scrapbook
  • "Unorganized" Notes
  • The Best Public Datasets for Machine Learning and Data Science
  • Practice Coding
  • plaid-API project
  • Biotech
    • Machine Learning vs. Deep Learning
  • Machine Learning for Computer Graphics
  • Books (on GitHub)
  • Ideas/Thoughts
  • Ziva for feature animation: Stylized simulation and machine learning-ready workflows
  • Tools
  • 🪶math
    • Papers
    • Math for ML (coursera)
      • Linear Algebra
        • Wk1
        • Wk2
        • Wk3
        • Wk4
        • Wk5
      • Multivariate Calculus
    • Improving your Algorithms & Data Structure Skills
    • Algorithms
    • Algorithms (MIT)
      • Lecture 1: Algorithmic Thinking, Peak Finding
    • Algorithms (khan academy)
      • Binary Search
      • Asymptotic notation
      • Sorting
      • Insertion sort
      • Recursion
      • Solve Hanoi recursively
      • Merge Sort
      • Representing graphs
      • The breadth-first search algorithm
      • Breadth First Search in JavaScript
      • Breadth-first vs Depth-first Tree Traversal in Javascript
    • Algorithms (udacity)
      • Social Network
    • Udacity
      • Linear Algebra Refresher /w Python
    • math-notes
      • functions
      • differential calculus
      • derivative
      • extras
      • Exponentials & logarithms
      • Trigonometry
    • Probability (MIT)
      • Unit 1
        • Probability Models and Axioms
        • Mathematical background: Sets; sequences, limits, and series; (un)countable sets.
    • Statistics and probability (khan academy)
      • Analyzing categorical data
      • Describing and comparing distributions
      • Outliers Definition
      • Mean Absolute Deviation (MAD)
      • Modeling data distribution
      • Exploring bivariate numerical data
      • Study Design
      • Probability
      • Counting, permutations, and combinations
      • Binomial variables
        • Binomial Distribution
        • Binomial mean and standard deviation formulas
        • Geometric random variable
      • Central Limit Theorem
      • Significance Tests (hypothesis testing)
    • Statistics (hackerrank)
      • Mean, Medium, Mode
      • Weighted Mean
      • Quartiles
      • Standard Deviation
      • Basic Probability
      • Conditional Probability
      • Permutations & Combinations
      • Binomial Distribution
      • Negative Binomial
      • Poisson Distribution
      • Normal Distribution
      • Central Limit Theorem
      • Important Concepts in Bayesian Statistics
  • 📽️PRODUCT
    • Product Strategy
    • Product Design
    • Product Development
    • Product Launch
  • 👨‍💻coding
    • of any interest
    • Maya API
      • Python API
    • Python
      • Understanding Class Inheritance in Python 3
      • 100+ Python challenging programming exercises
      • coding
      • Iterables vs. Iterators vs. Generators
      • Generator Expression
      • Stacks (LIFO) / Queues (FIFO)
      • What does -1 mean in numpy reshape?
      • Fold Left and Right in Python
      • Flatten a nested list of lists
      • Flatten a nested dictionary
      • Traverse A Tree
      • How to Implement Breadth-First Search
      • Breadth First Search
        • Level Order Tree Traversal
        • Breadth First Search or BFS for a Graph
        • BFS for Disconnected Graph
      • Trees and Tree Algorithms
      • Graph and its representations
      • Graph Data Structure Interview Questions
      • Graphs in Python
      • GitHub Repo's
    • Python in CG Production
    • GLSL/HLSL Shading programming
    • Deep Learning Specialization
      • Neural Networks and Deep Learning
      • Untitled
      • Untitled
      • Untitled
    • TensorFlow for AI, ML, and DL
      • Google ML Crash Course
      • TensorFlow C++ API
      • TensorFlow - coursera
      • Notes
      • An Introduction to different Types of Convolutions in Deep Learning
      • One by One [ 1 x 1 ] Convolution - counter-intuitively useful
      • SqueezeNet
      • Deep Compression
      • An Overview of ResNet and its Variants
      • Introducing capsule networks
      • What is a CapsNet or Capsule Network?
      • Xception
      • TensorFlow Eager
    • GitHub
      • Project README
    • Agile - User Stories
    • The Open-Source Data Science Masters
    • Coding Challenge Websites
    • Coding Interview
      • leetcode python
      • Data Structures
        • Arrays
        • Linked List
        • Hash Tables
        • Trees: Basic
        • Heaps, Stacks, Queues
        • Graphs
          • Shortest Path
      • Sorting & Searching
        • Depth-First Search & Breadth-First Search
        • Backtracking
        • Sorting
      • Dynamic Programming
        • Dynamic Programming: Basic
        • Dynamic Programming: Advanced
    • spaCy
    • Pandas
    • Python Packages
    • Julia
      • jupyter
    • macos
    • CPP
      • Debugging
      • Overview of memory management problems
      • What are lvalues and rvalues?
      • The Rule of Five
      • Concurrency
      • Avoiding Data Races
      • Mutex
      • The Monitor Object Pattern
      • Lambdas
      • Maya C++ API Programming Tips
      • How can I read and parse CSV files in C++?
      • Cpp NumPy
    • Advanced Machine Learning
