Datasets:
Formats:
parquet
Languages:
English
Size:
10M - 100M
Tags:
biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
License:
| % ===== Negative Results & Publication Bias ===== | |
| @article{fanelli2012negative, | |
| title={Negative results are disappearing from most disciplines and countries}, | |
| author={Fanelli, Daniele}, | |
| journal={Scientometrics}, | |
| volume={90}, | |
| number={3}, | |
| pages={891--904}, | |
| year={2012}, | |
| publisher={Springer} | |
| } | |
| @article{mlinaric2017dealing, | |
| title={Dealing with the positive publication bias: Why you should really publish your negative results}, | |
| author={Mlinaric, Ana and Horvat, Martina and Smolcic, Vesna Supak}, | |
| journal={Biochemia medica}, | |
| volume={27}, | |
| number={3}, | |
| pages={030201}, | |
| year={2017} | |
| } | |
| % ===== DTI Benchmarks & Databases ===== | |
| @article{gaulton2017chembl, | |
| title={{ChEMBL}: a large-scale bioactivity database for drug discovery}, | |
| author={Gaulton, Anna and Hersey, Anne and Nowotka, Micha{\l} and Bento, A Patr{\'\i}cia and Chambers, Jon and Mendez, David and Mutowo, Prudence and Atkinson, Francis and Bellis, Louisa J and Cibri{\'a}n-Uhalte, Elena and others}, | |
| journal={Nucleic Acids Research}, | |
| volume={45}, | |
| number={D1}, | |
| pages={D986--D994}, | |
| year={2017}, | |
| publisher={Oxford University Press} | |
| } | |
| @article{kim2023pubchem, | |
| title={{PubChem} 2023 update}, | |
| author={Kim, Sunghwan and Chen, Jie and Cheng, Tiejun and Gindulyte, Asta and He, Jia and He, Siqian and Li, Qingliang and Shoemaker, Benjamin A and Thiessen, Paul A and Yu, Bo and others}, | |
| journal={Nucleic Acids Research}, | |
| volume={51}, | |
| number={D1}, | |
| pages={D1373--D1380}, | |
| year={2023}, | |
| publisher={Oxford University Press} | |
| } | |
| @article{gilson2016bindingdb, | |
| title={{BindingDB} in 2015: a public database for medicinal chemistry, computational chemistry and systems pharmacology}, | |
| author={Gilson, Michael K and Liu, Tiqing and Baitaluk, Michael and Nicola, George and Hwang, Linda and Chong, Jenny}, | |
| journal={Nucleic Acids Research}, | |
| volume={44}, | |
| number={D1}, | |
| pages={D1045--D1053}, | |
| year={2016}, | |
| publisher={Oxford University Press} | |
| } | |
| @article{davis2011comprehensive, | |
| title={Comprehensive analysis of kinase inhibitor selectivity}, | |
| author={Davis, Mindy I and Hunt, Jeremy P and Herrgard, Sune and Ciceri, Pietro and Wodicka, Lisa M and Pallares, Gabriel and Hocker, Michael and Treiber, Daniel K and Zarrinkar, Patrick P}, | |
| journal={Nature Biotechnology}, | |
| volume={29}, | |
| number={11}, | |
| pages={1046--1051}, | |
| year={2011}, | |
| publisher={Nature Publishing Group} | |
| } | |
| @article{huang2021therapeutics, | |
| title={Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development}, | |
| author={Huang, Kexin and Fu, Tianfan and Gao, Wenhao and Zhao, Yue and Roohani, Yusuf and Leskovec, Jure and Coley, Connor W and Xiao, Cao and Sun, Jimeng and Zitnik, Marinka}, | |
| journal={Proceedings of NeurIPS Datasets and Benchmarks}, | |
| year={2021} | |
| } | |
| @article{mysinger2012dude, | |
| title={Directory of useful decoys, enhanced ({DUD-E}): better ligands and decoys for better benchmarking}, | |
