Machine Learning Scientist – Computational Pathology

Machine Learning Scientist – Computational Pathology

Job Description

20 petabytes of data! 2 million patient-years of information and 30 data domains from preclinical through Phase 3 trials! All waiting for you to unlock the next breakthrough in medicine.

The Pre-Clinical Safety Project Pathology group in the Novartis Institutes for Biomedical Research (NIBR), Basel, is looking for you, an inspiring leader and authority in machine/deep learning (ML/DL) and imaging data science. We seek a computational scientist to help us pioneer machine learning approaches for the analysis of histopathological whole slide images (WSI). Explore new ways to integrate WSI data with various data sources: in vivo (clinical observations, body and organ weights, clinical pathology and biomarker results and omics) and in vitro toxicology data (off target screening), publications, Real World Evidence (RWE), Electronic Health Records (EHR), clinical trials data, assay data, omics, clinical biomarkers and/or other sources to support decision-making for drug discovery.

• We want you to explore novel machine learning methods, extract reliable insight from Whole-slide images (WSI) and identify correlations with multiple related data sources helping us to better understand the mechanisms of toxicity and clinical translatability.

• Provide us with guidance on analysis methods, data visualization, data integration, computational infrastructure, HPC/Cloud workflows for computational pathology.

• Work with different line functions with a focus on digital pathology, secondary pharmacology and multi-modal data integration.

• Join our safety assessment teams with the responsibility of accelerating the application of computational pathology data annotation, analysis and building decision support algorithms.

• Share knowledge with colleagues and train them on ML and computational approaches including model understanding/interpretability.

• Represent us in external and intra-departmental collaborations.

• Engage with the broader data science community within Translational Medicine, with data science partners in functions across Novartis, as well as external partners.

Minimum requirements


• PhD or MS in a quantitative subject (e.g. computer science, engineering, statistics, mathematics, bioinformatics, computational biology or related field), including mathematical foundations for machine learning (including deep learning), signal processing and image processing.

• Solid background in image analysis, data visualization and machine learning.

• Practical experience in multiple programming languages including Python, C/C++ and Matlab. Experience with commonly used deep learning frameworks (e.g. TensorFlow, Pytorch, Caffe, etc.) and model architectures. Experience with Pandas, Numpy, Holoviews, Bokeh, Plotly, H5py, OpenCV and OpenSlide is a plus.

• Good technical experience and organizational skills to lead complex machine learning projects/initiatives. Demonstrated ability to design, implement and rollout analysis solutions.

• Experience in designing custom practical interactive visual data exploration interfaces for domain specialists.

• Extensive experience designing and implementing large data workflows (especially image data) using a scientific computing environment on Unix/Linux (HPC, Cloud). Experience in scaling and optimizing ML/DL models (on clusters of GPUs and CPUs) using frameworks such as Horovod.

• Shown experience in pulling and consolidating data from multiple systems, geographical locations and in varied formats. Experience with knowledge graph databases would be useful

750 million. That’s how many lives our products touch. And while we’re proud of that fact, in this world of digital and technological transformation, we must also ask ourselves this: how can we continue to improve and extend even more people’s lives?

We believe the answers are found when curious, courageous and collaborative people like you are empowered to ask new questions, make bolder decisions and take smarter risks.

We are Novartis. Join us and help us reimagine medicine.
Translational Medicine
Novartis Pharma AG
Research & Development
Full Time