      • Wk 1
      • Untitled
      • Untitled
      • Untitled
      • Untitled
  • data science
    • Resources
    • Tensorflow C++
    • Computerphile
      • Big Data
    • Google ML Crash Course
    • Kaggle
      • Data Versioning
      • The Basics of Rest APIs
      • How to Make an API
      • How to deploying your API
    • Jupiter Notebook Tips & Tricks
      • Jupyter
    • Image Datasets Notes
    • DS Cheatsheets
      • Websites & Blogs
      • Q&A
      • Strata
      • Data Visualisation
      • Matplotlib etc
      • Keras
      • Spark
      • Probability
      • Machine Learning
        • Fast Computation of AUC-ROC score
    • Data Visualisation
    • fast.ai
      • deep learning
      • How to work with Jupyter Notebook on a remote machine (Linux)
      • Up and Running With Fast.ai and Docker
      • AWS
    • Data Scientist
    • ML for Beginners (Video)
    • ML Mastery
      • Machine Learning Algorithms
      • Deep Learning With Python
    • Linear algebra cheat sheet for deep learning
    • DL_ML_Resources
    • Awesome Machine Learning
    • web scraping
    • SQL Style Guide
    • SQL - Tips & Tricks
  • 💡Ideas & Thoughts
    • Outdoors
    • Blog
      • markdown
      • How to survive your first day as an On-set VFX Supervisor
    • Book Recommendations by Demi Lee
  • career
    • Skills
    • learn.co
      • SQL
      • Distribution
      • Hypothesis Testing Glossary
      • Hypothesis Tests
      • Hypothesis & AB Testing
      • Combinatorics Continued and Maximum Likelihood Estimation
      • Bayesian Classification
      • Resampling and Monte Carlo Simulation
      • Extensions To Linear Models
      • Time Series
      • Distance Metrics
      • Graph Theory
      • Logistic Regression
      • MLE (Maximum Likelihood Estimation)
      • Gradient Descent
      • Decision Trees
      • Ensemble Methods
      • Spark
      • Machine Learning
      • Deep Learning
        • Backpropagation - math notation
        • PRACTICE DATASETS
        • Big Data
      • Deep Learning Resources
      • DL Datasets
      • DL Tutorials
      • Keras
      • Word2Vec
        • Word2Vec Tutorial Part 1 - The Skip-Gram Model
        • Word2Vec Tutorial Part 2 - Negative Sampling
        • An Intuitive Explanation of Convolutional Neural Networks
      • Mod 4 Project
        • Presentation
      • Mod 5 Project
      • Capstone Project Notes
        • Streaming large training and test files into Tensorflow's DNNClassifier
    • Carrier Prep
      • The Job Search
        • Building a Strong Job Search Foundation
        • Key Traits of Successful Job Seekers
        • Your Job Search Mindset
        • Confidence
        • Job Search Action Plan
        • CSC Weekly Activity
        • Managing Your Job Search
      • Your Online Presence
        • GitHub
      • Building Your Resume
        • Writing Your Resume Summary
        • Technical Experience
      • Effective Networking
        • 30 Second Elevator Pitch
        • Leveraging Your Network
        • Building an Online Network
        • Linkedin For Research And Networking
        • Building An In-Person Network
        • Opening The Line Of Communication
      • Applying to Jobs
        • Applying To Jobs Online
        • Cover Letters
      • Interviewing
        • Networking Coffees vs Formal Interviews
        • The Coffee Meeting/ Informational Interview
        • Communicating With Recruiters And HR Professional
        • Research Before an Interview
        • Preparing Questions for Interviews
        • Phone And Video/Virtual Interviews
        • Cultural/HR Interview Questions
        • The Salary Question
        • Talking About Apps/Projects You Built
        • Sending Thank You's After an Interview
      • Technical Interviewing
        • Technical Interviewing Formats
        • Code Challenge Best Practices
        • Technical Interviewing Resources
      • Communication
        • Following Up
        • When You Haven't Heard From an Employer
      • Job Offers
        • Approaching Salary Negotiations
      • Staying Current in the Tech Industry
      • Module 6 Post Work
      • Interview Prep
  • projects
    • Text Classification
    • TERRA-REF
    • saildrone
  • Computer Graphics
  • AI/ML
  • 3deeplearning
    • Fast and Deep Deformation Approximations
    • Compress and Denoise MoCap with Autoencoders
    • ‘Fast and Deep Deformation Approximations’ Implementation
    • Running a NeuralNet live in Maya in a Python DG Node
    • Implement a Substance like Normal Map Generator with a Convolutional Network
    • Deploying Neural Nets to the Maya C++ API
  • Tools/Plugins
  • AR/VR
  • Game Engine
  • Rigging
    • Deformer Ideas
    • Research
    • brave rabbit
    • Useful Rigging Links
  • Maya
    • Optimizing Node Graph for Parallel Evaluation
  • Houdini
    • Stuff
    • Popular Built-in VEX Attributes (Global Variables)
Powered by GitBook
On this page
  • Senior Software Engineer - Machine Learning Platform
  • About the Role
  • Responsibilities:
  • What We're Looking For:
  • Nice to Haves:
  • Onsite
  • Problems we are looking to solve
  • Pipelines
  • Notes
  • Toolkits
  • Reading
  • Pipeline(s)
  • Books
  • Software

