, each leaf labeled by a string of length at most k, and a binary string alignment function ⊗, an implied alignment can be generated to describe the alignment of a dynamic homology for [Formula: see text]. This is done by first decorating each node of [Formula: see text] with an alignment context using ⊗, in a post-order traversal, then, during a subsequent pre-order traversal, inferring on which edges insertion and deletion events occurred using those internal node decorations. RESULTS: Previous descriptions of the implied alignment algorithm suggest a technique of "back-propagation" with time complexity [Formula: see text]. Here we describe an implied alignment algorithm with complexity [Formula: see text]. For well-behaved data, such as molecular sequences, the runtime approaches the best-case complexity of Ω(k∗n). CONCLUSIONS: The reduction in the time complexity of the algorithm dramatically improves both its utility in generating multiple sequence alignments and its heuristic utility.

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.

Full frame distilled prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.

metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesInsufficient payload (model declined to judge)
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Simulation or modeling · Consensus signal: none
GenreCandidate signal: Methods · Consensus signal: Methods
Teacher disagreement score0.866
Threshold uncertainty score1.000

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0000.000
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0000.001
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0010.000
Research integrity0.0000.000
Insufficient payload (model declined to judge)0.0000.001

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.

Opus teacher head0.034
GPT teacher head0.236
Teacher spread0.202 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it