Machine Learning Engineer (Data science / Deep learning)

Salary for this Role:

From £48,600 with benefits, subject to skills and experience

Job Title:

Machine Learning Engineer (Data science / Deep learning)

Reports to:

Amy Strange

Closing Date:

19/Jan/2025 23.59 GMT

Job Description:

Machine Learning Engineer (Data science / Deep learning)

From £48,600 with benefits, subject to skills and experience

Contract term: 3 years

Reports to: Amy Strange, Software Engineering and AI Facility Lead and MANIFEST Consortium Lead, Prof. Samra Turajlic

The role will be placed in the Software Engineering and AI facility and will support the MANIFEST research platform led by Prof. Samra Turajlic (Cancer Dynamics Laboratory).

The Research Group & Project

THE MANIFEST RESEARCH PLATFORM

Harnessing the immune system to treat cancer has revolutionised survival outcomes for many patients. Immune checkpoint inhibitor therapies which unleash the brakes from immune cells to kill cancer cells, have become standard of care for many cancer subtypes. The success of existing, emerging and future immunotherapies and their routine use in the NHS is dependent on the appropriate tools, data and technology to rationalise their use and manage their side effects. Nevertheless, almost no biomarkers today can effectively distinguish responders from non-responders, predict toxicity, or guide treatment choices.

An exciting Machine Learning Engineer post is available in the Cancer Dynamics Laboratory. The post holder would work across multiple on-going projects of the lab, including a dedicated role within the MANIFEST project (“Multiomic ANalysis of Immunotherapy Features Evidencing Success and Toxicity”), a newly formed ambitious multi-stakeholder consortium involving academic, industry and NHS partners to deliver deep multi-omic profiling for patients with cancer undergoing immunotherapy. The MANIFEST consortium represents a diverse group of UK-wide experts in cancer research and clinical care comprising major NHS trusts, academic institutes and universities, and industry partners. This grant is funded by the UK Office of Life Sciences (OLS) and the Medical Research Council (MRC).

MANIFEST addresses the critical challenge in cancer treatment: predicting how patients will respond to immunotherapy. By integrating multio-omic data and innovative methodologies, this platform aims to enhance treatment precision and effectiveness.

More information about research interests and on-going projects of Cancer Dynamics Laboratory can be found here: https://www.crick.ac.uk/research/labs/samra-turajlic

More information about MANIFEST can be found here: https://www.manifest-io.org.uk/about.

SUMMARY OF THE ROLE

We are looking for a data scientist / machine learning engineer to join the project team to work on integrated and multimodal approaches to predicting immune-oncology response for the unique dataset being compiled as part of the MANIFEST consortium. Specifically, this role will be focussed on multiomics (RNASeq, WES, WGS), blood and clinical data initially but there may be opportunity to expand into imaging modalities later on. This is an opportunity to develop state-of-the-art deep learning methods for a remarkable dataset.

The post holder will work closely with the Software Engineering and AI team and Cancer Dynamics lab within the Francis Crick Institute. They will also interact closely with other laboratory staff from the MANIFEST platform, as well as with post-docs, students, scientists, technicians from the lab, and scientific partners of MANIFEST.

Key Responsibilities

These include but are not limited to:

• To develop machine learning based analyses approaches in accordance with the requirements of the project

• Stay current with the latest thinking in the field through building a library of related publications

• Develop approaches to evaluate the performance of ML models in relation to project objectives

• Design and develop high-quality, optimised and maintainable pipelines and software to meet project needs

• Work in close collaboration with clinical scientists, bioinformaticians and other project team members both within the Facility and MANIFEST platform to understand the full range of data and meta-data being produced for the project

• Assist with creating and supporting a productive and efficient standardised model development work-flow as appropriate for the project (including versioning and automation)

• Produce, update or otherwise maintain documentation for project, and present results updates back to the project team and other collaborators

• Assist with workload planning by providing estimates

• Provide engineering support and mentoring as required to other members of the project team

• To attend, and report research results at regular group meetings.

