Benchmarks with provenance, scope, realism and explicit gaps.

Expert-authored life-science workflow tasks spanning evidence handling, analysis, experimental design, reasoning, validation, translation and scientific communication.

Metrics

Rubric-based task performance across expert-authored scientific workflows

Access

Public benchmark description and evaluation materials

Evidence

Independent expert-authored workflow benchmark

Evidence strength

Prospective / blind evaluation

BioAtlas use

Evaluate scientific-agent usefulness on realistic life-science work, not only question answering or recall.

Broad scientific reasoning across biology, chemistry, longevity, materials and related scientific domains.

Metrics

Task-dependent classification, regression and reasoning metrics

Access

Public leaderboard / explorer

Evidence

Developer-maintained benchmark portal

Evidence strength

Retrospective random split

BioAtlas use

Cross-domain scientific-reasoning reference; keep task-level results separate from model evidence records.

Scientific data-analysis reasoning across descriptive, exploratory, inferential, predictive, causal and mechanistic analysis.

Metrics

Task-appropriate reasoning and analysis accuracy

Access

Research benchmark / paper

Evidence

Research benchmark

Evidence strength

Retrospective random split

BioAtlas use

Prevents scientific reasoning from being collapsed into one undifferentiated score.

LLM-oriented drug-discovery reasoning across molecular properties, synergy, drug-protein interactions and perturbation responses.

Metrics

Task accuracy plus explanation / reasoning quality

Access

Research benchmark / paper

Evidence

Research benchmark

Evidence strength

Retrospective random split

BioAtlas use

Separates domain reasoning quality from conventional QSAR or structure-prediction metrics.

Unified evaluation across drug-discovery and development tasks, mixing curated public datasets with proprietary evaluations.

Metrics

Representative normalized task metrics plus rank-based aggregation

Access

Public leaderboard; underlying access varies by benchmark

Evidence

Developer-maintained benchmark portal

Evidence strength

Mixed / benchmark-dependent

BioAtlas use

Reference pipeline coverage and scoring design while preserving public/proprietary provenance at the individual benchmark level.

Proprietary internal evaluations spanning scientific and drug-discovery tasks.

Metrics

Task-dependent metrics aggregated into an Insilico Score

Access

Public leaderboard; benchmark contents partly proprietary

Evidence

Developer-reported proprietary benchmark

Evidence strength

Opaque / proprietary evaluation

BioAtlas use

Track as proprietary benchmark evidence; never present opaque internal scores as independently reproduced results.

Open benchmark ecosystem for therapeutic ML tasks spanning ADMET, efficacy, drug-target interaction, drug combinations and related discovery problems.

Metrics

Dataset-appropriate classification, regression and ranking metrics

Access

Open public datasets and leaderboards

Evidence

Independent public benchmark ecosystem

Evidence strength

Mixed: random, group and temporal splits

BioAtlas use

Independent public anchor for vendor/model claims and a source of realistic split designs including temporal generalization.

Reproducible drug-discovery benchmark platform that packages dataset, split, metric and evaluation logic as explicit benchmark objects.

Metrics

Benchmark-defined metrics with standardized splits and evaluation logic

Access

Public benchmark hub

Evidence

Independent public benchmark platform

Evidence strength

Mixed: scaffold, group and OOD-capable splits

BioAtlas use

Strong architectural reference for reproducible benchmark records: dataset + split + metric + evaluation logic.

Registry of biological and drug-discovery benchmarks, initiatives, organizations and experimental-validation status.

Metrics

Registry-level metadata rather than one universal model metric

Access

Public benchmark registry

Evidence

Independent benchmark intelligence registry

Evidence strength

Mixed: retrospective through clinical

BioAtlas use

Competitive reference for benchmark discovery; BioAtlas differentiates via provenance, leakage risk, applicability and decision relevance.

Canonical benchmark collection for molecular machine learning across quantum, physical chemistry, biophysics and physiology tasks.

Metrics

ROC-AUC, RMSE, MAE and dataset-specific metrics

Access

Public datasets / benchmark definitions

Evidence

Peer-reviewed public benchmark

Evidence strength

Random / scaffold split depending on task

BioAtlas use

Baseline historical reference; flag when newer OOD or temporal benchmarks provide stronger evidence.

Multi-objective molecular optimization under structural and property constraints.

Metrics

Success rate plus task-specific property and similarity constraints

Access

Public research benchmark

Evidence

Research benchmark

Evidence strength

Constraint-based retrospective evaluation

BioAtlas use

Track separately from ADMET prediction because constrained molecular optimization tests a distinct capability.

Functional-group chemistry reasoning and quantitative comparison tasks.

Metrics

Accuracy and error metrics depending on task

Access

Research benchmark / reported evaluation

Evidence

Research benchmark

Evidence strength

Retrospective evaluation

BioAtlas use

Adds chemistry-reasoning coverage that molecular property prediction alone does not capture.

Large benchmark for protein mutation-effect and fitness prediction across deep mutational scanning and clinical variants.

Metrics

Rank correlation and task-specific mutation-effect metrics

Access

Public datasets and leaderboard

Evidence

Independent public benchmark

Evidence strength

Cross-assay / protein generalization

BioAtlas use

Core benchmark family for protein language/foundation models; expose biological strata instead of only a global score.

