Awesome List Updates on Dec 02, 2021

15 awesome lists updated today.

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1. Dive Into Machine Learning

Tools you'll need / If you prefer local installation

• Python. Python 3 is the best option.

• Jupyter Notebook. (Formerly known as IPython Notebook.)

• Some scientific computing packages:
  • numpy
  • pandas
  • scikit-learn
  • matplotlib

Other courses / Take my tips with a grain of salt

• Data science courses as Jupyter Notebooks:
  • Practical Data Science
  • Python Data Science Handbook, as Jupyter Notebooks

• Coursera's Data Science Specialization

• Harvard CS109: Data Science

• An epic Quora thread: How can I become a data scientist?

Supplement: Learning Pandas well / Some communities to know about!

• Here are some docs I found especially helpful as I continued learning:
  • Cookbook
  • Data Structures, esp. DataFrame section
  • Reshaping by pivoting DataFrames
  • Computational tools and StackExchange thread: "What is covariance in plain language?"
  • Group By (split, apply, and combine DataFrames)
  • Visualizing your DataFrames

Supplement: Troubleshooting / Risks - some starting points

• Awesome Production Machine Learning (⭐19k), "a curated list of awesome open source libraries to deploy, monitor, version and scale your machine learning." It includes a section about privacy-preserving ML (⭐19k), by the way!

• The High Cost of Maintaining Machine Learning Systems

• 11 Clever Methods of Overfitting and How to Avoid Them

• "So, you want to build an ethical algorithm?" An interactive tool to prompt discussions (source) (⭐72)

More Data Science materials / Aside: Bayesian Statistics and Machine Learning

• The free book Probabilistic Programming and Bayesian Methods for Hackers. Made with a "computation/understanding-first, mathematics-second point of view." Uses PyMC (⭐9.1k). It's available in print too!

• Like learning by playing? Me too. Try 19 Questions (⭐15), "a machine learning game which asks you questions and guesses an object you are thinking about," and explains which Bayesian statistics techniques it's using!

• Time Series Forecasting with Bayesian Modeling by Michael Grogan, a 5-project series - paid but the first project is free.

• Bayesian Modelling in Python (⭐2.5k). Uses PyMC (⭐9.1k) as well.

2. Urban and Regional Planning Resources

Educational and Informational Resources / Literature Resources

• Automated Decision-Making and the Law Clearinghouse Project - The aim of this clearinghouse project thus is to highlight seminal and impactful articles focused on issues of AI Decision-Making and the law.

3. Awesome Cytodata

Software / Genetic Perturbations

• Cytominer (⭐51) - Methods for image-based cell profiling in R.

• BioProfiling.jl (⭐13) - Toolkit for filtering and curation of morphological profiles in Julia.

• PyCytominer (⭐120) - Methods for image-based cell profiling in Python.

• ImJoy - A platform compiling tool for deep-learning based image analyses with a GUI.

Publications / Reviews

• Large-scale image-based screening and profiling of cellular phenotypes - Overview of image-based profiling, including its applications and challenges.

• How cells explore shape space: A quantitative statistical perspective of cellular morphogenesis - Discussion on the biology of cell shape changes based on quantitative descriptors.

• Machine learning and image-based profiling in drug discovery - Introduction to morphological profiling and discussion on what machine learning has to offer.

Publications / Applications

• Mapping the perturbome network of cellular perturbations - Image-based profiling and network analysis of drug combinations.

• Morphological profiling of human T and NK lymphocytes by high-content cell imaging - Image-based profiling of actin organization at the immunological synapse.

• A subcellular map of the human proteome - Classification of protein subcellular location from confocal microscopy images of the Human Protein Atlas.

• A multi-scale map of cell structure fusing protein images and interactions - Combining confocal imaging and mass spectrometry representations of proteins to predict physical proximity and characterize cellular organization.

• Predicting cell health phenotypes using image-based morphology profiling - Image-based profiles as predictors of apoptosis, proliferation and other cell health descriptors.

• Systematic genetics and single‐cell imaging reveal widespread morphological pleiotropy and cell‐to‐cell variability - Analysis of single-cell profiles to characterize variability, pleiotropy and incomplete penetrance.

