On ARGs, pedigrees, and genetic relatedness matrices
Bibliographic record
Abstract
Genetic relatedness is a central concept in genetics, underpinning studies of population and quantitative genetics in human, animal, and plant settings. It is typically stored as a genetic relatedness matrix, whose elements are pairwise relatedness values between individuals. This relatedness has been defined in various contexts based on pedigree, genotype, phylogeny, coalescent times, and, recently, ancestral recombination graph. For some downstream applications, including association studies, using ancestral recombination graph-based genetic relatedness matrices has led to better performance relative to the genotype genetic relatedness matrix. However, they present computational challenges due to their inherent quadratic time and space complexity. Here, we first discuss the different definitions of relatedness in a unifying context, making use of the additive model of a quantitative trait to provide a definition of "branch relatedness" and the corresponding "branch genetic relatedness matrix". We explore the relationship between branch relatedness and pedigree relatedness (i.e. kinship) through a case study of French-Canadian individuals that have a known pedigree. Through the tree sequence encoding of an ancestral recombination graph, we then derive an efficient algorithm for computing products between the branch genetic relatedness matrix and a general vector, without explicitly forming the branch genetic relatedness matrix. This algorithm leverages the sparse encoding of genomes with the tree sequence and hence enables large-scale computations with the branch genetic relatedness matrix. We demonstrate the power of this algorithm by developing a randomized principal components algorithm for tree sequences that easily scales to millions of genomes. All algorithms are implemented in the open source tskit Python package. Taken together, this work consolidates the different notions of relatedness as branch relatedness and, by leveraging the tree sequence encoding of an ancestral recombination graph, provides efficient algorithms that enable computations with the branch genetic relatedness matrix that scale to mega-scale genomic datasets.
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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 | 0.003 | 0.019 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.003 | 0.006 |
| Open science | 0.002 | 0.004 |
| Research integrity | 0.001 | 0.004 |
| Insufficient payload (model declined to judge) | 0.009 | 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".