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Stefan G. Creadore

Publications and source records attributed to Stefan G. Creadore.

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When Agent Metrics Measure Different Things: An Evidence-Grounded Audit of the Praxa AI Pipeline

Agent evaluations can be numerically correct while measuring a different construct from the one implied by their labels. We present a retrospective measurement audit of selected Praxa AI implementation files, historical evaluation artifacts, and operational records. A 139-case offline routing report contains 112 passes and 27 failures despite zero gating failures, because known gaps are explicitly exempted from the gate. An identifier-free export represents 8,843 tool-attempt rows: 8,395 recorded durations and 448 missing values. Of the durations, 121 equal the signed 32-bit maximum and carry abandoned-client labels; inspected database code clamps elapsed lifecycle age. The pooled recorded 99th percentile is 2,147,483,647 ms, versus 38,118.31 ms among server-observed completed calls. This is a stratum contrast, not a treatment effect. In a documented single-trajectory compaction pilot, the reported follow-up input reduction is 94.39%, but the reduction across the trigger and follow-up calls together is 46.54%. We reproduce the descriptive calculations, verify 91 timing statistics through a separate weighted rational-arithmetic implementation, and execute 13 scoring-function and 12 analysis-verifier tests. Finite-completion bounds show how missing durations limit all-row timing statements without imputing values. The contribution is a source-linked case study and reusable verification package for separating gate policy, lifecycle timing, and request-level accounting from broader agent-performance claims. Historical provider runs and the full current pipeline were not independently reproduced; general capability superiority and population-level statistical significance are not established.

cs.SE

Plato-Bio: verification-first biological novelty screening with temporal rediscovery and structural benchmarks

Large language model research agents can connect literature retrieval, analysis code, and manuscript preparation, but coherent output does not establish scientific validity. We developed Plato-Bio, a biology-routed extension of the open Plato/Denario architecture that couples explicit workflow states with provenance records, citation checks, claim-to-evidence links, scoped file writes, and publication gates. A source audit identified and repaired three defects that could distort evaluation: loss of task domain in the default factory, omission of declared method signals from scoring, and evidence sidecars that lacked the drafted-claim denominator. On the current clean revision, the full Python suite completed with 931 passes, six skips, and no failures or errors; targeted biology, genomics, evidence/citation, and adversarial-safety suites likewise completed without failure. We evaluated two narrow use cases. In a frozen historical rediscovery task, independent pre-1986 literature bridges ranked the later-studied relation between fish oil and Raynaud phenomenon first; TF-IDF ranked it second and corpus frequency third. This single curated task measures retrospective ranking, not prospective discovery. In a separate comparison of AlphaFold models with experimental structures for 15 human proteins, 11 targets had high-confidence-core C-alpha RMSD below 1 Angstrom (median 0.501 Angstrom). Four targets exceeded 2 Angstrom, and confidence masking reduced the SUMO1 discrepancy from 16.61 to 2.58 Angstrom over 74 residues. The workflow emitted 27 traceable discrepancy regions, all retained as unvalidated hypotheses. Plato-Bio therefore provides reproducible software contracts and auditable screening baselines; broader claims of agent efficacy or biological novelty require preregistered evaluation, independent review, and prospective validation.

cs.AI