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acefesan/dl-bio

https://github.com/acefesan/dl-bio · scanned 2026-06-17 01:28 UTC (1 month, 2 weeks ago)

47 raw signals (0 security + 47 graph)

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UNIFIED Repobility · multi-layer engine · AI coders

Complete repo analysis

Last scanned 1 month, 2 weeks ago · v2 · last Δ -15.8 (diff) · 28 actionable findings from 1 signal source. 19 repeated signals grouped for readability. Security checks, system graph analysis, and verified AI-agent feedback are merged into one review queue.

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66.7% cov · 28 findings

Severity distribution — click a segment to filter

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Severity: Critical 0 High 0 Medium 13 Low 15 9-Layer: Software Security Quality Integrity Frontend Hardware Data Network Cicd Source: Security checks 0 System graph 28 Crowd 0 Layer: Software 9 Network 3 Hardware 2 Security 2 Cicd 1 Quality 11

Exclude dismissed / FP Exclude test files

All 752 nodes from the latest scan, grouped by kind. Each node is a unit the engine identified (file, function, endpoint, table…). Most users won't need this view — it's primarily for debugging the engine's graph extraction or for AI agents that want to enumerate the project structure.

Label	Layer	Status	Path
`get_git_commit`	software	healthy	`write_artifact_metadata.py:30`
`check_git_clean`	software	healthy	`write_artifact_metadata.py:38`
`main`	software	healthy	`write_artifact_metadata.py:46`
`__call__`	software	healthy	`chapters/chapter2/05_go_prediction.py:61`
`load_split`	software	healthy	`chapters/chapter2/05_go_prediction.py:76`
`make_batches`	software	healthy	`chapters/chapter2/05_go_prediction.py:99`
`train_step`	software	healthy	`chapters/chapter2/05_go_prediction.py:117`
`loss_fn`	software	dead	`chapters/chapter2/05_go_prediction.py:119`
`compute_per_target_metrics`	software	healthy	`chapters/chapter2/05_go_prediction.py:129`
`evaluate`	software	healthy	`chapters/chapter2/05_go_prediction.py:151`
`train_model`	software	healthy	`chapters/chapter2/05_go_prediction.py:173`
`plot_comparison`	software	healthy	`chapters/chapter2/05_go_prediction.py:257`
`plot_final_bar`	software	healthy	`chapters/chapter2/05_go_prediction.py:304`
`main`	software	healthy	`chapters/chapter2/05_go_prediction.py:335`
`load_sequences`	software	healthy	`chapters/chapter2/02_build_dataset.py:45`
`load_taxonomy`	software	healthy	`chapters/chapter2/02_build_dataset.py:63`
`fetch_taxonomy_names_batch`	software	healthy	`chapters/chapter2/02_build_dataset.py:71`
`load_labels`	software	healthy	`chapters/chapter2/02_build_dataset.py:104`