• Large‐scale image‐based profiling of single‐cell phenotypes in arrayed CRISPR‐Cas9 gene perturbation screens - Demonstrates feasibility of imaging arrayed CRISPR screens and offers a way to characterize transfection efficacy in individual cells.

• A chemical-genetic interaction map of small molecules using high-throughput imaging in cancer cells - Profiling the morphological changes induced in 1280 compounds in 12 knockout cell lines.

• Time-resolved mapping of genetic interactions to model rewiring of signaling pathways - Changes in genetic interactions across time based on multiple morphological descriptors.

• High-Content Imaging of Unbiased Chemical Perturbations Reveals that the Phenotypic Plasticity of the Actin Cytoskeleton Is Constrained - Defining morphological clusters in a large compound screen.

• A map of directional genetic interactions in a metazoan cell - Characterizing genetic interactions by integrating 21 phenotypic descriptors.

• Evaluation of Gene Expression and Phenotypic Profiling Data as Quantitative Descriptors for Predicting Drug Targets and Mechanisms of Action - Benchmarking profiling modalities, including image-based profiles, for mechanism of action prediction.

Publications / Methods

• Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting - Selfsupervised method to learn feature representations of single cells in microscopy images without labelled training data.

• A BaSiC tool for background and shading correction of optical microscopy images - Illumination-correction method accounting for space- and time-dependent biases.

• Cellpose: a generalist algorithm for cellular segmentation - Generalist deep learning model for cell and nucleus segmentation with pre-trained weights.

• Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments - DeepCell: collection of deep learning segmentation models.

• Improving Phenotypic Measurements in High-Content Imaging Screens - Embedding single-cell and compound profiles using transfer learning, examplified on mechanism of action prediction.

• The Multidimensional Perturbation Value - Proposing a score to define significant activity in screens.

• CytoGAN: Generative Modeling of Cell Images - Generative network displaying potential for learning latent representation of biological conditions from cell images.

• Self-supervised feature extraction from image time series in plant phenotyping using triplet networks - Direct extraction of phenotypic features from plant images.

4. Awesome Developer First

Databases & Spreadsheets

• PlanetScale - Hosted managed MySQL database, CI integration & auto scaling.

5. Awesome Selfhosted

Software / Money, Budgeting & Management

• IHateMoney - Manage your shared expenses, easily. (Demo, Source Code (⭐1.3k)) BSD-3-Clause Docker/Python

6. Awesome Vue

Components & Libraries / UI Components

• vue3-emoji-picker (⭐218) - Simple and Powerful Emoji Picker for Vue3.

7. Awesome Flutter

Forms / Image Picker

• Form Builder (⭐1.6k) - Framework that simplifies building forms, validating fields, reacting to changes, and collecting the final user input by Danvick Miller

• Reactive Forms (⭐487) - Model-driven approach to handling Forms inputs and validations, heavily inspired in Angular's Reactive Forms.

8. Awesome Circuitpython

Contributing / Contribution Workflow Overview

• Fork this repository (⭐679) on GitHub.

• Merge adafruit or main.

9. Awesome Vite

Svelte / Integrations

• vite-plugin-svelte (⭐928) - Adds Svelte support. Official plugin of Svelte team.

10. Awesome Lowcode

Automation

• Data Fetcher for Airtable - Connect Airtable to any API using the Data Fetcher app.

11. Awesome Python Typing

Tools / Linters

• flake8-type-checking (⭐118) - Plugin to help you guard any type-annotation-only import correctly.

12. Tools

UI Builders

• Windframe

13. Awesome Generative Deep Art

Improving Google Colab experience / Deforum

• 7 ways to load external data into Google Colab | by B. Chen | Towards Data Science

• 10 tricks for a better Google Colab experience | by Cyprien NIELLY | Towards Data Science

• Quickly share ML WebApps from Google Colab using ngrok for Free | by AbdulMajedRaja RS | Towards Data Science

• Jupyter Widgets for Interactivity in Google Colab: notebook with examples of using Jupyter Widgets in Colab, allowing interactive inputs

14. Awesome Ddd

Video Collections

• The Art of Discovering Bounded Contexts by Nick Tune - Session from 2017 DevoxxUK on how to define bounded contexts

15. Awesome Digital History

Archives and primary sources / Global

• Karlsruher Virtueller Katalog - Book search engine for finding hundreds of millions of media in catalogs worldwide.

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