Senior Bio Machine Learning Scientist - 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 is recruiting a Senior BioMachine Learning (BioML) Scientist to lead machine learning R&D for the ADAPT project, a new precision cancer therapy initiative funded by ARPA-H. The overall goal of the ADAPT project is to use advanced AI/ML technologies to deliver the right therapy to the right patients at the right time. ADAPT will revolutionize cancer treatment by using predictive biomarkers and interpretable AI/ML to create dynamical cancer treatment strategies and personalized therapies for patients suffering with metastatic cancers.

Under general supervision, the Senior BioMachine Learning Scientist will oversee bioML research projects and objectives toward the successful completion of the APRA-H ADAPT program goals. This role will require expertise in bioinformatics, machine learning, systems biology, and project leadership, with a deep understanding of modern cancer biology. In particular, this position will:

-Lead the design and implementation of machine learning approaches for drug recommendation in cancer.-Serve as a computational lead in interdisciplinary teams, collaborating with 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 complex, multimodal datasets, including genomic, proteomic, and transcriptomic, and clinical data.-Develop multi-modal data fusion pipelines 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 biomarker data.-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 guidance to junior researchers, including PhD students and postdocs, fostering expertise in bioML and its applications in oncology.-Lead the development and dissemination of robust, scalable bioinformatics software, ensuring alignment with FAIR data principles and accessibility to the broader research community.-Prepare detailed reports, publications, and presentations showcasing progress on ADAPT program goals, and represent the lab at national and international conferences.-Collaborate closely with the Ideker Lab's Program Manager to identify and pursue new funding opportunities, align lab objectives with emerging trends in precision medicine, and contribute to grant proposals to support long-term research initiatives.-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.

In general, this position involves a hybrid of multiple computational / data / Cyberinfrastructure (CI) dominated fields such as, but not limited to, bioinformatics, geological information services (GIS), data analytics, and computational chemistry. Applies computational, computer science, data science and cyber infrastructure (CI) research and development principles, with relevant domain science knowledge, to perform research and technology integration and development. Responsibilities include research, design, development, analysis, operation, and support of high performance computing (HPC) and data science research, software, tools and hardware resources. Develops data algorithms and performs computations, statistical analyses, interpretation and reporting of research. This specialty / function exists for those positions whose primary responsibility is to do research and use computational and data science technology as a tool to accomplish the research.

Applies skills as a seasoned, experienced IT research professional in diverse research application areas. Usescomputational, computer science, data science, and CI software research and development principles, with relevant domain science knowledge where applicable, along with professional programming concepts for medium-sized projects or portions of larger projects. Develops and optimizes a variety of computational, data science, and CI research tools and components. Performs research on current and future HPC, data, and CI technologies, hardware and software projects. Works on algorithm development, optimization, programming, performance analysis and / or benchmarking assignments of moderate scope where the tasks involve knowledge of either domain / computer science research requirements and / or CI design / implementation requirements.

• Seven years of related experience, education/training, OR an Bachelor's degree in related area plus three years of related experience/training.

• Demonstrated broad 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 understand research computing / data / CI needs, mapping use cases to requirements and how systems / software / infrastructure can support those needs and meet the requirements. Demonstrated ability to develop and implement such solutions.

• Demonstrated experience and ability to collaborate effectively with all levels of staff; technical, students, faculty and administrators.

• Self-motivated and works independently and as part of a team. Able to learn effectively and meet deadlines.

• Intermediate knowledge of HPC / data science / CI.

• Advanced 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 HPC or data science or CI applications and tools.

• Demonstrated ability to regularly interface with management.

• Demonstrated ability to contribute research and technical content to grant proposals.

• Demonstrated effective communication and interpersonal skills. 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.

• Proven skills and experience in independently resolving broad computing / data / CI problems using introductory and / or intermediate principles.

• Thorough 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.

• Proven ability to successfully work on multiple concurrent projects

• Employment is subject to a criminal background check.

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