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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

DOI: 10.64898/2026.08.31.748056

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Records in this release that cite this source. A record can cite several sources.

Results

Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.

ValueMetricModel or configurationDatasetEvaluation
0.902 unitlessConcordance index (Davis DeepDTA holdout fold)DeepDTA with 1D conv. protein and 1D conv. drug representationDavis holdout test fold (DeepDTA split)DeepDTA (1D conv.; 1D conv.) on Davis
0.224 unit-unreportedMSE (Davis DeepDTA holdout fold)DeepDTA with 1D conv. protein and 1D conv. drug representationDavis holdout test fold (DeepDTA split)DeepDTA (1D conv.; 1D conv.) on Davis
0.863 unitlessConcordance index (KIBA DeepDTA holdout fold)DeepDTA with 1D conv. protein and 1D conv. drug representationKIBA holdout test fold (DeepDTA split)DeepDTA (1D conv.; 1D conv.) on KIBA
0.194 unit-unreportedMSE (KIBA DeepDTA holdout fold)DeepDTA with 1D conv. protein and 1D conv. drug representationKIBA holdout test fold (DeepDTA split)DeepDTA (1D conv.; 1D conv.) on KIBA
0.906 unitlessConcordance index (Davis DeepDTA holdout fold)DeepGraphDTA with 1D conv. (8) protein and GAT-GCN drug representationDavis holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (8); GAT-GCN) on Davis
0.175 unit-unreportedMSE (Davis DeepDTA holdout fold)DeepGraphDTA with 1D conv. (8) protein and GAT-GCN drug representationDavis holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (8); GAT-GCN) on Davis
0.901 unitlessConcordance index (KIBA DeepDTA holdout fold)DeepGraphDTA with 1D conv. (8) protein and GCN drug representationKIBA holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (8); GCN) on KIBA
0.128 unit-unreportedMSE (KIBA DeepDTA holdout fold)DeepGraphDTA with 1D conv. (8) protein and GCN drug representationKIBA holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (8); GCN) on KIBA
0.907 unitlessConcordance index (Davis DeepDTA holdout fold)DeepGraphDTA with 1D conv. (16) protein and GAT drug representationDavis holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (16); GAT) on Davis
0.176 unit-unreportedMSE (Davis DeepDTA holdout fold)DeepGraphDTA with 1D conv. (16) protein and GAT drug representationDavis holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (16); GAT) on Davis
0.906 unitlessConcordance index (Davis DeepDTA holdout fold)DeepGraphDTA with 1D conv. (16) protein and GCN drug representationDavis holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (16); GCN) on Davis
0.174 unit-unreportedMSE (Davis DeepDTA holdout fold)DeepGraphDTA with 1D conv. (16) protein and GCN drug representationDavis holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (16); GCN) on Davis
0.888 unitlessConcordance index (KIBA DeepDTA holdout fold)DeepGraphDTA with 1D conv. (16) protein and GIN drug representationKIBA holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (16); GIN) on KIBA
0.145 unit-unreportedMSE (KIBA DeepDTA holdout fold)DeepGraphDTA with 1D conv. (16) protein and GIN drug representationKIBA holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (16); GIN) on KIBA
0.872 unitlessConcordance index (KIBA DeepDTA holdout fold)DeepGraphDTA with 1D conv. (24) protein and GAT drug representationKIBA holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (24); GAT) on KIBA
0.173 unit-unreportedMSE (KIBA DeepDTA holdout fold)DeepGraphDTA with 1D conv. (24) protein and GAT drug representationKIBA holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (24); GAT) on KIBA
0.903 unitlessConcordance index (KIBA DeepDTA holdout fold)DeepGraphDTA with 1D conv. (32) protein and GAT-GCN drug representationKIBA holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (32); GAT-GCN) on KIBA
0.125 unit-unreportedMSE (KIBA DeepDTA holdout fold)DeepGraphDTA with 1D conv. (32) protein and GAT-GCN drug representationKIBA holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (32); GAT-GCN) on KIBA
0.909 unitlessConcordance index (Davis DeepDTA holdout fold)DeepGraphDTA with 1D conv. (32) protein and GIN drug representationDavis holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (32); GIN) on Davis
0.172 unit-unreportedMSE (Davis DeepDTA holdout fold)DeepGraphDTA with 1D conv. (32) protein and GIN drug representationDavis holdout test fold (DeepDTA split)DeepGraphDTA (1D conv. (32); GIN) on Davis
0.889 unitlessConcordance index (Davis DeepDTA holdout fold)GraphDTA with 1D conv. protein and GAT-GCN drug representationDavis holdout test fold (DeepDTA split)GraphDTA (1D conv.; GAT-GCN) on Davis
0.227 unit-unreportedMSE (Davis DeepDTA holdout fold)GraphDTA with 1D conv. protein and GAT-GCN drug representationDavis holdout test fold (DeepDTA split)GraphDTA (1D conv.; GAT-GCN) on Davis
0.890 unitlessConcordance index (KIBA DeepDTA holdout fold)GraphDTA with 1D conv. protein and GAT-GCN drug representationKIBA holdout test fold (DeepDTA split)GraphDTA (1D conv.; GAT-GCN) on KIBA
0.145 unit-unreportedMSE (KIBA DeepDTA holdout fold)GraphDTA with 1D conv. protein and GAT-GCN drug representationKIBA holdout test fold (DeepDTA split)GraphDTA (1D conv.; GAT-GCN) on KIBA
