Archives for September 2021

Check out our new paper at ICIP on multi-scale segmentation of brain structure from X-ray microCT image volumes!  [Check out our paper here!]

Abstract:   Methods for resolving the brain’s microstructure are rapidly improving, allowing us to image large brain volumes at high resolutions. As a result, the interrogation of samples spanning multiple diversified brain regions is becoming increasingly common. Understanding these samples often requires multiscale processing: segmentation of the detailed microstructure and large-scale modelling of the macrostructure. Current brain mapping algorithms often analyze data only at a single scale, and optimization for each scale occurs independently, potentially limiting the consistency, performance, and interpretability. In this work we introduce a deep learning framework for segmentation of brain structure at multiple scales. We leverage a modified U-Net architecture with a multi-task learning objective and unsupervised pre-training to simultaneously model both the micro and macro architecture of the brain. We successfully apply our methods to a heterogeneous, three-dimensional, X-ray micro-CT dataset spanning multiple regions in the mouse brain, and show that our approach consistently outperforms another multi-task architecture, and is competitive with strong single-task baselines at both scales.

Henry presented his paper on Bayesian Optimization at the Conference on Uncertainty in AI (UAI)! [Check out the paper here!]

Abstract:  Most existing black-box optimization methods assume that all variables in the system being optimized have equal cost and can change freely at each iteration. However, in many real-world systems, inputs are passed through a sequence of different operations or modules, making variables in earlier stages of processing more costly to update. Such structure induces a dynamic cost from switching variables in the early parts of a data processing pipeline. In this work, we propose a new algorithm for switch-cost-aware optimization called Lazy Modular Bayesian Optimization (LaMBO). This method efficiently identifies the global optimum while minimizing cost through a passive change of variables in early modules. The method is theoretically grounded which achieves a vanishing regret regularized with switching cost. We apply LaMBO to multiple synthetic functions and a three-stage image segmentation pipeline used in a neuroimaging task, where we obtain promising improvements over existing cost-aware Bayesian optimization algorithms. Our results demonstrate that LaMBO is an effective strategy for black-box optimization capable of minimizing switching costs.