Log-correlation Distance And Fourier Transform With Kullback-Leibler Divergence Distance For Construction Of Vertebrate Phylogeny Using Complete Mitochondrial Genomes
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Bibliographic record
Abstract
For vertebrate mitochondrial genomes, some phylogenies have been built by various methods with or without sequence alignment. These methods are important for the problem of classification and evolution. In this paper, we propose two approaches to analyze the phylogenetic relationship of 64 vertebrates using complete mitochondrial genomes without sequence alignment. The first approach combines discrete Fourier transform (DFT) with Kullback-Leibler divergence (KLD) distance. The second one directly uses a log-correlation distance. Both methods are based on compositional vectors of DNA sequences or protein sequences from the complete genome. The phylogenetic trees show that the mitochondrial genomes are separated into three major groups. One group corresponds to mammals; one group corresponds to fish; and the other one is Archosauria (including birds and reptiles). In particular, the structure of the tree based on log-correlation distance are roughly in agreement in topology with the current known phylogenies of vertebrates.
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Full frame distilled prediction
Teacher imitationNot 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.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it