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Machine Learning Engineer (Senior/ Staff)
Deep Genomics
Toronto, Ontario
About Us
Deep Genomics is a startup company that aims to revolutionize drug development by leveraging expertise in artificial intelligence (AI) to decode RNA biology. Our proprietary platform, the AI Workbench, enables us to decode the enormous complexity of RNA biology to find novel targets, mechanisms, and molecules that are not accessible through traditional methods. We use this advanced technology to develop steric-blocking oligonucleotides (SBOs) that achieve expression increase for the treatment of genetic disease. Founded in 2015, our multidisciplinary team includes expertise in a diverse range of disciplines including those found in a traditional drug company, as well as machine learning, laboratory automation, and software engineering.  Deep Genomics is based in Toronto, Ontario with additional locations in  Cambridge, Massachusetts and Montreal, Quebec.

Where You Fit In
As an ML Engineer you will be a part of the core ML group responsible for developing the models that power our AI workbench. You will be responsible for designing, developing, and deploying machine learning models as well as the software infrastructure for rapid and reproducible model development.

What you will do:

    • Work with our ML scientists to develop models and algorithms using state-of-the-art neural network methodologies.
    • Develop evaluation, visualization, and productivity tools for streamlining machine learning research.
    • Adapt our algorithms and architectures to best exploit modern cloud computing environments (GPUs/TPUs)
    • Keep up-to-date with the latest ML research and techniques, and apply them to our solutions.
    • Mentor and guide junior machine learning engineers.

What you bring:

    • Solid Engineering and Computer Science fundamentals, ideally with a degree in CS, Math, or equivalent experience.
    • 5+ years of professional experience as a software developer/engineer
    • Experience in architecting, developing, and deploying large software systems in a leading position
    • Expertise with implementation details of large neural-network architectures such as Transformers with frameworks like PyTorch, Tensorflow, Keras, JAX, etc.
    • Experience with CloudML and MLOps tools (e.g. Kubeflow, AWS Sagemaker, Google AI Platform, Azure Machine Learning).
    • Excellent communication skills and the ability to work in a team environment.

Nice to have:

    • Experience within the biotechnology or healthcare space.

What we offer:

    • A highly competitive salary and meaningful equity compensation (ESOPs)
    • A wide array of company-paid benefits
    • Exceptional opportunities for learning and growth working alongside a world-class team of researchers and software developers working at the intersection of the most exciting areas of science and technology.
Deep Genomics thanks all applicants, however only those selected for an interview will be contacted.    

Deep Genomics welcomes and encourages applications from people with disabilities. Accommodations are available on request for candidates taking part in all aspects of the selection process
Full-time
Senior
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Software Engineering Infrastructure Intern (Jan 2024-Aug 2024)
Deep Genomics
Toronto, Ontario
About Us
Deep Genomics is a startup company that aims to revolutionize drug development by leveraging expertise in artificial intelligence (AI) to decode RNA biology. Our proprietary platform, the AI Workbench, enables us to decode the enormous complexity of RNA biology to find novel targets, mechanisms, and molecules that are not accessible through traditional methods. We use this advanced technology to develop steric-blocking oligonucleotides (SBOs) that achieve expression increase for the treatment of genetic disease. Founded in 2015, our multidisciplinary team includes expertise in a diverse range of disciplines including those found in a traditional drug company, as well as machine learning, laboratory automation, and software engineering.  Deep Genomics is based in Toronto, Ontario with an additional location in Cambridge, Massachusetts,

Where You Fit In
We’re looking for a highly motivated software engineer intern to be part of our multidisciplinary team that is revolutionizing drug development through AI. Deep Genomics is poised to become the foremost AI-powered genetic medicine company by using data-driven approaches at every step of the drug design process.
You’d work alongside experienced software engineers to build world-class tools and services for our internal platform, which powers the core components of the company: analysis and ingestion of raw data from various lab experiments (both manual and through our robotics platforms), powering the ML data and compute backends (e.g. running large-scale computational processes in the cloud), and state-of-the-art bioinformatics tools. The focus of this position is our compute infrastructure, particularly the ergonomics of the tools we use to run large workloads in the cloud.

What you bring:

    • Prior experience with cloud computing and Docker
    • Solid knowledge of Python
    • Solid understanding of Unix shell programming and related tools
    • Basic knowledge of networks (if you've ever configured a proxy, you'll be OK)

Nice to have:

    • Familiarity with workflow engines, in particular Cromwell
    • Prior DevOps experience (CI/CD, dev tooling, compute infrastructure)
    • Knowledge of Kubernetes fundamentals
    • Experience with Envoy, Ngnix, Tailscale, or adjacent tools
    • Prior experience with Golang a plus

What we offer:

    • A highly competitive salary 
    • Exceptional opportunities for learning and growth working alongside a world-class team of researchers and software developers working at the intersection of the most exciting areas of science and technology.
Deep Genomics thanks all applicants, however only those selected for an interview will be contacted.    

