Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction
bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF · Preprint
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Results
Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.
Models, benchmarks and other records
Models (4)
Methods (2)
Configurations (23)
- DeepDTA with 1D conv. protein and 1D conv. drug representation
- DeepGraphDTA with 1D conv. (8) protein and GAT-GCN drug representation
- DeepGraphDTA with 1D conv. (8) protein and GCN drug representation
- DeepGraphDTA with 1D conv. (16) protein and GAT drug representation
- DeepGraphDTA with 1D conv. (16) protein and GCN drug representation
- DeepGraphDTA with 1D conv. (16) protein and GIN drug representation
- DeepGraphDTA with 1D conv. (24) protein and GAT drug representation
- DeepGraphDTA with 1D conv. (32) protein and GAT-GCN drug representation
- DeepGraphDTA with 1D conv. (32) protein and GIN drug representation
- GraphDTA with 1D conv. protein and GAT drug representation
- GraphDTA with 1D conv. protein and GAT-GCN drug representation
- GraphDTA with 1D conv. protein and GCN drug representation
- GraphDTA with 1D conv. protein and GIN drug representation
- KronRLS with Similarity vector protein and Similarity vector drug representation
- PGraphDTA with ESM2 650M protein and GAT drug representation
- PLM-GraphDTA with ESMC 600M protein and GAT drug representation
- PLM-GraphDTA with ESMC 600M protein and GAT-GCN drug representation
- PLM-GraphDTA with ESMC 600M protein and GCN drug representation
- PLM-GraphDTA with ESMC 600M protein and GIN drug representation
- PLM-GraphDTA with ProstT5 protein and GAT drug representation
- PLM-GraphDTA with ProstT5 protein and GAT-GCN drug representation
- PLM-GraphDTA with ProstT5 protein and GCN drug representation
- SimBoost with Similarity features protein and Similarity features drug representation
Benchmarks (1)
Protocols (2)
Datasets (2)
Evaluations (32)
- DeepDTA (1D conv.; 1D conv.) on Davis
- DeepDTA (1D conv.; 1D conv.) on KIBA
- DeepGraphDTA (1D conv. (8); GAT-GCN) on Davis
- DeepGraphDTA (1D conv. (8); GCN) on KIBA
- DeepGraphDTA (1D conv. (16); GAT) on Davis
- DeepGraphDTA (1D conv. (16); GCN) on Davis
- DeepGraphDTA (1D conv. (16); GIN) on KIBA
- DeepGraphDTA (1D conv. (24); GAT) on KIBA
- DeepGraphDTA (1D conv. (32); GAT-GCN) on KIBA
- DeepGraphDTA (1D conv. (32); GIN) on Davis
- GraphDTA (1D conv.; GAT-GCN) on Davis
- GraphDTA (1D conv.; GAT-GCN) on KIBA
- GraphDTA (1D conv.; GAT) on Davis
- GraphDTA (1D conv.; GAT) on KIBA
- GraphDTA (1D conv.; GCN) on Davis
- GraphDTA (1D conv.; GCN) on KIBA
- GraphDTA (1D conv.; GIN) on Davis
- GraphDTA (1D conv.; GIN) on KIBA
- KronRLS (Similarity vector; Similarity vector) on Davis
- KronRLS (Similarity vector; Similarity vector) on KIBA
- PGraphDTA (ESM2 650M; GAT) on Davis
- PGraphDTA (ESM2 650M; GAT) on KIBA
- PLM-GraphDTA (ESMC 600M; GAT-GCN) on Davis
- PLM-GraphDTA (ESMC 600M; GAT) on Davis
- PLM-GraphDTA (ESMC 600M; GCN) on Davis
Evidence
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Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
25 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.artifact_sha256 11b88d5ab2964b581430454d0d9e7848739819d52ec2e338e2a6412cbd259163 Source metadata | Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction No field-specific location recorded Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF | catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Artifact url https://www.biorxiv.org/content/10.64898/2026.08.31.748056v1.full.pdf Source metadata | Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction No field-specific location recorded Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF | catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Code url https://github.com/matija-marijan/PLM-GraphDTA Source metadata | Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction No field-specific location recorded Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF | catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Doi 10.64898/2026.08.31.748056 Source metadata | Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction No field-specific location recorded Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF | catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Evidence concerns1 values
| Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction No field-specific location recorded Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF | catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Licence CC-BY-NC-4.0 Source metadata | Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction No field-specific location recorded Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF | catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Limitations5 values
| Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction No field-specific location recorded Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF | catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Media type application/pdf Source metadata | Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction No field-specific location recorded Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF | catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Publication status preprint Source metadata | Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction No field-specific location recorded Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF | catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Retrieved at 2026-10-11T21:27:40Z Source metadata | Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction No field-specific location recorded Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF | catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Primary source retrieved and hashed for the 2026-10-11 microbial and interactions literature pass.
Technical metadata and extraction receipts
Stable ID: lit-interactions-20261011-plmdta-source-marijan2026
- areas
- molecular-interactions
- contexts
- research
- url
- https://doi.org/10.64898/2026.08.31.748056
- artifact url
- https://www.biorxiv.org/content/10.64898/2026.08.31.748056v1.full.pdf
- version
- bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF
- retrieved at
- 2026-10-11T21:27:40Z
- artifact sha256
- 11b88d5ab2964b581430454d0d9e7848739819d52ec2e338e2a6412cbd259163
- doi
- 10.64898/2026.08.31.748056
- publication status
- preprint
- licence
- CC-BY-NC-4.0
- media type
- application/pdf
- code url
- https://github.com/matija-marijan/PLM-GraphDTA
- limitations
- bioRxiv adds a per-request banner, so the PDF hash describes this one retrieval.; Values were read from the pdftotext (poppler 26.08.0) layout text layer, SHA-256 e9b9dff90c731fe69f34a8649daf95d4f69449b1b8143da9ea7c72af4e11edd4. The PDF is not archived in the repository.; Tables 2 and 3 print one PLM per drug backbone (the 5-fold CV winner); the per-PLM comparison (ESM2 8M/150M/650M, ESMC 300M/600M, DeepFRI, ProstT5) is in Appendix D figures and was not read.; Cold-start results (Figures 4 and 5) are figures only and were not read.; Italic and bold marking of best values is not carried by the text layer.
- evidence concerns
- source id: lit-interactions-20261011-plmdta-source-marijan2026; message: Table 3 KIBA rows KronRLS, SimBoost and DeepDTA equal the values printed in Ozturk et al. 2018, while the proposed models are 5-seed means; the rows may not share a training run or protocol. Do not compare these three rows against the proposed models automatically.; source locator: Table 3, rows KronRLS, SimBoost, DeepDTA; artifact sha256: 11b88d5ab2964b581430454d0d9e7848739819d52ec2e338e2a6412cbd259163; reviewed at: 2026-10-11T00:00:00Z; review method: ai-assisted-source-review
- review
- method: source-hash-verification; method note: PDF re-downloaded; the per-request bioRxiv banner changes the PDF hash, so the pdftotext -layout text layer was rehashed instead and matches the recorded text-layer hash.; reviewer: claude; reviewer note: Claude review agent reviewer-mi-2, independent of the extractor lit-microbial-interactions; no human review claimed; date: 2026-10-11