MétaCan
Menu
Back to cohort
Record W4285580083 · doi:10.4230/lipics.sea.2022.16

RLBWT Tricks

2021· preprint· en· W4285580083 on OpenAlex

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.

affAt least one author lists a Canadian institution in the pinned OpenAlex snapshot.

Bibliographic record

VenueDROPS (Schloss Dagstuhl – Leibniz Center for Informatics) · 2021
Typepreprint
Languageen
FieldComputer Science
TopicAlgorithms and Data Compression
Canadian institutionsDalhousie University
FundersNational Institute of Allergy and Infectious DiseasesNational Human Genome Research Institute
KeywordsRowPermutation (music)Table (database)Constant (computer programming)Computer scienceSpeedupLimitingAlgorithmRank (graph theory)Compression (physics)ComputationCombinatoricsParallel computingMathematicsDatabasePhysicsProgramming language

Abstract

fetched live from OpenAlex

Until recently, most experts would probably have agreed we cannot backwards-step in constant time with a run-length compressed Burrows-Wheeler Transform (RLBWT), since doing so relies on rank queries on sparse bitvectors and those inherit lower bounds from predecessor queries. At ICALP '21, however, Nishimoto and Tabei described a new, simple and constant-time implementation. For a permutation $π$, it stores an $O (r)$-space table -- where $r$ is the number of positions $i$ where either $i = 0$ or $π(i + 1) \neq π(i) + 1$ -- that enables the computation of successive values of $π(i)$ by table look-ups and linear scans. Nishimoto and Tabei showed how to increase the number of rows in the table to bound the length of the linear scans such that the query time for computing $π(i)$ is constant while maintaining $O (r)$-space. In this paper we refine Nishimoto and Tabei's approach, including a time-space tradeoff, and experimentally evaluate different implementations demonstrating the practicality of part of their result. We show that even without adding rows to the table, in practice we almost always scan only a few entries during queries. We propose a decomposition scheme of the permutation $π$ corresponding to the LF-mapping that allows an improved compression of the data structure, while limiting the query time. We tested our implementation on real-world genomic datasets and found that without compression of the table, backward-stepping is drastically faster than with sparse bitvector implementations but, unfortunately, also uses drastically more space. After compression, backward-stepping is competitive both in time and space with the best existing implementations.

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)0.001
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesMeta-epidemiology (narrow), Scholarly communication, Open science
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Other design · Consensus signal: none
GenreCandidate signal: Methods · Consensus signal: Methods
Teacher disagreement score0.703
Threshold uncertainty score0.999

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0010.000
Meta-epidemiology (narrow)0.0010.001
Meta-epidemiology (broad)0.0010.001
Bibliometrics0.0000.000
Science and technology studies0.0000.000
Scholarly communication0.0030.003
Open science0.0040.009
Research integrity0.0010.002
Insufficient payload (model declined to judge)0.0000.000

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 head0.020
GPT teacher head0.268
Teacher spread0.248 · 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