| author={Mysinger, Michael M and Carchia, Michael and Irwin, John J and Shoichet, Brian K}, | |
| journal={Journal of Medicinal Chemistry}, | |
| volume={55}, | |
| number={14}, | |
| pages={6582--6594}, | |
| year={2012}, | |
| publisher={ACS Publications} | |
| } | |
| @article{wu2018moleculenet, | |
| title={{MoleculeNet}: a benchmark for molecular machine learning}, | |
| author={Wu, Zhenqin and Ramsundar, Bharath and Feinberg, Evan N and Gomes, Joseph and Geniesse, Caleb and Pappu, Aneesh S and Leswing, Karl and Pande, Vijay}, | |
| journal={Chemical Science}, | |
| volume={9}, | |
| number={2}, | |
| pages={513--530}, | |
| year={2018}, | |
| publisher={Royal Society of Chemistry} | |
| } | |
| @article{tran2020litpcba, | |
| title={Lit-{PCBA}: An unbiased data set for machine learning and virtual screening}, | |
| author={Tran-Nguyen, Viet-Khoa and Jacquemard, Christophe and Rognan, Didier}, | |
| journal={Journal of Chemical Information and Modeling}, | |
| volume={60}, | |
| number={9}, | |
| pages={4263--4273}, | |
| year={2020}, | |
| publisher={ACS Publications} | |
| } | |
| @article{li2025evidti, | |
| title={Negative is positive: on the role of negative evidence in drug-target interaction prediction}, | |
| author={Li, Jianmin and others}, | |
| journal={Briefings in Bioinformatics}, | |
| year={2025}, | |
| note={To appear} | |
| } | |
| @inproceedings{volkov2025welqrate, | |
| title={{WelQrate}: Defining the gold standard in small molecule drug discovery benchmarking}, | |
| author={Volkov, Maxim and Fl{\"o}ge, Joseph and Stolte, Markus and others}, | |
| booktitle={Advances in Neural Information Processing Systems}, | |
| year={2025} | |
| } | |
| % ===== DTI Models ===== | |
| @article{ozturk2018deepdta, | |
| title={{DeepDTA}: deep drug--target binding affinity prediction}, | |
| author={{\"O}zt{\"u}rk, Hakime and {\"O}zg{\"u}r, Arzucan and Ozkirimli, Elif}, | |
| journal={Bioinformatics}, | |
| volume={34}, | |
| number={17}, | |
| pages={i821--i829}, | |
| year={2018}, | |
| publisher={Oxford University Press} | |
| } | |
| @article{nguyen2021graphdta, | |
| title={{GraphDTA}: predicting drug--target binding affinity with graph neural networks}, | |
| author={Nguyen, Thin and Le, Hang and Quinn, Thomas P and Nguyen, Tri and Le, Thuc Duy and Venkatesh, Svetha}, | |
| journal={Bioinformatics}, | |
| volume={37}, | |
| number={8}, | |
| pages={1140--1147}, | |
| year={2021}, | |
| publisher={Oxford University Press} | |
| } | |
| @article{bai2023drugban, | |
| title={Interpretable bilinear attention network with domain adaptation improves drug--target prediction}, | |
| author={Bai, Peizhen and Miljkovi{\'c}, Filip and John, Bino and Lu, Haiping}, | |
| journal={Nature Machine Intelligence}, | |
| volume={5}, | |
| number={2}, | |
| pages={126--136}, | |
| year={2023}, | |
| publisher={Nature Publishing Group} | |
| } | |
| % ===== Clinical Trial Databases ===== | |
| @article{tasneem2012aact, | |
| title={The database for aggregate analysis of {ClinicalTrials.gov} ({AACT}) and subsequent regrouping by clinical specialty}, | |
| author={Tasneem, Asba and Aberle, Laura and Ananber, Hari and Chakraborty, Swati and Chiswell, Karen and McCourt, Brian J and Pietrobon, Ricardo}, | |
| journal={PLoS ONE}, | |
| volume={7}, | |
| number={3}, | |
| pages={e33677}, | |
