Senior Director of Bio Machine Learning - 136085

The Ideker Laboratory is in the Division of Human Genetics and Precision Medicine at UC San Diego School of Medicine. We are a vibrant research team of 30-40 staff, postdocs, graduate students, and undergraduate students known for its dynamic and collaborative environment. We perform bioinformatics research coupled with wet-lab investigations, working in the areas of network biology, data-driven hierarchical modeling, and machine learning applied to biomedicine. We also support multiple open-source software projects, some with 100K+ users. One of the main research goals of the Ideker Lab is to create artificially intelligent, mechanistic models of cancer for translation of patient data to precision diagnosis and treatment. We are advancing this goal by developing "visible" predictive machine learning approaches to model the flow of genetic information to translate genotype to phenotype and, importantly, to identify the molecular functions and mechanisms by which these predictions are made.

The Ideker Laboratory at UC San Diego is recruiting a Senior Director of BioMachine Learning (BioML) to lead machine learning research and development at the Center for Dynamic Digital Tumors, a recently launched national precision oncology initiative (digitaltumors.org). This center forms the central AI prediction hub of the ARPA-H ADAPT program (arpa-h.gov/explore-funding/programs/adapt).

The overall goal of the project is to use advanced AI/ML technologies to deliver the right therapy to the right patients at the right time. The project will revolutionize cancer treatment via interpretable AI/ML models which learn to predict patient drug responses, enabling dynamical cancer treatment strategies and personalized therapies for patients with metastatic cancers. This position will oversee AI/ML research projects and objectives toward the successful completion of the APRA-H ADAPT program goals.

In particular, the position will:- Direct a team of 3-4 talented AI/ML professionals and trainees in the design and implementation of a drug recommender system for cancer.

• Foster interdisciplinary collaborations among biologists, oncologists, statisticians, and other computational/ML scientists to translate computational findings into therapeutic strategies.

• Design, debug, and optimize algorithms and computational techniques to analyze and fuse complex, multimodal datasets, including genomic, transcriptomic and proteomic data from various sources for biomarker discovery and therapy recommendation.

• Create and validate computational tools to track tumor changes and adapt therapy plans in real-time using insights from clinical data.

• Oversee creation of a central benchmarking platform for standardizing AI/ML models.

• Contribute to the creation and maintenance of a central cancer treatment and analysis platform, ensuring accurate and timely data availability for clinicians and researchers.

• Provide mentorship and guidance to junior researchers, including PhD students and postdocs, fostering expertise in bioML and its applications in oncology.

• Prepare detailed reports, publications, and presentations showcasing progress on ADAPT program goals, and represent the lab at national and international conferences.

In addition to the main ADAPT initiative, we expect that this position will work on and potentially lead other projects within the Ideker Lab research portfolio as needed.

Additional details and responsibilities:- Has wide-ranging, extensive experience with computational, computer science, data science, and CI software research and development principles, with relevant domain science knowledge where applicable, performs up to and including the most complex research, technology and software development projects with sitewide, institution-wide and / or multi-institutional scope.

• Represents organization at national and international meetings, conferences and committees.

• Considered research and technology expert in multiple aspects of HPC, data science, and CI.

• Advises on and resolves highly complex research and technology projects / issues.

• Directs the design, implementation and selection of new hardware and software technologies for advancing complex HPC, data science, and CI projects.

• Presents research and technical briefings to senior management, institution-wide, national and international audiences.

• Contributes to the research and technical direction in one or more technical specialties.

• Performs advanced research and technology development to contribute to design of future HPC, data science, and CI hardware and software systems.

• Bachelor's degree in related area and / or equivalent experience / training plus seven (7) or more years of relevant experience.

• Expert knowledge of HPC / data science / CI.

• Expert skills and demonstrated experience associated with one or more of the following: HPC hardware and software power and performance analysis and research, design, modification, implementation and deployment of diverse and complex HPC or data science or CI applications and tools of campus wide / multi-institutional scope.

• Demonstrated ability to effectively communicate with executive-level management on a regular basis as well as funding agency program managers / directors.

• Demonstrated ability to communicate technical information to technical and non-technical personnel at various levels in the organization and to external research and education audiences as well as senior research, academic and government officials.

• Expert skills and experience in independently resolving highly complex computing / data / CI problems using introductory and / or intermediate principles.

• Self-motivated and works independently and as part of a team.

• Expert experience working in a complex computing / data / CI environment encompassing all or some of the following: HPC, data science infrastructure and tools / software, and diverse domain science application base.

• Expert ability to successfully lead and manage multiple concurrent projects. Excellent research and technology project leadership and management skills.

• Expert ability to independently plan, guide and execute innovative scientific research programs and development projects to completion by selecting approaches, and interpreting and evaluating results with researchers, staff and colleagues and supervisors.

• Demonstrated expert experience in one or more of the following: optimizing, benchmarking, HPC performance and power modeling, analyzing hardware, software, and applications for HPC / data / CI.

• Proven ability to establish realistic research priorities and lead, motivate and guide colleagues and staff for a sustained effort.

• Advanced knowledge of deep learning model architectures and modern AI/ML technologies. Experience in deep learning is essential, including but not limited to transformer models, transfer and meta-learning, and multi-modal data fusion approaches.

• PhD in Computer Science, Statistics, Mathematics, Bioinformatics, or related discipline.

• Three (3) years of relevant work experience in industry or academia.

• Demonstrated ability to develop and lead one or multi-institutional national scale proposals and acquire funding.

• Prior experience in bioinformatics and cancer biology.

• Employment is subject to a criminal background check.