AI Computational Biology Math Paper Template

Use this template when a paper connects AI methods, computational biology objects, and mathematical objectives. Keep missing metadata as to verify; do not invent authors, metrics, artifacts, or benchmark details.

Frontmatter

---
title: Paper Title
status: reading
paper:
  title: to verify
  authors: to verify
  venue: to verify
  year: to verify
  url: to verify
tags:
  - papers
---

Summary

• One-line question: to verify
• Main contribution: to verify
• Main axis: AI method / computational biology object / Math objective / benchmark / system / agent workflow
• Secondary axes: to verify
• Public source: to verify
• Reading status: Reading status

Routing

Route	Fill
AI intake	AI paper intake
Computational biology intake	Computational Biology paper intake or not applicable
Formula intake	Formula intake
Formula explanation	Formula explanation ladder
Benchmark intake	Benchmark intake
Claim routing	Claim routing
Cross-axis contract	AI Computational Biology Math contract
Readiness gate	AI Computational Biology Math readiness gate
Coverage check	Coverage matrix

Claim

State claims as paper claims, not facts.

Claim	Evidence	Status
to verify	figure/table/section to verify	to verify

Claim-Type Gate

Select all that apply before summarizing the result.

Claim Type	Applies?	Required Check
architecture improvement	to verify	fair baseline, ablation, parameter/compute boundary
SSL or pretraining	to verify	pretraining unit, positive/corruption rule, transfer split
generative model	to verify	sampler budget, validity/diversity/novelty/utility, invalid denominator
energy or score model	to verify	energy/score/force definition, sampler or negative process, validity after filtering
constrained generation	to verify	hard constraint vs penalty/projection/repair/filter, invalid-output denominator
property or activity prediction	to verify	label semantics, target/assay context, split unit
protein modeling	to verify	sequence/structure source, PLM/MSA/template policy, family split
docking or pose	to verify	receptor/ligand preparation, pose metric, failed docking handling
benchmark result	to verify	allowed information, selection rule, baseline, uncertainty
formula or estimator	to verify	variables, distributions, objective, estimator assumptions
agent or tool workflow	to verify	tool boundary, verifier, memory, success/failure definition

Evidence level:

evidence_level: mentioned # mentioned | specified | supported | bounded | reproducible

Method

• Input object: to verify
• Output object: to verify
• Representation: to verify
• Architecture: to verify
• Learning signal: to verify
• Objective: to verify
• Inference or sampling procedure: to verify
• Constraint or filtering rule: to verify

Representation Contract

Field	Value
Raw unit	molecule / protein / residue / atom / complex / text / image / graph / assay row / to verify
Model input	token / graph / coordinate / embedding / pair feature / latent / to verify
Tokenization or graph construction	to verify
Positional or geometric encoding	to verify
Context source	target / pocket / assay / retrieval / template / prompt / not applicable
Information available at inference	to verify
Information that must be excluded	labels, future data, ground-truth structures, private context, or to verify

Formula Slot

Rewrite the key equation with symbol definitions. Use level 3 from Formula explanation ladder when the paper’s claim depends on the equation.

$$\mathcal{J}(\theta )={\mathbb{E}}_{u\sim q(u)}\left[{\ell }_{\theta }(u)\right]$$

• $u$: to verify
• $q(u)$: to verify
• ${\ell }_{\theta }(u)$: to verify
• $\theta$: to verify
• Explanation level: name / canonical formula / operational form / claim contract / derivation
• Relation to evaluation metric: to verify

Objective and Metric Alignment

Field	Value
Training objective	to verify
Objective family	likelihood / contrastive / score / energy / velocity / reward / constraint / metric / to verify
Model-selection metric	to verify
Reported metric	to verify
Claimed utility	to verify
Mismatch risk	to verify

Computational Biology Contract

Use not applicable only when the paper is not about computational biology.

Field	Value
Biological object	molecule / ligand / protein / pocket / complex / assay / genome region / not applicable
Example unit	to verify
Label semantics	endpoint, unit, direction, threshold, censoring, source, or not applicable
Preprocessing	molecule standardization, protein cleaning, coordinate source, or not applicable
Split unit	scaffold, protein family, complex pair, assay/source, time, template-aware, or to verify
Leakage risks	duplicate, scaffold, homolog, template, assay/source, coordinate-frame, or to verify

Public Boundary

Field	Value
Uses only public sources	to verify
No private paths, servers, accounts, ports, or credentials	yes
No collaborator-private details	yes
No unpublished internal results	yes
Sensitive details removed or generalized	to verify

Benchmark

Field	Value
Dataset or benchmark	to verify
Task	to verify
Split	to verify
Metric	to verify
Metric family	classification / regression / ranking / probability / generation / pose / enrichment / to verify
Baseline	to verify
Model-selection rule	to verify
Uncertainty or seed variation	to verify
Allowed information	training data, templates, retrieval corpus, prompt examples, or to verify

Evidence and Limits

• Strongest evidence: to verify
• Weakest evidence: to verify
• Missing baseline or ablation: to verify
• Failure modes: to verify
• Applicability domain: to verify
• Public artifact availability: Artifact availability
• Implementation readiness: Implementation readiness
• Reproduction plan: Reproduction plan
• Reproducibility status: Reproducibility checklist

Concept Updates

• Object/entity note to update: to verify
• Modality/task note to update: to verify
• Architecture or learning note to update: to verify
• Math note to update: to verify
• Constraint/objective note to update: Constrained optimization, Energy-based model, or not applicable
• Evaluation or benchmark note to update: to verify
• Potential Korean post route: use the post workflow from the Posts section when a reader-facing essay is needed.
• Promotion readiness: AI computational biology math readiness gate

Related

• Paper note format
• Paper review workflow
• AI Computational Biology Math contract
• AI computational biology math readiness gate
• Formula explanation ladder
• Coverage matrix
• Claim extraction
• Evidence table
• Benchmark card