0.893 unitlessConcordance index (Davis DeepDTA holdout fold)GraphDTA with 1D conv. protein and GAT drug representationDavis holdout test fold (DeepDTA split)GraphDTA (1D conv.; GAT) on Davis
0.255 unit-unreportedMSE (Davis DeepDTA holdout fold)GraphDTA with 1D conv. protein and GAT drug representationDavis holdout test fold (DeepDTA split)GraphDTA (1D conv.; GAT) on Davis
0.866 unitlessConcordance index (KIBA DeepDTA holdout fold)GraphDTA with 1D conv. protein and GAT drug representationKIBA holdout test fold (DeepDTA split)GraphDTA (1D conv.; GAT) on KIBA
0.178 unit-unreportedMSE (KIBA DeepDTA holdout fold)GraphDTA with 1D conv. protein and GAT drug representationKIBA holdout test fold (DeepDTA split)GraphDTA (1D conv.; GAT) on KIBA
0.880 unitlessConcordance index (Davis DeepDTA holdout fold)GraphDTA with 1D conv. protein and GCN drug representationDavis holdout test fold (DeepDTA split)GraphDTA (1D conv.; GCN) on Davis
0.237 unit-unreportedMSE (Davis DeepDTA holdout fold)GraphDTA with 1D conv. protein and GCN drug representationDavis holdout test fold (DeepDTA split)GraphDTA (1D conv.; GCN) on Davis
0.892 unitlessConcordance index (KIBA DeepDTA holdout fold)GraphDTA with 1D conv. protein and GCN drug representationKIBA holdout test fold (DeepDTA split)GraphDTA (1D conv.; GCN) on KIBA
0.144 unit-unreportedMSE (KIBA DeepDTA holdout fold)GraphDTA with 1D conv. protein and GCN drug representationKIBA holdout test fold (DeepDTA split)GraphDTA (1D conv.; GCN) on KIBA
0.897 unitlessConcordance index (Davis DeepDTA holdout fold)GraphDTA with 1D conv. protein and GIN drug representationDavis holdout test fold (DeepDTA split)GraphDTA (1D conv.; GIN) on Davis
0.199 unit-unreportedMSE (Davis DeepDTA holdout fold)GraphDTA with 1D conv. protein and GIN drug representationDavis holdout test fold (DeepDTA split)GraphDTA (1D conv.; GIN) on Davis
0.884 unitlessConcordance index (KIBA DeepDTA holdout fold)GraphDTA with 1D conv. protein and GIN drug representationKIBA holdout test fold (DeepDTA split)GraphDTA (1D conv.; GIN) on KIBA
0.149 unit-unreportedMSE (KIBA DeepDTA holdout fold)GraphDTA with 1D conv. protein and GIN drug representationKIBA holdout test fold (DeepDTA split)GraphDTA (1D conv.; GIN) on KIBA
0.870 unitlessConcordance index (Davis DeepDTA holdout fold)KronRLS with Similarity vector protein and Similarity vector drug representationDavis holdout test fold (DeepDTA split)KronRLS (Similarity vector; Similarity vector) on Davis
0.359 unit-unreportedMSE (Davis DeepDTA holdout fold)KronRLS with Similarity vector protein and Similarity vector drug representationDavis holdout test fold (DeepDTA split)KronRLS (Similarity vector; Similarity vector) on Davis
0.782 unitlessConcordance index (KIBA DeepDTA holdout fold)KronRLS with Similarity vector protein and Similarity vector drug representationKIBA holdout test fold (DeepDTA split)KronRLS (Similarity vector; Similarity vector) on KIBA
0.411 unit-unreportedMSE (KIBA DeepDTA holdout fold)KronRLS with Similarity vector protein and Similarity vector drug representationKIBA holdout test fold (DeepDTA split)KronRLS (Similarity vector; Similarity vector) on KIBA
0.898 unitlessConcordance index (Davis DeepDTA holdout fold)PGraphDTA with ESM2 650M protein and GAT drug representationDavis holdout test fold (DeepDTA split)PGraphDTA (ESM2 650M; GAT) on Davis
0.206 unit-unreportedMSE (Davis DeepDTA holdout fold)PGraphDTA with ESM2 650M protein and GAT drug representationDavis holdout test fold (DeepDTA split)PGraphDTA (ESM2 650M; GAT) on Davis
0.872 unitlessConcordance index (KIBA DeepDTA holdout fold)PGraphDTA with ESM2 650M protein and GAT drug representationKIBA holdout test fold (DeepDTA split)PGraphDTA (ESM2 650M; GAT) on KIBA
0.160 unit-unreportedMSE (KIBA DeepDTA holdout fold)PGraphDTA with ESM2 650M protein and GAT drug representationKIBA holdout test fold (DeepDTA split)PGraphDTA (ESM2 650M; GAT) on KIBA
0.910 unitlessConcordance index (Davis DeepDTA holdout fold)PLM-GraphDTA with ESMC 600M protein and GAT-GCN drug representationDavis holdout test fold (DeepDTA split)PLM-GraphDTA (ESMC 600M; GAT-GCN) on Davis
0.169 unit-unreportedMSE (Davis DeepDTA holdout fold)PLM-GraphDTA with ESMC 600M protein and GAT-GCN drug representationDavis holdout test fold (DeepDTA split)PLM-GraphDTA (ESMC 600M; GAT-GCN) on Davis
0.908 unitlessConcordance index (Davis DeepDTA holdout fold)PLM-GraphDTA with ESMC 600M protein and GAT drug representationDavis holdout test fold (DeepDTA split)PLM-GraphDTA (ESMC 600M; GAT) on Davis
0.174 unit-unreportedMSE (Davis DeepDTA holdout fold)PLM-GraphDTA with ESMC 600M protein and GAT drug representationDavis holdout test fold (DeepDTA split)PLM-GraphDTA (ESMC 600M; GAT) on Davis
0.906 unitlessConcordance index (Davis DeepDTA holdout fold)PLM-GraphDTA with ESMC 600M protein and GCN drug representationDavis holdout test fold (DeepDTA split)PLM-GraphDTA (ESMC 600M; GCN) on Davis
0.167 unit-unreportedMSE (Davis DeepDTA holdout fold)PLM-GraphDTA with ESMC 600M protein and GCN drug representationDavis holdout test fold (DeepDTA split)PLM-GraphDTA (ESMC 600M; GCN) on Davis

