{"id":15906004,"url":"https://github.com/lucacappelletti94/master-in-bioinformatics-and-functional-genomics","last_synced_at":"2025-09-01T17:47:57.305Z","repository":{"id":98555308,"uuid":"182020474","full_name":"LucaCappelletti94/Master-in-Bioinformatics-and-Functional-genomics","owner":"LucaCappelletti94","description":"Some exercises and example for the neural networks section of the course.","archived":false,"fork":false,"pushed_at":"2020-05-01T17:34:05.000Z","size":39170,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-02T22:42:50.706Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/LucaCappelletti94.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}},"created_at":"2019-04-18T05:14:29.000Z","updated_at":"2020-07-27T11:03:45.000Z","dependencies_parsed_at":null,"dependency_job_id":"d64f37e6-aaf1-4240-9aeb-2ef367b6403e","html_url":"https://github.com/LucaCappelletti94/Master-in-Bioinformatics-and-Functional-genomics","commit_stats":{"total_commits":39,"total_committers":1,"mean_commits":39.0,"dds":0.0,"last_synced_commit":"691040e17777ce3519bca8fc03126279756f0d4d"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/LucaCappelletti94/Master-in-Bioinformatics-and-Functional-genomics","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2FMaster-in-Bioinformatics-and-Functional-genomics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2FMaster-in-Bioinformatics-and-Functional-genomics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2FMaster-in-Bioinformatics-and-Functional-genomics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2FMaster-in-Bioinformatics-and-Functional-genomics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LucaCappelletti94","download_url":"https://codeload.github.com/LucaCappelletti94/Master-in-Bioinformatics-and-Functional-genomics/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2FMaster-in-Bioinformatics-and-Functional-genomics/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273166937,"owners_count":25057178,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-09-01T02:00:09.058Z","response_time":120,"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":"2024-10-06T13:20:31.815Z","updated_at":"2025-09-01T17:47:57.280Z","avatar_url":"https://github.com/LucaCappelletti94.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Master in Bioinformatics and Functional genomics\nSome exercises and example for the neural networks section of the course.\n\n## Setup\nTo setup everything needed for the lessons, once you have python and git installed on your system, please run the following script in your terminal:\n```bash\n  git clone https://github.com/LucaCappelletti94/Master-in-Bioinformatics-and-Functional-genomics.git\n  cd Master-in-Bioinformatics-and-Functional-genomics\n  python -m pip install --upgrade -r requirements.txt\n```\n\n## Lessons\n### [1 - Lesson on MLP](https://github.com/LucaCappelletti94/Master-in-Bioinformatics-and-Functional-genomics/tree/master/1%20-%20Lesson%20on%20MLP)\n\nIn [this lesson](https://github.com/LucaCappelletti94/Master-in-Bioinformatics-and-Functional-genomics/tree/master/1%20-%20Lesson%20on%20MLP), we will learn how to use a multi-layer perceptron to predict the values of an arbitraty *unknown* function.\n\n### [2 - Practice on MLP](https://github.com/LucaCappelletti94/Master-in-Bioinformatics-and-Functional-genomics/tree/master/2%20-%20Practice%20on%20MLP)\n\nIn [this lesson](https://github.com/LucaCappelletti94/Master-in-Bioinformatics-and-Functional-genomics/tree/master/2%20-%20Practice%20on%20MLP), after learning how to load and execute a preliminary analysis on a real dataset, we will create an MLP model and introduce the concept of Dropout layers. Guided free experimentation will follow.\n\n### [3 - Lesson and practice on CNN](https://github.com/LucaCappelletti94/Master-in-Bioinformatics-and-Functional-genomics/tree/master/3%20-%20Lesson%20on%20CNN)\n\nIn [this lesson](https://github.com/LucaCappelletti94/Master-in-Bioinformatics-and-Functional-genomics/tree/master/3%20-%20Lesson%20on%20CNN) we will learn how to create a convolutional neural network that can learn patterns, afterwards we will proceed to create a neural network that repairs a pattern.\n\n### [4 - Lesson on prediction active regulatory regions](https://github.com/LucaCappelletti94/Master-in-Bioinformatics-and-Functional-genomics/tree/master/4%20-%20Lesson%20on%20prediction%20active%20regulatory%20regions)\nIn [this lesson](https://github.com/LucaCappelletti94/Master-in-Bioinformatics-and-Functional-genomics/tree/master/4%20-%20Lesson%20on%20prediction%20active%20regulatory%20regions) we have practiced with the preparation of the active regulatory regions dataset (retrieving data, one-hot encoding data, quick dataset analysis, preparation of the labels for training) and used the data for training a simple MLP.\n\n### 5 - 27/05/2019 - Creating, testing and deploying a neural network\n\nIn this lesson, in a step by step fashion, we created a MLP trained on the standard dataset Boston Housing and proceeded with guided experimentation in class with its model structure. Afterwards, a simple pytest test was created to test the model in a CI fashion.\nFinally, a simple example of the neural network deployment for production was shown.\n\n## Additional materials\nIn this brief course we could not touch as deeply as we would like to a number of topics, so here are a few links that any of you could explore. I tried to select only materials that I enjoyed and that I would love to watch again.\n\n### 3Blue1Brown\nThis is a youtube channel with great animations which can show you in an enjoyable way what a neural network is:\n- [What is a neural network?](https://www.youtube.com/watch?v=aircAruvnKk\u0026t=1s)\n- [Gradient Descent](https://www.youtube.com/watch?v=IHZwWFHWa-w)\n- [Backpropagation - high level](https://www.youtube.com/watch?v=Ilg3gGewQ5U)\n- [Backpropagation - low level](https://www.youtube.com/watch?v=tIeHLnjs5U8)\n\n### Tesla\nThe presentation of how they cracked autonomous driving at Tesla:\n- [Tesla: autopilot day](https://www.youtube.com/watch?v=Ucp0TTmvqOE)\n\n### Welch labs\nA small video playplist on neural networks:\n- [Neural networks demistified](https://www.youtube.com/watch?v=bxe2T-V8XRs)\n\n### Kurtzgesagt\nThe rise of automation\n- [The Rise of the Machines – Why Automation is Different this Time](https://www.youtube.com/watch?v=WSKi8HfcxEk\u0026t=27s)\n\n### CGP Grey\nA video showing how artificial intelligence will be taking our jobs way before it becomes sentient:\n- [Humans need not apply](https://www.youtube.com/watch?v=7Pq-S557XQU)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flucacappelletti94%2Fmaster-in-bioinformatics-and-functional-genomics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flucacappelletti94%2Fmaster-in-bioinformatics-and-functional-genomics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flucacappelletti94%2Fmaster-in-bioinformatics-and-functional-genomics/lists"}