Deep Genomics welcomes and encourages applications from people with disabilities. Accommodations are available on request for candidates taking part in all aspects of the selection process
Internship
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Senior Data Scientist
Deep Genomics
Toronto, Ontario
About Us
Deep Genomics is a startup company that aims to revolutionize drug development by leveraging expertise in artificial intelligence (AI) to decode RNA biology. Our proprietary platform, the AI Workbench, enables us to decode the enormous complexity of RNA biology to find novel targets, mechanisms, and molecules that are not accessible through traditional methods. We use this advanced technology to develop steric-blocking oligonucleotides (SBOs) that achieve expression increase for the treatment of genetic disease. Founded in 2015, our multidisciplinary team includes expertise in a diverse range of disciplines including those found in a traditional drug company, as well as machine learning, laboratory automation, and software engineering.  Deep Genomics is based in Toronto, Ontario with an additional location in Cambridge, Massachusetts.

Where You Fit In 
We are looking for a Senior Data Scientist to join our team of machine learning scientists, software engineers, and wet lab biologists. Your role will focus on collaborating closely with bench scientists to design experiments and analyze data. You will also work alongside machine learning scientists, applying ML models to practical, impactful projects.

What you will do:

    • Collaborate with wet lab scientists on experimental design and data analysis.
    • Develop and maintain tools for automating data analysis pipelines.
    • Benchmark internal and external machine learning models, focusing on applications like variant effect prediction and RNA therapeutic design.
    • Mentor and guide junior data scientists, fostering a supportive and collaborative environment for team growth and learning.

What you bring:

    • An MSc or PhD in computational biology, biostatistics, or a related field.
    • At least three years of experience working with experimental teams.
    • A strong understanding of statistics.
    • Solid experience in software engineering best practices, such as version control, unit testing, and continuous integration.

Nice to have:

    • Experience with deep learning models applied to biology

What we offer:

    • A highly competitive salary and meaningful equity compensation (ESOPs)
    • A wide array of company-paid benefits
    • Exceptional opportunities for learning and growth working alongside a world-class team of researchers and software developers working at the intersection of the most exciting areas of science and technology.
Deep Genomics thanks all applicants, however only those selected for an interview will be contacted.    

Deep Genomics welcomes and encourages applications from people with disabilities. Accommodations are available on request for candidates taking part in all aspects of the selection process.
Full-time
Senior
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Head of Machine Learning
Deep Genomics
Toronto, Ontario
About Us

Deep Genomics is a startup company that aims to revolutionize drug development using artificial intelligence built to decode RNA biology and RNA therapeutics. Our proprietary AI platform enables us to decode the enormous complexity of RNA biology to find novel targets, mechanisms, and molecules that are not accessible through traditional methods. We use this advanced technology to discover genetic targets for human diseases, and develop RNA therapeutics, with a focus on steric-blocking oligonucleotides (SBOs) that achieve expression increase for the treatment of genetic disease. Founded in 2015, our multidisciplinary team includes expertise in a diverse range of disciplines including those found in a traditional drug company, as well as machine learning, statistical genetics, applied data science, deep bioinformatics, software engineering and laboratory automation. Deep Genomics is based in Toronto, Ontario and Cambridge, Massachusetts.

Opportunity

As the Head of Machine Learning, you will assume a pivotal role in leading a dynamic, cross-disciplinary team of ML scientists, ML engineers, and computational biologists, and collaborating closely with our applied data science, statistical genetics and software engineering teams. You will be responsible for guiding and shaping our strategy for developing differentiating ML capabilities for drug development, and working directly with the executive team to achieve ML goals that directly impact company objectives and are meaningful to our partners, our investors and our board of directors. You will play a key role in shaping the design and execution of ML research projects by harnessing the latest methodologies and best engineering practices, including foundation models, transformers and generative AI. In addition, your responsibilities will encompass team coordination, talent acquisition, and seamless collaboration with other departments within the organization. We are seeking a self-motivated individual with exceptional communication skills and a high degree of emotional intelligence. If you have the curiosity, passion, and collaborative spirit, let's work together!

What you bring:

    • A PhD in machine learning, computer science or other quantitative discipline; or equivalent industry experience.
    • Deep expertise in contemporary AI/ML methods and their applications to problems in genomics and related areas of biology.
    • Experience managing teams of ML scientists and engineers, including setting and tracking team goals and timelines, providing feedback to individuals and supporting their development, and coordinating with necessary support functions, such as software engineering, data science, bioinformatics and statistics.
    • Mentoring, developing and leading junior staff from different backgrounds across machine learning.
    • Technical leadership experience and familiarity with modern software engineering practices and tools such as Github, CI/CD pipelines, cloud frameworks, and others.
    • Demonstrated track record in building collaborations and an ability to communicate effectively with diverse teams and functions, including data scientists or computational biologists, engineers and experimental biologists.
    • Experience working under pressure, managing projects and delivering results on time.
    • An inspirational and energetic working style, coupled with the highest standards of scientific rigor and integrity.

What we offer:

    • Building technologies that can directly impact the lives of patients.
    • A competitive salary plus equity compensation (ESOPs).
    • A wide array of company-paid benefits.
    • Flexibility in remote working.
    • Exceptional opportunities for learning and growth in a world-class team of researchers and software developers, working at the intersection of the most exciting areas of science and technology.
Deep Genomics welcomes and encourages applications from people with disabilities. Accommodations are available on request for candidates taking part in all aspects of the selection process.

Deep Genomics thanks all applicants, however only those selected for an interview will be contacted.
Full-time
Senior
Deep Learning