Holistic protein-foundation-model evaluation across quality, novelty, diversity and robustness.

Metrics

Quality, novelty, diversity and robustness dimensions

Access

Public benchmark / leaderboard

Evidence

Research benchmark

Evidence strength

Multi-dimensional retrospective evaluation

BioAtlas use

Avoids ranking protein models on a single axis and captures robustness and novelty explicitly.

Peptide-therapeutics benchmark spanning canonical and noncanonical peptide prediction tasks.

Metrics

Dataset-specific classification and regression metrics

Access

Research benchmark / paper

Evidence

Research benchmark

Evidence strength

Standardized retrospective evaluation

BioAtlas use

Adds peptide-specific evaluation coverage that is not captured by small-molecule or general protein benchmarks.

Independent blind community assessment of protein-structure prediction and related structural-biology tasks.

Metrics

Structure-accuracy metrics defined by CASP category

Access

Public challenge results and evaluation materials

Evidence

Independent blind community benchmark

Evidence strength

Prospective / blind evaluation

BioAtlas use

Treat as a high-evidence structural benchmark because targets are assessed blind rather than retrospectively selected.

Large structural-model quality benchmark derived from CASP15/CASP16 models with global, local and interface-level annotations.

Metrics

Global, local and interface structural-quality metrics

Access

Research dataset / paper

Evidence

CASP-derived public benchmark

Evidence strength

Blind-challenge-derived evaluation

BioAtlas use

Useful for benchmarking model-quality assessment and confidence estimation against challenging blind-prediction outputs.

Large protein-ligand interaction resource with similarity-aware evaluation splits for proteins, ligands, pockets and interactions.

Metrics

Pose, interaction and task-specific structure metrics

Access

Open dataset and tooling

Evidence

Independent public benchmark resource

Evidence strength

OOD / similarity-controlled split

BioAtlas use

Top-priority docking benchmark because it supports novelty-aware evaluation instead of easy random splits.

Protein-ligand co-folding benchmark designed to test true zero-shot generalization and possible training-set memorization.

Metrics

Pose accuracy, pocket accuracy, training similarity and physical-validity checks

Access

Open benchmark repository

Evidence

Independent public generalization benchmark

Evidence strength

Out-of-distribution target or domain

BioAtlas use

Expose memorization/generalization risk directly alongside headline pose accuracy.

Realistic protein-ligand structure prediction including apo-to-holo, unknown-pocket and multi-ligand settings.

Metrics

Pose accuracy, physical validity and setting-specific structure metrics

Access

Public research benchmark

Evidence

Independent research benchmark

Evidence strength

OOD / realistic structural evaluation

BioAtlas use

Separate performance on familiar holo structures from harder deployment-like structural settings.

Docking generalization benchmark built around previously unseen protein classes and binding pockets.

Metrics

Pose-recovery and docking-generalization metrics

Access

Public research benchmark

Evidence

Independent research benchmark

Evidence strength

Out-of-distribution target or domain

BioAtlas use

Explicitly distinguish ordinary docking accuracy from generalization to novel targets and pockets.

Physical and chemical validity checks for generated or docked protein-ligand poses.

Metrics

Geometry, stereochemistry, clashes and interaction-validity checks

Access

Open benchmark / toolkit

Evidence

Independent public validation toolkit

Evidence strength

Orthogonal physical-validity evaluation

BioAtlas use

Use as an orthogonal validity layer so a low-RMSD pose is not automatically treated as physically credible.

Disease-specific therapeutic target-identification benchmarking with clinical retrieval and translational-readiness dimensions.

Metrics

Clinical-target retrieval plus druggability, structure availability, repurposing and experimental-readiness measures

Access

Public framework / published methodology

Evidence

Published / developer-maintained benchmark framework

Evidence strength

Retrospective translational benchmark

BioAtlas use

High-value target-discovery reference because retrieval and downstream actionability are scored separately.

Clinical-development benchmark for predicting trial outcomes, including Phase II outcome prediction.

Metrics

F1 and task-specific classification metrics

Access

Proprietary / reported through MMAI Gym materials

Evidence

Developer-reported proprietary benchmark

Evidence strength

Retrospective clinical prediction

BioAtlas use

Track with explicit proprietary status and without unsupported independent-reproduction claims.

Aging-biology reasoning from low-level biodata to phenotype-level conclusions.

Metrics

Task-specific classification, ranking and regression metrics

Access

Publication / benchmark materials

Evidence

Research benchmark

Evidence strength

Retrospective biological evaluation

BioAtlas use

Evaluate whether scientific models can reason over aging biology rather than only recall textual facts.

Single-cell foundation-model benchmark for drug-response and perturbation prediction across pooled, cross-dataset, fine-tuned and zero-shot settings.

Metrics

Prediction metrics across pooled, transfer and zero-shot scenarios

Access

Research benchmark / paper

Evidence

Independent research benchmark

Evidence strength

Cross-dataset / zero-shot evaluation

BioAtlas use

Adds deployment-relevant cell-response evaluation and distinguishes ordinary pooled performance from cross-dataset transfer.