CBIIT Speaker Series Page

Cancer patients and their doctors choose from a range of different treatment options. But often the chosen treatment is ineffective, reducing quality and length of life and increasing cost. Today treatment decisions and outcomes occur in isolation. All4Cure has built a patient-centered, web-based, knowledge sharing platform that graphically portrays treatments and responses extracted from the medical records of de-identified patients with multiple myeloma (the second most common form of blood cancer) for comment by a community of participating patients, clinicians and researchers. Having assembled more than 580 participants we will describe examples of patients have benefited from their participation.

Session details...

Cancer is a complex category of diseases caused in large part by genetic or genomic, transcriptomic, proteomic, and epigenomics alterations leading to abnormal cell proliferation.  Genes and their protein products rarely act in isolation. Therefore, it is necessary to utilize a comprehensive and integrated computational approach informed by systems biology and omics-oriented approaches to investigate the disruption of biological networks caused by genomic alterations.

In this talk, Dr. Meerzaman will describe two ongoing projects. The first focuses on Sequencing Quality Control Phase 2 (SEQC II), a collaborative project led by the Food and Drug Administration (FDA) that systematically investigated somatic mutations in paired breast cancer and normal cell lines and formulated best practices for identifying, or calling, genomic variations such as single-nucleotide polymorphisms, copy-number alterations, or single-nucleotide variants. Regarding the second project, Dr. Meerzaman will discuss methods developed by the CGBG team to use mutual exclusivity and pathway network interaction algorithms to identify low-frequency “driver” (that is, causative) genomic alterations at the pathway level.

Session details...

Deep learning methods have shown substantial promise across many tasks, including some relevant to biomedicine. I'll chat about some examples of how these algorithms can be used as well as the challenges that I expect us to face as we start using these on a massive scale. Also, as deep learning methods proliferate in the biomedical sciences, I expect that we will need to reconsider how we discuss reproducibility in computational research. I'll touch on a couple steps towards these objectives, but substantially more work will be needed.

Session details...

The success of an AI system depends on the amount and quality of data used to train it. The database that was key to the latest AI revolution (ImageNet) contains millions of real-life images labeled into thousands of categories. No data collections of comparable extent and quality exist for radiology data. By many, this is considered to be the biggest challenge for AI in radiology. Training of AI models requires medical images accompanied by metadata and expert annotations (e.g., spatial location of the finding, its clinical characteristics), ideally linked with the non-imaging part of the patient record (e.g., biopsy results, genomic and blood serum tests). Large volumes of clinical images are routinely collected, interpreted visually and analyzed quantitatively, both in clinical and research studies.

Nevertheless, the result is often optimized for reuse by a human — not an algorithm. Tremendous effort is often needed to prepare datasets for AI training, combine data sets across sites or collections, or aggregate versatile datasets as often required to develop robust models. With the recent advances in automated imaging-based tissue phenotyping (radiomics) and other relevant AI technologies, there is a new realization of the value of the large, structured AI-ready datasets.

There are many obstacles and few incentives for engineering datasets to optimize machine-level reusability. Non-technical issues aside, there are major challenges of choosing a data format, defining a data model, deciding what attributes of the data may be valuable for the future unforeseen use cases and how those can be captured in a structured and self-documenting manner, and identifying practical tools to help with those tasks. Over the past five years, we have directed our efforts to incrementally and collaboratively advance data engineering practices as applied to medical imaging research. We are extending the existing, broadly adopted DICOM standard, to support the needs of medical imaging research applications, and subsequent implementation into clinical systems. We develop open source tools that enable standardization of common outputs of image analysis. We established collaborations with a number of academic and industry groups to encourage, support and evaluate adoption of the standard. We have been leading efforts in training and outreach, aiming to educate the community about the capabilities of the standard and the supporting tools. In parallel with developing support for the generic data types commonly encountered in imaging research, we are also working on targeted solutions for the specific research workflows of interest in several cancer types.

In this talk, I will discuss our progress to date in developing the ecosystem of standards, tools, use cases, datasets, publications, and outreach activities that have the overarching goal of improving data engineering practices. I will also present some of our ongoing work developing integrated technology solutions that are used to support clinical research at our site, and the role of data as the backbone of downstream innovation.

Session details...