Examples
Interactive TMAP visualizations across chemistry, biology, and machine learning.
EGFR Kinase Inhibitors - SAR Navigation
Structure-activity relationships for 10,466 EGFR kinase inhibitors from ChEMBL (CHEMBL203). 677 activity cliffs detected, SAR continuity score 0.88.
Protein Fold Space - SCOPe ASTRAL 40%
15,177 protein domains across 1,257 folds from SCOPe ASTRAL 40%. Cross-class boundary edges: 19.1%. Mean subtree purity: 0.88.
Protein Function 3D - EC Class Map
35,000 proteins organized by embedding similarity. Color by EC class or phylum, search UniProt accessions, and open AlphaFold-backed 3D structure cards.
Oxford Pets - Breed Classifier Audit
3,669 images, 37 breeds, 90.4% linear probe accuracy. 302 boundary edges (8.2%) reveal confused breed pairs. Traces failure paths from misclassified to correct predictions.
MNIST Digits - Cosine Metric
70,000 handwritten digits (784D pixel vectors) with cosine metric. Trace paths between morphologically similar digits: 3 to 8, 4 to 9, 7 to 1.
Enamine Chemical Cluster - Molecular Properties
~6,000 molecules from Enamine cluster 65053. Multiple color layers: MW, LogP, ring count, QED, Murcko scaffolds. Demonstrates filtering and search panels.
Fashion-MNIST - Category Confusion Analysis
70,000 clothing items (784D) with cosine metric and image tooltips. 14.3% boundary edges. Top confused: Shirt vs T-shirt (1,844 edges), Coat vs Pullover (1,584 edges).
PBMC 3k - Single-Cell RNA-seq
2,638 peripheral blood cells, 8 cell types, euclidean metric on PCA. 5.8% boundary edges, subtree purity 0.88. Pseudotime and gene marker color layers.
Tox21 - Multi-Endpoint Toxicity
7,831 compounds screened across 12 toxicity endpoints. Each endpoint is a filterable color layer: toggle between NR-AR, NR-AhR, SR-MMP, SR-p53, and 8 more.
Approved Drugs - ATC Classification
3,039 approved drugs from ChEMBL (phase 4), filtered to MW >= 100. Colored by ATC therapeutic class. 62.8% boundary edges, subtree purity 0.47. SMILES tooltips, drug names.
COCONUT - Natural Products
25,000 natural products from the COCONUT database (738k total). NP classifier pathways (Terpenoids, Alkaloids, Shikimates, Polyketides, Fatty acids). 15.5% pathway boundary edges, subtree purity 0.76.
ESM-2 Protein Embeddings - Sequence Families
3,164 protein sequences embedded with ESM-2 (650M parameter model), cosine metric. Colored by protein family and sequence length.
ESM Atlas - Metagenomic Protein Universe
50,000 metagenomic proteins from the ESM Atlas, embedded with ESMC-600M and folded with ESMFold2. Two maps - raw 1,152-d embeddings and 16,384-d sparse-autoencoder features - with click-to-view predicted 3D structures.