Models, benchmarks and other records

Models (4)

Methods (2)

Configurations (23)

Benchmarks (1)

Protocols (2)

Datasets (2)

Evaluations (32)

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25 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
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attributes.artifact_sha256
11b88d5ab2964b581430454d0d9e7848739819d52ec2e338e2a6412cbd259163
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Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction

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Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF
Retrieved: 2026-10-11T21:27:40Z

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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

Original source ↗

No field-specific location recorded

Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF
Retrieved: 2026-10-11T21:27:40Z

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Code url
https://github.com/matija-marijan/PLM-GraphDTA
Source metadata
Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction

Original source ↗

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Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF
Retrieved: 2026-10-11T21:27:40Z

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10.64898/2026.08.31.748056
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Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction

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Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF
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1 values
  • 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
Source metadata
Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction

Original source ↗

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Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF
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CC-BY-NC-4.0
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Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction

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Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF
Retrieved: 2026-10-11T21:27:40Z

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Limitations
5 values
  • 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.
Source metadata
Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction

Original source ↗

No field-specific location recorded

Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF
Retrieved: 2026-10-11T21:27:40Z

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Media type
application/pdf
Source metadata
Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction

Original source ↗

No field-specific location recorded

Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF
Retrieved: 2026-10-11T21:27:40Z

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Publication status
preprint
Source metadata
Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction

Original source ↗

No field-specific location recorded

Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF
Retrieved: 2026-10-11T21:27:40Z

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Retrieved at
2026-10-11T21:27:40Z
Source metadata
Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction

Original source ↗

No field-specific location recorded

Version: bioRxiv 10.64898/2026.08.31.748056v1 (posted 2026-09-03); 24-page PDF
Retrieved: 2026-10-11T21:27:40Z

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

Primary source retrieved and hashed for the 2026-10-11 microbial and interactions literature pass.

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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
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