Complex information networks are ubiquitous with increasingly voluminous and diverse data: examples include social networks, medical health records, stock market, disaster response, and environmental science. Complex, partial, unstructured and time-varying multimodal data pose significant new challenges to knowledge discovery. Healthcare is an excellent example of a data offering all these challenges: patient health records, consisting of imaging data (CT scans, MRI, pathology images), physiological measurements, physician notes, disease states, treatment history including medication, and outcomes (well-being of the patient). The spatial variations (e.g., in 2D/3D images) and temporal behavior (response to medication, changes in imaging and other measurements) are further complicated because data sampling is not uniform in any of these dimensions. The primary mission of the Center for Multimodal Big Data Science is to address the grand challenge of developing novel computational methods leveraging image analysis, natural language processing, machine learning, system identification and database technologies to discover significant knowledge to provide a transformative impact on a broad spectrum of applications.
A central component in this research effort is the BisQue image management and analysis platform that has been developed in the lab over the past 10 years. BisQue specifically supports large scale, multi-dimensional multimodal-images and image analysis. Metadata is stored as arbitrarily nested and linked tag/value pairs, allowing for domain-specific data organization. Image analysis modules can be added to perform complex analysis tasks on compute clusters. Analysis results are stored within the database for further querying and processing. The data and analysis provenance is maintained for reproducibility of results. BisQue can be easily deployed in cloud computing environments or on computer clusters for scalability. The user interacts with BisQue via any modern web browser.
The interdisciplinary research projects built on top of BisQue span four main areas: marine science, plant biology, materials science, and healthcare.
LIMPID/BisQue + IDEAS Joint Workshop, Feb 3-5, 2020
The center we will be hosting the second LIMPID/BisQue workshop on Scalable Image Informatics. This is a joint meeting with the workshop on Applications of Machine Learning and Scalable Image Informatics to Materials Discovery, held as part of the NSF-sponsored IDEAS program on Data-Driven Approaches to Materials Discovery, at the University of California at Santa Barbara. Participation is by invitation only and we are expecting over 80 registered participants.
The three day joint workshop will take place at UCSB from February 3-5, 2020. The workshop will start at 8:00 AM on Monday, February 3rd and adjourn by 5:00 PM on Wednesday, February 5th.
This workshop will bring together researchers from Academia and National Laboratories who are developing or have adopted new experimental methods and measurement tools that provide very large and rich data sets, with early adopters of machine learning as well as leaders in the machine learning community. The main objective of the LIMPID/BisQue workshop is to identify key requirements for scalability and sustainability of software infrastructures to support multimodal data analysis and machine learning in diverse application areas such as life sciences, marine science, materials and health sciences. A key objective of the IDEAS workshop is to connect researchers in the data sciences field with domain researchers to foster a dialogue and establish the state-of-the-art in the application of machine learning to materials discovery related disciplines, and identify (i) the potential impact of, and opportunities for, data sciences in materials, with an emphasis on integrating experimental and computational materials; and (ii) the grand challenges at the intersection of materials discovery and machine learning.
Monday will focus on sustainable software infrastructure for multimodal informatics and machine learning for image applications. Tuesday will address data-driven approaches for advanced materials applications, effectively educating a workforce of data-driven innovators, and high-throughput approaches in computational mechanics. Wednesday will focus on accelerating data-intensive research with a range of applications, and AI and ML for high-dimensional and multi-scale datasets.
Samantha Daly, Mechanical Engineering, UCSB; B.S. Manjunath, Electrical and Computer Engineering, UCSB; Tresa Pollock, Materials, UCSB
EM2 data and Cellular segmentation
Material Science & Structural Analysis
Dream3D and Structural Analysis
Patient monitoring and analytics
Underwater image segmentation and classification
- “Structure-Forming Corals and Sponges and Their Use as Fish Habitat in Bering Sea Submarine Canyons”,PLoS ONE, vol. 7, no. 3, Mar. 2013.
- Frontiers in plant science, vol. 2, Jul. 2013.
- Springer, pp. 56--66, Copenhagen, Denmark, Nov. 2015.
- IEEE Proceedings, pp. 1--9, Nov. 2016.
- Springer, ECCV-ACVR, pp. 178--194, Amsterdam, The Netherlands, Nov. 2016.
BisQue has been used to manage and analyze 23.3 hours (884GB) of high definition video from dives in Bering Sea submarine canyons to evaluate the density of fishes, structure-forming corals and sponges and to document and describe fishing damage.
The BisQue image analysis platform was used to develop algorithms to assay phenotypes such as directional root-tip growth or comparisons of seed size differences.
In this project, we integrate the microstructure analysis software package Dream.3D into BisQue.
The Multimodal Multiview Network for Healthcare is a collaborative effort between researchers from the Electrical and Computer Engineering Department at the University of California Santa Barbara and the intesivists and medical practitioners from the Medical Intensive Care Unit (MICU) at Santa Barbara Cottage Hospital. The Objective of the research is to improve quality of care by monitoring patients and workflows in real ICU rooms. The network is non-disruptive and non-intrusive and the methods and protocols to protect and maintain the privacy of patients and staff.
The center we will be hosting the second LIMPID/BisQue workshop on Scalable Image Informatics.
UCSB researchers given the award from NSF’s Office of Advanced Cyberinfrastructure to build a large-scale distributed image-processing infrastructure (LIMPID) through a broad, interdisciplinary collaboration.
Software and Resources
Bisque is an advanced image database and analysis system for multimocal images. It supports large scale image databases, flexible experimental data management, metatdata and content based search, analysis integration and knowledge discovery. The system is based on scalable web services.
Read more about LIMPID/BisQue in this Outreach Article.
Distinguished Professor, Electrical and Computer Engineering Department
Director, Center for Multimodal Big Data Science and Healthcare
University of California
Santa Barbara, CA 93106-9560
Tel: (805) 893 7112
E-mail: manj [at] ucsb [dot] ed