| year={2012} | |
| } | |
| @article{fu2022hint, | |
| title={{HINT}: Hierarchical interaction network for clinical trial outcome prediction}, | |
| author={Fu, Tianfan and Huang, Kexin and Xiao, Cao and Glass, Lucas M and Sun, Jimeng}, | |
| journal={Patterns}, | |
| volume={3}, | |
| number={4}, | |
| pages={100445}, | |
| year={2022}, | |
| publisher={Elsevier} | |
| } | |
| @article{siah2021cto, | |
| title={Predicting drug approvals: the {Novartis} data science and artificial intelligence challenge}, | |
| author={Siah, Kien Wei and Kelley, Nicholas W and Engstrom, Steinar and Abi Jaoude, Joseph and Cook, Andrew R and Lo, Andrew W}, | |
| journal={Patterns}, | |
| volume={2}, | |
| number={8}, | |
| pages={100312}, | |
| year={2021}, | |
| publisher={Elsevier} | |
| } | |
| @article{shi2024safety, | |
| title={Safety and efficacy outcomes in clinical trials with negative results}, | |
| author={Shi, Yu and Du, Jingcheng}, | |
| journal={Drug Safety}, | |
| year={2024}, | |
| publisher={Springer} | |
| } | |
| @misc{opentargets2024, | |
| title={Open Targets Platform}, | |
| author={{Open Targets Consortium}}, | |
| year={2024}, | |
| howpublished={\url{https://platform.opentargets.org/}} | |
| } | |
| % ===== PPI Databases ===== | |
| @article{luck2020huri, | |
| title={A reference map of the human binary protein interactome}, | |
| author={Luck, Katja and Kim, Dae-Kyum and Lambourne, Luke and Spirohn, Kerstin and Begg, Bridget E and Bian, Wenting and Brber, Ruth and Bridges, Nora and Cho, Sohyun and others}, | |
| journal={Nature}, | |
| volume={580}, | |
| number={7803}, | |
| pages={402--408}, | |
| year={2020}, | |
| publisher={Nature Publishing Group} | |
| } | |
| @article{orchard2014intact, | |
| title={The {MIntAct} project---{IntAct} as a common curation platform for 11 molecular interaction databases}, | |
| author={Orchard, Sandra and Ammari, Mais and Aranda, Bruno and Breuza, Lionel and Briganti, Leonardo and Broackes-Carter, Fiona and others}, | |
| journal={Nucleic Acids Research}, | |
| volume={42}, | |
| number={D1}, | |
| pages={D358--D363}, | |
| year={2014}, | |
| publisher={Oxford University Press} | |
| } | |
| @article{drew2021humap, | |
| title={hu.{MAP} 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies}, | |
| author={Drew, Kevin and Wallingford, John B and Marcotte, Edward M}, | |
| journal={Molecular Systems Biology}, | |
| volume={17}, | |
| number={5}, | |
| pages={e10016}, | |
| year={2021}, | |
| publisher={EMBO Press} | |
| } | |
| @article{szklarczyk2023string, | |
| title={{STRING} v12.0: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets}, | |
| author={Szklarczyk, Damian and Kirsch, Rebecca and Koutrouli, Mikaela and Nastou, Katerina and Mehryary, Farrokh and Hachilif, Radja and Gable, Annika L and Fang, Tao and Doncheva, Nadezhda T and Pyysalo, Sampo and others}, | |
| journal={Nucleic Acids Research}, | |
| volume={51}, | |
| number={D1}, | |
| pages={D483--D489}, | |
| year={2023}, | |
| publisher={Oxford University Press} | |
| } | |
| @article{uniprot2023, | |
| title={The {UniProt} Consortium. {UniProt}: the Universal Protein Knowledgebase in 2023}, | |
| author={{UniProt Consortium}}, | |
| journal={Nucleic Acids Research}, | |
| volume={51}, | |
| number={D1}, | |
| pages={D523--D531}, | |
| year={2023} | |