`load_go_descriptions`	software	healthy	`chapters/chapter2/02_build_dataset.py:113`
`load_embeddings`	software	healthy	`chapters/chapter2/02_build_dataset.py:121`
`fetch_hogs_from_oma`	software	healthy	`chapters/chapter2/02_build_dataset.py:137`
`load_hog_cache`	software	healthy	`chapters/chapter2/02_build_dataset.py:249`
`build_dataset`	software	healthy	`chapters/chapter2/02_build_dataset.py:263`
`create_metadata`	software	healthy	`chapters/chapter2/02_build_dataset.py:351`
`main`	software	healthy	`chapters/chapter2/02_build_dataset.py:420`
`load_common_proteins`	software	healthy	`chapters/chapter2/05_model_size_clustering.py:44`
`get_taxa_and_sample`	software	healthy	`chapters/chapter2/05_model_size_clustering.py:65`
`load_embeddings_for_sample`	software	healthy	`chapters/chapter2/05_model_size_clustering.py:90`
`run_analysis`	software	healthy	`chapters/chapter2/05_model_size_clustering.py:99`
`main`	software	healthy	`chapters/chapter2/05_model_size_clustering.py:133`
`parse_args`	software	healthy	`chapters/chapter2/04_pretrain_esm2.py:48`
`tokenize_sequences`	software	healthy	`chapters/chapter2/04_pretrain_esm2.py:92`
`main`	software	healthy	`chapters/chapter2/04_pretrain_esm2.py:103`
`load_data`	software	healthy	`chapters/chapter2/07_whitening_analysis.py:24`
`run_analysis`	software	healthy	`chapters/chapter2/07_whitening_analysis.py:48`
`load_training_log`	software	healthy	`chapters/chapter2/analyze_training_dynamics.py:28`
`plot_loss_curves`	software	healthy	`chapters/chapter2/analyze_training_dynamics.py:58`
`plot_generalization_gap`	software	healthy	`chapters/chapter2/analyze_training_dynamics.py:74`
`plot_grad_norm`	software	healthy	`chapters/chapter2/analyze_training_dynamics.py:94`
`compute_weight_metrics`	software	healthy	`chapters/chapter2/analyze_training_dynamics.py:107`
`analyze_weight_dynamics`	software	healthy	`chapters/chapter2/analyze_training_dynamics.py:151`
`plot_weight_norms`	software	healthy	`chapters/chapter2/analyze_training_dynamics.py:168`
`plot_effective_rank`	software	healthy	`chapters/chapter2/analyze_training_dynamics.py:180`
`plot_layer_rank_heatmap`	software	healthy	`chapters/chapter2/analyze_training_dynamics.py:203`
`main`	software	healthy	`chapters/chapter2/analyze_training_dynamics.py:238`
`oma_get`	software	healthy	`chapters/chapter2/fetch_mammalia.py:63`
`fetch_species_metadata`	software	healthy	`chapters/chapter2/fetch_mammalia.py:93`
`fetch_protein_list`	software	healthy	`chapters/chapter2/fetch_mammalia.py:109`
`phase_fetch_lists`	software	healthy	`chapters/chapter2/fetch_mammalia.py:146`
`hog_balanced_sample`	software	healthy	`chapters/chapter2/fetch_mammalia.py:192`