Biotech

Previousplaid-API projectNextMachine Learning vs. Deep Learning

Last updated 6 years ago

Senior Software Engineer - Machine Learning Platform

About the Role

Freenome is looking for engineers to help us develop software to combat cancer and other age-related diseases. You will work as part of an interdisciplinary team of engineers and scientists building our internal machine learning platform. As an early team member, you’ll take the lead on major projects and collaborate actively with our world-class team of engineers, scientists, designers and product managers. You’ll design and build the systems used to power our Discovery Platform, the heart of Freenome’s experimental analyses. Since we’re a small team, you’ll also have an opportunity to determine the course of a broad range of projects and help shape the direction of the Engineering team at Freenome.

Freenome’s software systems provide the “nervous system” for the company by tracking sample analysis from start to finish, empowering and assisting lab technicians and scientists, and automating our growing collection of cancer-fighting robots. This nervous system is built using modern software development technologies and methodologies.

Responsibilities:

  • Work closely with machine learning, bioinformatics, and product management teams to understand needs and then architect, roadmap, and lead development of the next phase of Freenome’s discovery software platform

  • Deep understanding of the role of the discovery platform for Freenome’s product development process and partnerships, and guidance of its purposeful evolution in support of these efforts

  • Own group charter and build a focused, collaborative engineering team

  • Develop and deploy reliable, maintainable, scalable, and fault-tolerant services

  • Guide and champion engineering hygiene and culture as a core part of the engineering backbone

What We're Looking For:

  • Ability to understand, plan, and develop for key aspects of Freenome’s multi-analyze discovery analysis platform:

    • Heterogeneous data organization, accessibility, and modeling

    • Rapid, iterative, reproducible experimentation and analysis

    • Simple navigation to arbitrary states and checkpoints within the analysis tree

    • Clear interpretation and presentation of discovery insights in reports

  • 5+ years experience as a part of a software development team successfully shipping a machine learning, deep learning, data science, analytical, or similar platform

  • Management or team lead experience

  • Knowledge of optimal methods for modern data storage systems, distributed systems, service architecture, and pipelining or workflow management.

  • Track record of building distributed systems with service endpoints and distributed storage.

  • Understanding of, and practical experience with, statistical and machine learning methods.

  • Degree in computer science, mathematics, statistics, or related field or equivalent work experience

  • Proficiency in a general-purpose programming language: Python, Java, C, C++, etc

  • Excellent written and verbal communication skills

  • A mindful, transparent, and humane approach to your work and your interactions with others

Nice to Haves:

  • Deep knowledge of Python

  • PostgreSQL or similar relational database experience

  • Experience with Google Cloud Platform, or another cloud computing service

  • Domain-specific experience in computational biology, genomics or a related field

  • Experience in scientific parallel computing

  • Experience in high-performance computing, including SIMD or GPU performance optimization

  • Experience with use of automated regression testing, version control, and deployment systems

Onsite

  1. A hands-on coding question. Writing some light classes, functions etc. No algorithms or anything tricky, just solving a problem with code.

  2. An algorithmic whiteboard question. This requires no coding or coding knowledge. A computer science background will help but is not required. The problem is around the subject matter of bioinformatics analysis but does not require prior knowledge.

  3. A infrastructure design whiteboard question. No coding. This is an exercise on the whiteboard to design the infrastructure and systems needed to create a web app that many users will use. This involves infrastructure, scaling, efficiency, and other considerations for a big user base.