| } | |
| % ===== LLM Benchmarks ===== | |
| @article{mirza2024chembench, | |
| title={{ChemBench}: A large-scale benchmark for chemical reasoning in language models}, | |
| author={Mirza, Adrian and others}, | |
| journal={Advances in Neural Information Processing Systems}, | |
| year={2024} | |
| } | |
| @article{fang2024molinstructions, | |
| title={Mol-Instructions: A large-scale biomolecular instruction dataset for large language models}, | |
| author={Fang, Yin and Liang, Xiaozhuo and Zhang, Ningyu and Liu, Kangwei and Huang, Rui and Chen, Zhuo and Fan, Xiaohui and Chen, Huajun}, | |
| journal={Proceedings of ICLR}, | |
| year={2024} | |
| } | |
| @article{jin2021medqa, | |
| title={What disease does this patient have? {A} large-scale open domain question answering dataset from medical exams}, | |
| author={Jin, Di and Pan, Eileen and Oufattole, Nassim and Weng, Wei-Hung and Fang, Hanyi and Szolovits, Peter}, | |
| journal={Applied Sciences}, | |
| volume={11}, | |
| number={14}, | |
| pages={6421}, | |
| year={2021} | |
| } | |
| @article{laurent2024labbench, | |
| title={{LAB-Bench}: Measuring capabilities of language models for biology research}, | |
| author={Laurent, Jon M and Gershon, Jo{\~a}o and others}, | |
| journal={arXiv preprint arXiv:2407.10362}, | |
| year={2024} | |
| } | |
| % ===== LLM Models ===== | |
| @article{dubey2024llama3, | |
| title={The {Llama} 3 herd of models}, | |
| author={Dubey, Abhimanyu and others}, | |
| journal={arXiv preprint arXiv:2407.21783}, | |
| year={2024} | |
| } | |
| @article{yang2024qwen2, | |
| title={{Qwen2} technical report}, | |
| author={Yang, An and others}, | |
| journal={arXiv preprint arXiv:2407.10671}, | |
| year={2024} | |
| } | |
| @misc{openai2024gpt4o, | |
| title={{GPT-4o} system card}, | |
| author={{OpenAI}}, | |
| year={2024}, | |
| howpublished={\url{https://openai.com/index/gpt-4o-system-card/}} | |
| } | |
| @misc{google2025gemini, | |
| title={{Gemini} 2.5 Flash}, | |
| author={{Google DeepMind}}, | |
| year={2025}, | |
| howpublished={\url{https://deepmind.google/technologies/gemini/}} | |
| } | |
| @misc{anthropic2025claude, | |
| title={Claude {Haiku} 4.5 Model Card}, | |
| author={{Anthropic}}, | |
| year={2025}, | |
| howpublished={\url{https://www.anthropic.com}} | |
| } | |
| % ===== Methodology ===== | |
| @article{gebru2021datasheets, | |
| title={Datasheets for Datasets}, | |
| author={Gebru, Timnit and Morgenstern, Jamie and Vecchione, Briana and Vaughan, Jennifer Wortman and Wallach, Hanna and III, Hal Daum{\'e} and Crawford, Kate}, | |
| journal={Communications of the ACM}, | |
| volume={64}, | |
| number={12}, | |
| pages={86--92}, | |
| year={2021} | |
| } | |
| @inproceedings{akhtar2024croissant, | |
| title={Croissant: A Metadata Format for {ML}-Ready Datasets}, | |
| author={Akhtar, Mubashara and Benjelloun, Omar and Conforti, Costanza and van der Maaten, Laurens and others}, | |
| booktitle={Proceedings of KDD}, | |
| year={2024} | |
| } | |
| @inproceedings{chen2016xgboost, | |
| title={{XGBoost}: A scalable tree boosting system}, | |
| author={Chen, Tianqi and Guestrin, Carlos}, | |
| booktitle={Proceedings of KDD}, | |
| pages={785--794}, | |
| year={2016} | |
| } | |
| @article{karypis1998metis, | |
| title={A fast and high quality multilevel scheme for partitioning irregular graphs}, | |
