Papers · mechanistic thesis layer

Daily hypothesis proposals from the trusted evidence graph

Each paper below is a mechanistic synthesis produced by Protean's thesis layer over the trusted-tier evidence already vetted by the runtime. These are proposals, not peer-reviewed findings. Paragraphs marked *[INFERRED]* are model-synthesized; acceptance requires the experimental program outlined in each thesis's §8.

Daily thesis status · 2026-07-02

No new mechanistic thesis passed the novelty/evidence thresholds today. The latest published thesis is thesis_2e56530bb9511cdd (2026-06-09T01:16:23Z). This is a computational/advisory status note produced by the daily thesis rail — a proposal-layer heartbeat, not a peer-reviewed finding and not biological proof. New theses publish automatically when the runtime emits a hypothesis that clears novelty and trusted-evidence thresholds.

23 day(s) since the last published thesis · computational/advisory · not biological proof

thesis_2e56530bb9511cdd · published 2026-06-09 01:16 UTC · ollama/deepseek-r1:latest
Conformational constraint handles should be tested explicitly
evidence_strength 0.35uncertainty 0.34supporting 5contradicting 5
protease resistancestructural motif
thesis_3e705fe3bd850ff8 · published 2026-06-03 05:20 UTC · openai-codex/gpt-5.5
Validation risk subgrouping of peptide candidates by failure similarity
evidence_strength 0.45uncertainty 0.40supporting 5contradicting 5
aging pathwaysantimicrobialstructural motif
thesis_4acdde2bff30943a · published 2026-06-03 05:20 UTC · openai-codex/gpt-5.5
Validation candidate subgroups distinguished by proximity to known failure signals
evidence_strength 0.40uncertainty 0.40supporting 5contradicting 5
aging pathwaysantimicrobialstructural motif
thesis_56fcc3d546a1d4a7 · published 2026-06-03 05:20 UTC · openai-codex/gpt-5.5
Peptide candidates for protease-resistance assays distinguished by cleavage-rule score
evidence_strength 0.35uncertainty 0.41supporting 5contradicting 5
protease resistance
thesis_5cca396371c715fb · published 2026-06-03 05:20 UTC · deepseek-r1:latest
Embedding novelty should be separated from stability-like motifs — antimicrobial
evidence_strength 0.50uncertainty 0.47supporting 5contradicting 2
antimicrobialinflammationneuropeptide signalingprotease resistancestructural motif
thesis_60fbbee1a56f57ed · published 2026-06-03 05:20 UTC · openai-codex/gpt-5.5
Distinguishing validation risk subgroups by similarity to known failure signals
evidence_strength 0.45uncertainty 0.40supporting 5contradicting 5
aging pathwaysantimicrobialstructural motif
thesis_79bbaa13db547838 · published 2026-06-03 05:20 UTC · openai-codex/gpt-5.5
Candidate validation subgroups distinguished by proximity to known failure signals
evidence_strength 0.45uncertainty 0.40supporting 5contradicting 5
aging pathwaysantimicrobialstructural motif
thesis_9ca1642c5d35b252 · published 2026-06-03 05:20 UTC · openai-codex/gpt-5.5
Distinguishing constrained from linear antimicrobial peptides by structural constraint handles
evidence_strength 0.50uncertainty 0.39supporting 2contradicting 2
antimicrobialneuropeptide signalingprotease resistancestructural motif
thesis_b50734ac395de503 · published 2026-06-03 05:20 UTC · openai-codex/gpt-5.5
Antimicrobial candidate subgrouping by proximity to known failure signals
evidence_strength 0.35uncertainty 0.16supporting 5contradicting 0
antimicrobialprotease resistancestructural motif
thesis_d6d68637d5edeec8 · published 2026-06-03 05:20 UTC · openai-codex/gpt-5.5
Distinguishing constrained peptide candidates by cyclization, disulfide, and high-proline handles
evidence_strength 0.35uncertainty 0.33supporting 5contradicting 5
structural motif
thesis_e6f07d388d3d3492 · published 2026-06-03 05:20 UTC · openai-codex/gpt-5.5
Antimicrobial candidates versus validation-risk subgroups by failure-similarity proximity
evidence_strength 0.35uncertainty 0.16supporting 5contradicting 0
antimicrobialprotease resistancestructural motif
thesis_f114bfe88a0980bb · published 2026-06-03 05:20 UTC · openai-codex/gpt-5.5
Separating constrained from linear peptide candidates by conformational constraint handles
evidence_strength 0.35uncertainty 0.33supporting 5contradicting 5
structural motif
thesis_f4b4de17768e13bd · published 2026-06-03 05:20 UTC · openai-codex/gpt-5.5
Peptide validation risk subgroups by proximity to known failure signals
evidence_strength 0.45uncertainty 0.40supporting 5contradicting 5
aging pathwaysantimicrobialstructural motif

Daily hypothesis proposals from the trusted evidence graph

Conformational constraint handles should be tested explicitly

Validation risk subgrouping of peptide candidates by failure similarity

Validation candidate subgroups distinguished by proximity to known failure signals

Peptide candidates for protease-resistance assays distinguished by cleavage-rule score

Embedding novelty should be separated from stability-like motifs — antimicrobial

Distinguishing validation risk subgroups by similarity to known failure signals

Candidate validation subgroups distinguished by proximity to known failure signals

Distinguishing constrained from linear antimicrobial peptides by structural constraint handles

Antimicrobial candidate subgrouping by proximity to known failure signals

Distinguishing constrained peptide candidates by cyclization, disulfide, and high-proline handles

Antimicrobial candidates versus validation-risk subgroups by failure-similarity proximity

Separating constrained from linear peptide candidates by conformational constraint handles

Peptide validation risk subgroups by proximity to known failure signals