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GenMol: A Drug Discovery Generalist with Discrete Diffusion

This is the official code repository for the paper titled GenMol: A Drug Discovery Generalist with Discrete Diffusion (ICML 2025).

Contribution

We introduce GenMol, a model for unified and versatile molecule generation by building masked discrete diffusion that generates SAFE molecular sequences.
We propose fragment remasking, an effective strategy for exploring chemical space using molecular fragments as the unit of exploration.
We propose molecular context guidance (MCG), a guidance scheme for GenMol to effectively utilize molecular context information.
We validate the efficacy and versatility of GenMol on a wide range of drug discovery tasks.

License

Copyright @ 2025, NVIDIA Corporation. All rights reserved.
\nThe source code is made available under Apache-2.0.
\nThe model weights are made available under the NVIDIA Open Model License.

Citation

If you find this repository and our paper useful, we kindly request to cite our work.

@article{lee2025genmol,\n  title     = {GenMol: A Drug Discovery Generalist with Discrete Diffusion},\n  author    = {Lee, Seul and Kreis, Karsten and Veccham, Srimukh Prasad and Liu, Meng and Reidenbach, Danny and Peng, Yuxing and Paliwal, Saee and Nie, Weili and Vahdat, Arash},\n  journal   = {International Conference on Machine Learning},\n  year      = {2025}\n}\n

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GenMol: A Drug Discovery Generalist with Discrete Diffusion

\n\nThis is the official code repository for the paper titled [GenMol: A Drug Discovery Generalist with Discrete Diffusion](https://arxiv.org/abs/2501.06158) (ICML 2025).\n\n\n## Contribution\n+ We introduce GenMol, a model for unified and versatile molecule generation by building masked discrete diffusion that generates SAFE molecular sequences.\n+ We propose fragment remasking, an effective strategy for exploring chemical space using molecular fragments as the unit of exploration.\n+ We propose molecular context guidance (MCG), a guidance scheme for GenMol to effectively utilize molecular context information.\n+ We validate the efficacy and versatility of GenMol on a wide range of drug discovery tasks.\n\n## License\nCopyright @ 2025, NVIDIA Corporation. All rights reserved.
\nThe source code is made available under Apache-2.0.
\nThe model weights are made available under the [NVIDIA Open Model License](https://www.nvidia.com/en-us/agreements/enterprise-software/nvidia-open-model-license/).\n\n## Citation\nIf you find this repository and our paper useful, we kindly request to cite our work.\n```BibTex\n@article{lee2025genmol,\n title = {GenMol: A Drug Discovery Generalist with Discrete Diffusion},\n author = {Lee, Seul and Kreis, Karsten and Veccham, Srimukh Prasad and Liu, Meng and Reidenbach, Danny and Peng, Yuxing and Paliwal, Saee and Nie, Weili and Vahdat, Arash},\n journal = {International Conference on Machine Learning},\n year = {2025}\n}\n```","displayName","GenMol",["D",1759598112564],"publisher","NVIDIA BioNeMo","latestVersion","versions","collectionCounts","imageUrl","/api/image/nvidia/clara/resources/genmol_v2","rawImageUrl","canGuestDownload","latestVersionSizeInBytes","licenseTerms","isMultinodeEnabled","isMultiArchitecture","bias","explainability","privacy","safetyAndSecurity","featureLabels",[],"displayLabels",[238,239,240,241],"policyLabels",[],"systemLabels",[],"products",[],"hasNimMetadata",{"_207":255,"_243":256,"_244":257,"_246":247},{"_207":251,"_243":252,"_244":253,"_246":247},{"_207":249,"_243":249,"_244":250,"_246":247},{"_207":242,"_243":242,"_244":245,"_246":247},"NSPECT-AACA-8XYG","value","filter",{"_248":247,"_243":242},"category","label","field","Model",{"_248":74,"_243":249},"Healthcare","indus_healthcare",{"_248":254,"_243":252},"industry","Drug Discovery","uscs_drug_discovery",{"_248":258,"_243":256},"application",{"_108":1433,"_110":1434},"ngcApps",[1386],"csaApiBaseUrl","https://www.nvidia.com/ai-agents/csa-agent/dcsm","datadogRum",{"_1367":1368,"_1369":1370,"_1371":1372,"_1373":1374,"_1375":270,"_139":294,"_1376":1377,"_1378":56,"_1379":87,"_1380":87,"_1381":1382,"_1383":87,"_1384":1385},"amplitude",{"_1364":1365,"_966":-7,"_1366":31},"disableJs","environment","prod","featureFlagsBlob","JTdCJTIydGVzdEZsYWclMjIlM0FmYWxzZSUyQyUyMnNob3dTZWFyY2hMYWJlbFNldEZpbHRlcnMlMjIlM0FmYWxzZSUyQyUyMmNoaW5hTmltRGlzdHJpYnV0b3JzUmVkZXNpZ24lMjIlM0F0cnVlJTJDJTIyZW5hYmxlQ3NhV2lkZ2V0JTIyJTNBZmFsc2UlMkMlMjJlbmFibGVQcm9kdWN0R3JvdXBpbmdCeVN1YnNjcmlwdGlvbiUyMiUzQWZhbHNlJTJDJTIyY29udGFpbmVyU2Nhbm5pbmdSZWRlc2lnbk0xJTIyJTNBdHJ1ZSU3RA==","featureFlagsGuarded","isDevLikeEnv","isPlaywright","isMobileDevice","categorizedOrgs",{"_1358":1359,"_1360":1361,"_1362":1363},"currentOrgContext","currentContextRoles",[],"enterpriseOrgs",[],"locale","en","ngcApiOrigin","ngcHelmOrigin","origin","https://catalog.ngc.nvidia.com","usesMocks","theme","year",2026,"1.7.3","defaultSearchSuggestions",{"_1241":183,"_1242":1243,"_1244":1245,"_1246":59},"announcements",[],"consentState",{"_331":1231,"_1232":87,"_1233":31,"_1234":31,"_1235":1236},"consentConfig",{"_313":314,"_315":316,"_317":318,"_319":320,"_321":322,"_323":324,"_325":326,"_327":328,"_329":330,"_331":332},"showContactAdmin",1784032427617,[],[],[308,309,310,311,312],{"_45":60,"_47":71,"_49":103,"_51":-5,"_53":-5,"_55":56},{"_45":60,"_47":69,"_49":103,"_51":-5,"_53":-5,"_55":56},{"_45":60,"_47":61,"_49":103,"_51":-5,"_53":-5,"_55":56},{"_45":57,"_47":58,"_49":103,"_51":-5,"_53":-5,"_55":56},{"_45":46,"_47":48,"_49":103,"_51":-5,"_53":-5,"_55":56},"mainInfoText","We and our third-party partners (including social media, advertising, and analytics partners) use cookies and other tracking technologies to collect, store, monitor, and process certain information about you when you visit our website. The information collected might relate to you, your preferences, or your device. We use that information to make the site work, analyze performance and traffic on our website, provide a more personalized web experience, and assist in our marketing efforts.

