{"id":20893188,"url":"https://github.com/keiserlab/deepfish","last_synced_at":"2026-04-30T05:32:37.575Z","repository":{"id":223963937,"uuid":"758260880","full_name":"keiserlab/deepfish","owner":"keiserlab","description":null,"archived":false,"fork":false,"pushed_at":"2025-03-30T17:04:26.000Z","size":44,"stargazers_count":1,"open_issues_count":1,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-12-28T22:58:05.555Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/keiserlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-02-15T23:53:30.000Z","updated_at":"2025-09-20T07:02:48.000Z","dependencies_parsed_at":"2024-02-23T01:29:29.128Z","dependency_job_id":"edbe966d-ad65-4cff-8e10-c1a1834d458a","html_url":"https://github.com/keiserlab/deepfish","commit_stats":null,"previous_names":["keiserlab/deepfish"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/keiserlab/deepfish","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keiserlab%2Fdeepfish","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keiserlab%2Fdeepfish/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keiserlab%2Fdeepfish/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keiserlab%2Fdeepfish/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/keiserlab","download_url":"https://codeload.github.com/keiserlab/deepfish/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keiserlab%2Fdeepfish/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32456165,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-29T22:27:22.272Z","status":"online","status_checked_at":"2026-04-30T02:00:05.929Z","response_time":57,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-18T10:14:55.574Z","updated_at":"2026-04-30T05:32:32.565Z","avatar_url":"https://github.com/keiserlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DeepFish\n\n## This is the deepfish repo to accompany the manuscript titled \"Deep phenotypic profiling of neuroactive drugs in larval zebrafish\" ([doi:10.1101/2024.02.22.581657](https://doi.org/10.1101/2024.02.22.581657))\n\n### **Environment setup:** \n\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp; To train the Twin-NN and Twin-DN models, create a new conda environment from the provided requirements file as follows: `conda create --name deepfish_env --file deepfish_env_req_simple.txt`.\\\n\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp; The code was tested and model training was performed on NVIDIA a GeForce GTX 1080 Ti GPU and a CentOS Linux kernel 3.10.0 operating system with an x86-64 architecture.\n\n### **Data:**\n\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp; Download data from provided zenodo repo: 10.5281/zenodo.15107536 (v2), https://zenodo.org/records/15107536. Put the data in the 'Data/' directory or whichever directory you prefer (just make sure to edit the path in the config.yaml file) \n\n### **To train models:**\n\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp; Use provided config file or choose custom training parameters (config.yaml file). Activate conda environment: `conda activate deepfish_env` \\\n\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp; We provide the pre-enumerated training and test pairs in the data repo as numpy arrays as described in the methods section. You can use a different train/ test splitting approach, just save the resulting pairs to a numpy array and place in the Data directory.\\\n\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp; Run main training loop: `python TwinMain.py`\n\n### **Expected Results:** ###\n\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp; Expected training results provided in output log files in the Results/ directory for the two models, Twin-NN and Twin-DN.\\\nTwin-NN runtime: about 10 minutes on a single GPU for 25 epochs, with batch size of 32. GPU memory utilization: 2.8 GB.\\\nTwin-DN: about 4 hours on a single GPU for 25 epochs, with batch size of 8. GPU memory utilization: 8.5 GB. \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkeiserlab%2Fdeepfish","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkeiserlab%2Fdeepfish","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkeiserlab%2Fdeepfish/lists"}