Showing first 50 of this kind. Full payload available via the JSON button at the top of the page.

Label	Layer	Status	Path
`AGENTS.md`	software	healthy	`AGENTS.md`
`write_artifact_metadata.py`	software	healthy	`write_artifact_metadata.py`
`README.md`	software	healthy	`README.md`
`.markdownlint.json`	software	healthy	`.markdownlint.json`
`pyproject.toml`	software	healthy	`pyproject.toml`
`.lychee.toml`	software	healthy	`.lychee.toml`
`WORKSTREAMS.md`	software	healthy	`WORKSTREAMS.md`
`hygiene.yml`	software	healthy	`.github/workflows/hygiene.yml`
`05_go_prediction.py`	software	healthy	`chapters/chapter2/05_go_prediction.py`
`02_build_dataset.py`	software	healthy	`chapters/chapter2/02_build_dataset.py`
`05_model_size_clustering.py`	software	healthy	`chapters/chapter2/05_model_size_clustering.py`
`04_pretrain_esm2.py`	software	healthy	`chapters/chapter2/04_pretrain_esm2.py`
`07_whitening_analysis.py`	software	healthy	`chapters/chapter2/07_whitening_analysis.py`
`run_200epoch_sweep.sh`	software	healthy	`chapters/chapter2/run_200epoch_sweep.sh`
`analyze_training_dynamics.py`	software	healthy	`chapters/chapter2/analyze_training_dynamics.py`
`run_60epoch_scaled_lr.sh`	software	healthy	`chapters/chapter2/run_60epoch_scaled_lr.sh`
`fetch_mammalia.py`	software	healthy	`chapters/chapter2/fetch_mammalia.py`
`esm2_3b.json`	software	healthy	`chapters/chapter2/esm2_3b.json`
`config.json`	software	healthy	`chapters/chapter2/config.json`
`esm2_150m.json`	software	healthy	`chapters/chapter2/esm2_150m.json`
`README.md`	software	healthy	`chapters/chapter2/README.md`
`03_clustering_analysis.py`	software	healthy	`chapters/chapter2/03_clustering_analysis.py`
`04_subtree_hog_analysis.py`	software	healthy	`chapters/chapter2/04_subtree_hog_analysis.py`
`06_go_grid_search.py`	software	healthy	`chapters/chapter2/06_go_grid_search.py`
`run_1m_sweep.sh`	software	healthy	`chapters/chapter2/run_1m_sweep.sh`
`pretrain_esm2.py`	software	healthy	`chapters/chapter2/pretrain_esm2.py`
`01_compute_embeddings.py`	software	healthy	`chapters/chapter2/01_compute_embeddings.py`
`run_1m_sweep_500k.sh`	software	healthy	`chapters/chapter2/run_1m_sweep_500k.sh`
`hog_umap_interactive.py`	software	healthy	`chapters/chapter2/hog_umap_interactive.py`
`run.py`	software	healthy	`chapters/chapter2/run.py`
`hog_umap.py`	software	healthy	`chapters/chapter2/hog_umap.py`
`compute_embeddings.py`	software	healthy	`chapters/chapter2/archive/compute_embeddings.py`
`umap_embeddings.py`	software	healthy	`chapters/chapter2/archive/scripts/umap_embeddings.py`
`umap_by_hog.py`	software	healthy	`chapters/chapter2/archive/scripts/umap_by_hog.py`
`sensitivity_analysis_corrected.py`	software	healthy	`chapters/chapter2/archive/scripts/sensitivity_analysis_corr…`
`build_cafa3_dataset.py`	software	healthy	`chapters/chapter2/archive/scripts/build_cafa3_dataset.py`
`sensitivity_analysis.py`	software	healthy	`chapters/chapter2/archive/scripts/sensitivity_analysis.py`
`deep_hog_analysis.py`	software	healthy	`chapters/chapter2/archive/scripts/deep_hog_analysis.py`
`generate_comparison_report.py`	software	healthy	`chapters/chapter2/archive/scripts/generate_comparison_repor…`
`esm2_taxonomy_bias.md`	software	healthy	`chapters/chapter2/archive/analysis/esm2_taxonomy_bias.md`
`formal_metrics_and_semantics.md`	software	healthy	`chapters/chapter2/archive/analysis/formal_metrics_and_seman…`
`CORRECTED_ANALYSIS_README.md`	software	healthy	`chapters/chapter2/archive/analysis/CORRECTED_ANALYSIS_READM…`
`CORRECTED_ANALYSIS_GUIDE.md`	software	healthy	`chapters/chapter2/archive/analysis/CORRECTED_ANALYSIS_GUIDE…`
`umap_stability_summary.json`	software	healthy	`chapters/chapter2/archive/analysis/umap_stability_summary.j…`
`README.md`	software	healthy	`chapters/chapter2/archive/analysis/README.md`
`CRITICAL_REVIEW.md`	software	healthy	`chapters/chapter2/archive/analysis/CRITICAL_REVIEW.md`
`CORRECTED_FINDINGS_SUMMARY.md`	software	healthy	`chapters/chapter2/archive/analysis/CORRECTED_FINDINGS_SUMMA…`
`IMPLEMENTATION_COMPLETE.md`	software	healthy	`chapters/chapter2/archive/analysis/IMPLEMENTATION_COMPLETE.…`
`comparison_report.md`	software	healthy	`chapters/chapter2/archive/analysis/comparison_report/compar…`
`sensitivity_results.json`	software	healthy	`chapters/chapter2/archive/analysis/sensitivity_analysis/sen…`

Showing first 50 of this kind. Full payload available via the JSON button at the top of the page.