• To write and present work to MANIFEST stakeholders as required.

• To engage in relevant MANIFEST programme workflows with academic, NHS and industry partners.

Person Specification

The post holder should embody and demonstrate our core Crick values: bold, imaginative, open, dynamic and collegial, in addition to the following:

Essential skills/experience

• Strong mathematical/statistical background with demonstrable experience in developing deep learning algorithms for research

• Expert level technical programming skills, with emphasis on Python (NumPy, PyTorch etc) and preferably experience with R

• Experience of applying deep learning techniques to omics datasets

• Ability to read machine learning research articles and implement the algorithms described

• Experience of working with high performance computing clusters (Bash, Slurm etc)

• Good understanding of MLOps for experiment tracking, model and data versioning, hyperparameter tuning and results visualisation

• Experience in database technologies: SQL, NoSQL.

• An understanding of good software engineering principles

• An understanding of reproducibility, repeatability and replicability for scientific software

• Able to work both autonomously and collaboratively in multidisciplinary teams

• Excellent communication skills, with the ability to build effective relationships at all levels and the ability to communicate technical concepts to a non-technical audience

• First- rate problem solving skills

• Able to work accurately under pressure and delivering with tight deadlines

• Degree in Computer Science, Machine Learning or equivalent experience and a demonstrable track record of working on these types of problems with impactful results

Desirable skills/experience

• Familiarity with SOTA methods for combining multi--omics datasets ideally including natural language methods

• Knowledge of XAI approaches, uncertainty quantification and safety in the use of AI in a medical setting

• Background knowledge of immune-oncology

• Experience of working with clinical data and/or developing tools ultimately to be used in a clinical environment

• Experience with other technologies/languages (C++, Matlab, Nextflow)

• Working experience in large-scale omics data analysis applications and databases

• Experience of working with Public Cloud (AWS/GCP/Azure)

• Experience of Agile or similar delivery oriented project methods and tools

• Building data visualisation tools

• A publication history in applicable domains

• Technical writing skills

About Us

At the Crick, we conduct research at the forefront of biomedical research. We combine rigour with an open and collaborative culture, and are outward-looking, reflecting our status as a partnership of six organisations aiming to pool knowledge, ideas and resources.

We have a wide research portfolio with no divisions or departments, bringing biomedical researchers together with clinicians, physical scientists and applied scientists from our pharmaceutical partners.

We aim to attract the most talented researchers and support them to tackle innovative research questions. Our science technology platforms provide our researchers with access to state-of-the-art technology and expertise.

We provide an excellent learning environment with dedicated education programmes in public engagement with science, education and personal development, and a postdoc training programme that prepares scientists for leadership roles in science.

• If you are interested in applying for this role, please apply via our website.

• All offers of employment are subject to successful security screening and continuous eligibility to work in the United Kingdom.

• If you require a visa to work in the UK we will help support your application should you be successful

Find out what benefits the Crick has to offer:

For more information on our great pay and benefits package please click here: https://www.crick.ac.uk/careers-and-study/life-at-the-crick/pay-and-benefits

Equality, Diversity & Inclusion:

We welcome applications from all backgrounds. We are committed to providing equal employment opportunities, regardless of ethnicity, nationality, gender, sexual orientation, gender identity, religion, pregnancy, age, disability, or civil partnership, marital or family status. We particularly welcome applications from people who are Minority Ethnic as they are currently underrepresented in the Crick at this level.

Diversity is essential to excellence in scientific endeavour. It increases breadth and perspective, leading to more innovation and creativity. We want the Crick to be a place where everyone feels valued and where diversity is celebrated and seen as part of the foundation for our Institute’s success.

The Crick is committed to creating equality of opportunity and promoting diversity and inclusivity. We all share in the responsibility to actively promote dignity, respect, inclusivity and equal treatment and it is our aim to ensure that these principles are reflected and implemented in all strategies, policies and practices.

Read more on our website: https://www.crick.ac.uk/careers-and-study/life-at-the-crick/equality-diversity-and-inclusion