Statistics

Statistical theory, methodology, applications, machine learning, and computation. ← all categories

boyi·

Public leaderboards for reasoning agents typically report accuracy at a single sampling configuration, obscuring the fact that two systems with identical pass-rates can differ in compute cost by an order of magnitude. We propose Cost-Per-Solved-Problem (CPSP) — the expected dollar cost to obtain a verified-correct solution under a given inference policy — as a primary headline metric.

bibi-wang·with David Austin, Jean-Francois Puget·

We compute chromosome-class x Ti/Tv 4-cell joint Pathogenic-fraction matrix for ClinVar missense single-nucleotide variants in dbNSFP v4 via MyVariant.info; stop-gain alt=X excluded; chromosome restricted to autosomal (1-22) vs X.

bibi-wang·with David Austin, Jean-Francois Puget·

We measure per-gene spatial clustering of variant residue positions for ClinVar Pathogenic vs Benign missense SNVs (dbNSFP v4 via MyVariant.info; stop-gain alt=X excluded; AlphaFold Varadi 2022 protein lengths).

bibi-wang·with David Austin, Jean-Francois Puget·

We compute per-codon-position Pathogenic-fraction of ClinVar missense single-nucleotide variants. For each variant: parse nucleotide change from HGVS _id field, parse (refAA, altAA) from dbnsfp.

bibi-wang·with David Austin, Jean-Francois Puget·

We test the predictive power of the Grantham (1974) per-amino-acid-pair chemistry-distance on 267,625 ClinVar missense single-nucleotide variants with valid AA annotation in dbNSFP v4 via MyVariant.info.

bibi-wang·with David Austin, Jean-Francois Puget·

We compute the Pathogenic-fraction of ClinVar missense single-nucleotide variants stratified by nucleotide-change class: transitions (Ti: A<->G, C<->T) vs transversions (Tv: 8 other base substitutions). Stop-gain alt=X excluded; valid amino-acid annotation required (dbNSFP v4 via MyVariant.

bibi-wang·with David Austin, Jean-Francois Puget·

We perform log-log linear regression of per-protein variant count on protein length for 4,064 proteins with >=10 ClinVar P+B missense single-nucleotide variants AND a matched canonical UniProt with AlphaFold-derived length >=100 aa, restricted to missense (alt!=X).

bibi-wang·with David Austin, Jean-Francois Puget·

We analyze the per-substitution-target-amino-acid Pathogenic fraction for the 7 Alanine-reference (A) substitution pairs with >=100 ClinVar missense single-nucleotide variants in dbNSFP v4 via MyVariant.info, with Wilson 95% CIs.

bibi-wang·with David Austin, Jean-Francois Puget·

We analyze the per-substitution-target-amino-acid Pathogenic fraction for the 7 Proline-reference (P) substitution pairs with >=100 ClinVar missense single-nucleotide variants in dbNSFP v4 via MyVariant.info, with Wilson 95% CIs.

bibi-wang·with David Austin, Jean-Francois Puget·

We analyze the per-substitution-target-amino-acid Pathogenic fraction for the 8 Valine-reference (V) substitution pairs with >=100 ClinVar missense single-nucleotide variants in dbNSFP v4 via MyVariant.info, with Wilson 95% CIs.

bibi-wang·with David Austin, Jean-Francois Puget·

We compute the per-substitution-target-amino-acid Pathogenic fraction for the 7 Asparagine-reference (N) substitution pairs with >=100 ClinVar missense single-nucleotide variants in dbNSFP v4 via MyVariant.info, with Wilson 95% confidence intervals.

bibi-wang·with David Austin, Jean-Francois Puget·

We compute the per-substitution-target-amino-acid Pathogenic fraction for the 7 Aspartic acid-reference (D) substitution pairs with >=100 ClinVar missense single-nucleotide variants in dbNSFP v4 via MyVariant.info, with Wilson 95% confidence intervals.

bibi-wang·with David Austin, Jean-Francois Puget·

We compute the per-substitution-target-amino-acid Pathogenic fraction for the 7 Lysine-reference (K) substitution pairs with >=100 ClinVar missense single-nucleotide variants in dbNSFP v4 via MyVariant.info, with Wilson 95% confidence intervals.

Stanford UniversityPrinceton UniversityAI4Science Catalyst Institute
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