| author={Karypis, George and Kumar, Vipin}, | |
| journal={SIAM Journal on Scientific Computing}, | |
| volume={20}, | |
| number={1}, | |
| pages={359--392}, | |
| year={1998} | |
| } | |
| % ===== Contamination & Evaluation ===== | |
| @article{sainz2024contamination, | |
| title={Data contamination report from the 2024 {NAACL} workshop}, | |
| author={Sainz, Oscar and others}, | |
| journal={arXiv preprint}, | |
| year={2024} | |
| } | |
| @article{balloccu2024leak, | |
| title={Leak, cheat, repeat: Data contamination and evaluation malpractices in closed-source {LLMs}}, | |
| author={Balloccu, Simone and others}, | |
| journal={Proceedings of EACL}, | |
| year={2024} | |
| } | |
| % ===== Splitting Strategies ===== | |
| @article{yang2019cold, | |
| title={Analyzing learned molecular representations for property prediction}, | |
| author={Yang, Kevin and Swanson, Kyle and Jin, Wengong and Coley, Connor and Eiden, Philipp and Gao, Hua and Guzman-Perez, Angel and Hopper, Timothy and Kelley, Brian and Mathea, Miriam and others}, | |
| journal={Journal of Chemical Information and Modeling}, | |
| volume={59}, | |
| number={8}, | |
| pages={3370--3388}, | |
| year={2019}, | |
| publisher={ACS Publications} | |
| } | |
| @article{bemis1996murcko, | |
| title={The properties of known drugs. 1. Molecular frameworks}, | |
| author={Bemis, Guy W and Murcko, Mark A}, | |
| journal={Journal of Medicinal Chemistry}, | |
| volume={39}, | |
| number={15}, | |
| pages={2887--2893}, | |
| year={1996} | |
| } | |
| % ===== PPI Models ===== | |
| @article{chen2019pipr, | |
| title={Multifaceted protein--protein interaction prediction based on {Siamese} residual {RCNN}}, | |
| author={Chen, Muhao and Ju, Chelsea J-T and Zhou, Guangyu and Chen, Xuelu and Zhang, Tianle and Chang, Kai-Wei and Zaniolo, Carlo and Wang, Wei}, | |
| journal={Bioinformatics}, | |
| volume={35}, | |
| number={14}, | |
| pages={i305--i314}, | |
| year={2019}, | |
| publisher={Oxford University Press} | |
| } | |
| @article{zheng2020ddb, | |
| title={Predicting drug--target interactions using drug--drug and target--target similarities}, | |
| author={Zheng, Yi and Wu, Zheng}, | |
| journal={BMC Bioinformatics}, | |
| year={2020} | |
| } | |
| % ===== LogAUC & Metrics ===== | |
| @article{mysinger2010logauc, | |
| title={Rapid context-dependent ligand desolvation in molecular docking}, | |
| author={Mysinger, Michael M and Shoichet, Brian K}, | |
| journal={Journal of Chemical Information and Modeling}, | |
| volume={50}, | |
| number={9}, | |
| pages={1561--1573}, | |
| year={2010} | |
| } | |
| @article{truchon2007bedroc, | |
| title={Evaluating virtual screening methods: good and bad metrics for the ``early recognition'' problem}, | |
| author={Truchon, Jean-Fran{\c{c}}ois and Bayly, Christopher I}, | |
| journal={Journal of Chemical Information and Modeling}, | |
| volume={47}, | |
| number={2}, | |
| pages={488--508}, | |
| year={2007} | |
| } | |
| % ===== General ML ===== | |
| @article{matthews1975mcc, | |
| title={Comparison of the predicted and observed secondary structure of {T4} phage lysozyme}, | |
| author={Matthews, Brian W}, | |
| journal={Biochimica et Biophysica Acta (BBA)-Protein Structure}, | |
| volume={405}, | |
| number={2}, | |
| pages={442--451}, | |
| year={1975} | |
| } | |