Label	Layer	Status	Path
`.github`	software	healthy	`.github`
`workflows`	software	healthy	`.github/workflows`
`chapters`	software	healthy	`chapters`
`chapter2`	software	healthy	`chapters/chapter2`
`archive`	software	healthy	`chapters/chapter2/archive`
`scripts`	software	healthy	`chapters/chapter2/archive/scripts`
`analysis`	software	healthy	`chapters/chapter2/archive/analysis`
`comparison_report`	software	healthy	`chapters/chapter2/archive/analysis/comparison_report`
`sensitivity_analysis`	software	healthy	`chapters/chapter2/archive/analysis/sensitivity_analysis`
`sensitivity_analysis_corrected`	software	healthy	`chapters/chapter2/archive/analysis/sensitivity_analysis_cor…`
`hog_analysis`	software	healthy	`chapters/chapter2/archive/analysis/hog_analysis`
`deep_hog_analysis`	software	healthy	`chapters/chapter2/archive/analysis/deep_hog_analysis`
`results`	software	healthy	`chapters/chapter2/results`
`whitening`	software	healthy	`chapters/chapter2/results/whitening`
`lab`	software	healthy	`chapters/chapter2/lab`
`006_subtree_depth_sweep`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep`
`figures`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures`
`650m`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/650m`
`seed_42`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/650m/…`
`level_3`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/650m/…`
`level_2`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/650m/…`
`level_1`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/650m/…`
`150m`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m`
`seed_789`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`level_3`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`level_2`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`level_1`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`seed_123`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`level_3`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`level_2`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`level_1`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`seed_456`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`level_3`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`level_2`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`level_1`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`seed_42`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`level_3`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`level_2`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`level_1`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/150m/…`
`3b`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/3b`
`seed_789`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/3b/se…`
`level_3`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/3b/se…`
`level_2`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/3b/se…`
`level_1`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/3b/se…`
`seed_123`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/3b/se…`
`level_3`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/3b/se…`
`level_2`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/3b/se…`
`level_1`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/3b/se…`
`seed_456`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/3b/se…`
`level_3`	software	healthy	`chapters/chapter2/lab/006_subtree_depth_sweep/figures/3b/se…`

Showing first 50 of this kind. Full payload available via the JSON button at the top of the page.

Label	Layer	Status	Path
`GOPredictor`	software	healthy	`chapters/chapter2/05_go_prediction.py:55`
`GOPredictor`	software	healthy	`chapters/chapter2/06_go_grid_search.py:49`
`TimingStats`	software	healthy	`chapters/chapter2/01_compute_embeddings.py:39`
`TimingStats`	software	healthy	`chapters/chapter2/archive/compute_embeddings.py:25`

Label	Layer	Status	Path
`port:010`	network	healthy	`chapters/chapter2/run_200epoch_sweep.sh`
`port:200`	network	healthy	`chapters/chapter2/run_200epoch_sweep.sh`
`port:011`	network	healthy	`chapters/chapter2/run_60epoch_scaled_lr.sh`
`port:60`	network	healthy	`chapters/chapter2/run_60epoch_scaled_lr.sh`

Label	Layer	Status	Path
`100.125.228.82`	network	healthy	`chapters/chapter2/lab/010_divergence/upload_to_remarkable.sh`
`127.0.0.1`	network	healthy	`infra/github-runner/docker-compose.yml`
`169.254.169.254`	network	healthy	`projects/caffeine/lab/001_adora_expression/fetch_adora_cach…`

Label	Layer	Status	Path
`image::infra/github-runner/Dockerfile`	hardware	healthy	`infra/github-runner/Dockerfile`
`github-egress-proxy`	hardware	healthy	`infra/github-runner/docker-compose.yml`
`runner`	hardware	healthy	`infra/github-runner/docker-compose.yml`

Label	Layer	Status	Path
`vps::aws`	hardware	healthy	`projects/caffeine/lab/001_adora_expression/fetch_adora_cach…`
`vps::ec2`	hardware	healthy	`projects/caffeine/lab/001_adora_expression/fetch_adora_cach…`

Label	Layer	Status	Path
`acefesan__dl-bio`	software	healthy	`/data/fable5_failed_archive/acefesan__dl-bio`

Label	Layer	Status	Path
`gpu (detected)`	hardware	healthy	`chapters/chapter2/04_pretrain_esm2.py`

Label	Layer	Status	Path
`gha::hygiene`	cicd	healthy	`.github/workflows/hygiene.yml`

Label	Layer	Status	Path
`hygiene`	cicd	healthy	`.github/workflows/hygiene.yml`

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acefesan/dl-bio

Complete repo analysis

function 50+

file 50+

directory 50+

class 4

port 4

service 3

container 3

vps 2

repo 1

gpu 1

pipeline 1

job 1