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These cookies enable us to provide enhanced website functionality and personalization as well as make the marketing messages we send to you more relevant to your interests. 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The cookie is extended for an extra 15 minutes every time the user interacts with the website, up to the maximum user session duration (4 hours).","__sec_tid","__sec__fid","crowdsource.nvidia.com","This cookie name is associated with 6sense which is used to collect visitor data related to the user’s visit to the website, such as number of visits, average time spent on the website and which pages have been loaded, for the purpose of serving targeted advertisements.This cookie contains no identifying information and is used for diagnostic purposes by Impact Radius, a service we use to track signup commissions for our affiliate program. We have categorized it under Functionality because it is necessary for the operation of our affiliate program.","__sec__ghost","_gd_svisitor","info.nvidia.com","nvweb_A","_ga","This cookie name is associated with Google Universal Analytics - which is a significant update to Google's more commonly used analytics service. This cookie is used to distinguish unique users by assigning a randomly generated number as a client identifier. It is included in each page request in a site and used to calculate visitor, session and campaign data for the sites analytics reports. By default it is set to expire after 2 years, although this is customisable by website owners.","research.nvidia.com","_uetvid","This is a cookie utilised by Microsoft Bing Ads and is a tracking cookie. It allows us to engage with a user that has previously visited our website.","s_pltp","This cookie is typically associated with Adobe Analytics (formerly SiteCatalyst). It is used to identify the previous link clicked within the site, which helps in analyzing site usage patterns.","s_ecid","Adobe Analytics cookie containing the the Adobe Experience Cloud 1st party visitor id if the Analytics AMCV visitor id is not found.","This cookie name is used as a long-lived unique identifier of the visitor on the website. It is either correlated to the 6suuid or a unique value, and can be changed during the lifetime of this cookie.This cookie contains no identifying information and is used for diagnostic purposes by Impact Radius, a service we use to track signup commissions for our affiliate program. We have categorized it under Functionality because it is necessary for the operation of our affiliate program.","s_ips","This cookie is associated with Adobe Analytics. The cookie is used for measuring a visitor’s scroll activity to see how much of a page they view before moving on to another page.","_gd_session","tp","This cookie is associated with Adobe Analytics site tracking. It registers if the website's scroll-depth detection is active. This function remembers how far the user has scrolled on the current session across the website's sub-pages.","dmn_chk_-xxxxxxxxxxxx","com","Posthog Analytics","_hly_vid","This cookie _hly_vid is used to record website and server performance with each visit to the site. The data is aggregated and analyzed; therefore, it remains anonymous upon use.","_cs_id","blogs.nvidia.com","_session_id","resources.nvidia.com","This cookie creates an interim session ID used as an in-session user ID.\n","s_cc","This cookie is associated with the Adobe Site Catalyst. It determines whether cookies are enabled in the web browser.","_hjSessionUser_xxxxxx","Hotjar cookie that is set when a user first lands on a page with the Hotjar script. It is used to persist the Hotjar User ID, unique to that site on the browser. 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After this check, the cookie is removed.","s_tp","s_plt","This cookie is used to measure the time taken for pages to load, allowing website owners to identify slow loading pages and improve user experience.","This _gd_session cookie is used to collect visitor data related to the user's visit to the website, such as number of visits, average time spent on the website and which pages have been loaded, for the purpose of serving targeted advertisements.This cookie contains no identifying information and is used for diagnostic purposes by Impact Radius, a service we use to track signup commissions for our affiliate program. 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