Stefan Dvoretskii

Linmin Pei, Granger Sutton, Michael Rutherford et al.

The de-identification (deID) of protected health information (PHI) and personally identifiable information (PII) is a fundamental requirement for sharing medical images, particularly through public repositories, to ensure compliance with patient privacy laws. In addition, preservation of non-PHI metadata to inform and enable downstream development of imaging artificial intelligence (AI) is an important consideration in biomedical research. The goal of MIDI-B was to provide a standardized platform for benchmarking of DICOM image deID tools based on a set of rules conformant to the HIPAA Safe Harbor regulation, the DICOM Attribute Confidentiality Profiles, and best practices in preservation of research-critical metadata, as defined by The Cancer Imaging Archive (TCIA). The challenge employed a large, diverse, multi-center, and multi-modality set of real de-identified radiology images with synthetic PHI/PII inserted. The MIDI-B Challenge consisted of three phases: training, validation, and test. Eighty individuals registered for the challenge. In the training phase, we encouraged participants to tune their algorithms using their in-house or public data. The validation and test phases utilized the DICOM images containing synthetic identifiers (of 216 and 322 subjects, respectively). Ten teams successfully completed the test phase of the challenge. To measure success of a rule-based approach to image deID, scores were computed as the percentage of correct actions from the total number of required actions. The scores ranged from 97.91% to 99.93%. Participants employed a variety of open-source and proprietary tools with customized configurations, large language models, and optical character recognition (OCR). In this paper we provide a comprehensive report on the MIDI-B Challenge's design, implementation, results, and lessons learned.

Stefan Dvoretskii, Anwai Archit, Constantin Pape et al.

Modern bioimage analysis approaches are data hungry, making it necessary for researchers to scavenge data beyond those collected within their (bio)imaging facilities. In addition to scale, bioimaging datasets must be accompanied with suitable, high-quality annotations and metadata. Although established data repositories such as the Image Data Resource (IDR) and BioImage Archive offer rich metadata, their contents typically cannot be directly consumed by image analysis tools without substantial data wrangling. Such a tedious assembly and conversion of (meta)data can account for a dedicated amount of time investment for researchers, hindering the development of more powerful analysis tools. Here, we introduce BioimageAIpub, a workflow that streamlines bioimaging data conversion, enabling a seamless upload to HuggingFace, a widely used platform for sharing machine learning datasets and models.

Bradly Alicea, Rishabh Chakrabarty, Stefan Dvoretskii et al.

There is much to learn through synthesis of Developmental Biology, Cognitive Science and Computational Modeling. Our path forward involves a design for developmentally-inspired learning agents based on Braitenberg Vehicles. Continual developmental neurosimulation allows us to consider the role of developmental trajectories in bridging the related phenomena of nervous system morphogenesis, developmental learning, and plasticity. Being closely tied to continual learning, our approach is tightly integrated with developmental embodiment, and can be implemented using a type of agent called developmental Braitenberg Vehicles (dBVs). dBVs begin their lives as a set of undefined structures that transform into agent-based systems including a body, sensors, effectors, and nervous system. This phenotype is characterized in terms of developmental timing: with distinct morphogenetic, critical, and acquisition (developmental learning) periods. We further propose that network morphogenesis can be accomplished using a genetic algorithmic approach, while developmental learning can be implemented using a number of computational methodologies. This approach provides a framework for adaptive agent behavior that might result from a developmental approach: namely by exploiting critical periods or growth and acquisition, an explicitly embodied network architecture, and a distinction between the assembly of neuronal networks and active learning on these networks. In conclusion, we will consider agent learning and development at different timescales, from very short (<100ms) intervals to long-term evolution. The development, evolution, and learning in an embodied agent-based approach is key to an integrative view of biologically-inspired intelligence.