Problems we are looking to solve

Pipelines

Tools: Luigi, Airflow, Ludwig, Kubeflow, Horizon

​https://code.fb.com/core-data/introducing-fblearner-flow-facebook-s-ai-backbone/​‌

​https://code.fb.com/ml-applications/horizon/​‌

​https://www.reddit.com/r/bioinformatics/comments/5bu61o/anybody_using_luigi_for_their_pipeline

Notes

Machine Learning is a method of statistical learning where each instance in a dataset is described by a set of features or attributes. In contrast, the term “Deep Learning” is a method of statistical learning that extracts features or attributes from raw data. Deep Learning does this by utilising neural networks with many hidden layers, big data, and powerful computational resources. The terms seem somewhat interchangeable; however, with Deep Learning methods, the algorithm constructs representations of the data automatically. In contrast, data representations are hard-coded as a set of features in machine learning algorithms, requiring further processes such as feature selection and extraction, (such as PCA).

Toolkits

  1. Airflow

  2. Ludwig

  3. Luigi

  4. Horizon

  5. Kubeflow

Reading

Shotgun Sequencing

Special machines, known as sequencing machines are used to extract short random DNA sequences from a particular genome we wish to determine (target genome). Current DNA sequencing technologies cannot read one whole genome at once. It reads small pieces of between 20 and 30000 bases, depending on the technology used. These short pieces are called reads. Special software are used to assemble these reads according to how they overlap, in order to generate continuous strings called contigs. These contigs can be the whole target genome itself, or parts of the genome (as shown in the above figure).

The process of aligning and merging fragments from a longer DNA sequence, in order to reconstruct the original sequence is known as Sequence Assembly.

In order to obtain the whole genome sequence, we may need to generate more and more random reads, until the contigs match to the target genome.

Pipeline(s)

Pipe-filter pattern

This pattern can be used to structure systems which produce and process a stream of data. Each processing step is enclosed within a filter component. Data to be processed is passed through pipes. These pipes can be used for buffering or for synchronization purposes.

Usage

  • Compilers. The consecutive filters perform lexical analysis, parsing, semantic analysis, and code generation.

  • Workflows in bioinformatics.

Pipe-filter pattern

Blackboard pattern

This pattern is useful for problems for which no deterministic solution strategies are known. The blackboard pattern consists of 3 main components.

  • blackboard — a structured global memory containing objects from the solution space

  • knowledge source — specialized modules with their own representation

  • control component — selects, configures and executes modules.

All the components have access to the blackboard. Components may produce new data objects that are added to the blackboard. Components look for particular kinds of data on the blackboard, and may find these by pattern matching with the existing knowledge source.

Usage

  • Speech recognition

  • Vehicle identification and tracking

  • Protein structure identification

  • Sonar signals interpretation.

Blackboard pattern

Comparison of Architectural Patterns

The table given below summarizes the pros and cons of each architectural pattern.

Books

  1. Bioinformatics for Dummies by Cedric Notredame and Jean-Michel Claverie

  2. Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools by Supratim Choudhuri

  3. Bioinformatics Programming in Python: A Practical Course for Beginners by Ruediger-Marcus Flaig

  4. Bioinformatics Programming Using Python by Mitchell L. Model

  5. Python Programming for Biology: Bioinformatics and Beyond 1st Edition, Kindle Edition

    by Tim J. Stevens, Wayne Boucher

  6. http://biopython.org/DIST/docs/tutorial/Tutorial.html

Software

LogoFind Cancer Research Jobs: Join the Team, Join the Fight — Freenome
LogoKubeflowKubeflow
LogoTutorial: Luigi for Scientific Workflows | RIL Labsrilpartner
LogoAirbnb Engineering & Data Science
LogoIntroducing Ludwig, a Code-Free Deep Learning ToolboxUber Engineering Blog
LogoData pipelines, Luigi, Airflow: everything you need to knowMedium
LogoA Dummies’ Intro to BioinformaticsMedium
LogoBioinformaticsScienceDaily
LogoBioinformatics, Big Data, and CancerNational Cancer Institute
LogoStarting off in Bioinformatics — DNA Nucleotides and StrandsMedium
LogoDNA Sequence Data Analysis — Starting off in BioinformaticsMedium
LogoPairwise Sequence Alignment using BiopythonMedium
Logo10 Common Software Architectural Patterns in a nutshellMedium
LogoMultiple Sequence Alignment using Clustal Omega and T-CoffeeMedium
LogoBioinformatics Workflow Management SystemsMedium
LogoMolecular Phylogenetics using Bio.PhyloMedium
LogoList of sequence alignment softwareWikipedia
DNA sequencing - Bioinformatics.Org Wiki
LogoBiopython · Biopython