Robust neural circuit reconstruction from serial electron microscopy with convolutional recurrent networks

Recent successes in deep learning have started to impact neuroscience. Of particular significance are claims that current segmentation algorithms achieve "super-human" accuracy in an area known as connectomics. However, as we will show, these algorithms do not effectively generalize beyond the particular source and brain tissues used for training -- severely limiting their usability by the broader neuroscience community. To fill this gap, we describe a novel connectomics challenge for source- and tissue-agnostic reconstruction of neurons (STAR), which favors broad generalization over fitting specific datasets. We first demonstrate that current state-of-the-art approaches to neuron segmentation perform poorly on the challenge. We further describe a novel convolutional recurrent neural network module that combines short-range horizontal connections within a processing stage and long-range top-down connections between stages. The resulting architecture establishes the state of the art on the STAR challenge and represents a significant step towards widely usable and fully-automated connectomics analysis

Stable and expressive recurrent vision models

Primate vision depends on recurrent processing for reliable perception (Gilbert & Li, 2013). At the same time, there is a growing body of literature demonstrating that recurrent connections improve the learning efficiency and generalization of vision models on classic computer vision challenges. Why then, are current large-scale challenges dominated by feedforward networks? We posit that the effectiveness of recurrent vision models is bottlenecked by the widespread algorithm used for training them, "back-propagation through time" (BPTT), which has O(N) memory-complexity for training an N step model. Thus, recurrent vision model design is bounded by memory constraints, forcing a choice between rivaling the enormous capacity of leading feedforward models or trying to compensate for this deficit through granular and complex dynamics. Here, we develop a new learning algorithm, "contractor recurrent back-propagation" (C-RBP), which alleviates these issues by achieving constant O(1) memory-complexity with steps of recurrent processing. We demonstrate that recurrent vision models trained with C-RBP can detect long-range spatial dependencies in a synthetic contour tracing task that BPTT-trained models cannot. We further demonstrate that recurrent vision models trained with C-RBP to solve the large-scale Panoptic Segmentation MS-COCO challenge outperform the leading feedforward approach. C-RBP is a general-purpose learning algorithm for any application that can benefit from expansive recurrent dynamics. Code and data are available at https://github.com/c-rbp

Recurrent neural circuits for contour detection

We introduce a deep recurrent neural network architecture that approximates visual cortical circuits. We show that this architecture, which we refer to as the gamma-net, learns to solve contour detection tasks with better sample efficiency than state-of-the-art feedforward networks, while also exhibiting a classic perceptual illusion, known as the orientation-tilt illusion. Correcting this illusion significantly reduces gamma-net contour detection accuracy by driving it to prefer low-level edges over high-level object boundary contours. Overall, our study suggests that the orientation-tilt illusion is a byproduct of neural circuits that help biological visual systems achieve robust and efficient contour detection, and that incorporating these circuits in artificial neural networks can improve computer vision.Comment: Published in ICLR 202