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Some neurodegenerative diseases, like Parkinsons Disease (PD) and Spinocerebellar ataxia 3 (SCA3), are associated with distinct, altered gait and tremor movements that are reflective of the underlying disease etiology. Drosophila melanogaster models of neurodegeneration have illuminated our understanding of the molecular mechanisms of disease. However, it is unknown whether specific gait and tremor dysfunctions also occur in fly disease mutants. To answer this question, we developed a machine-learning image-analysis program, Feature Learning-based LImb segmentation and Tracking (FLLIT), that automatically tracks leg claw positions of freely moving flies recorded on high-speed video, producing a series of gait measurements. Notably, unlike other machine-learning methods, FLLIT generates its own training sets and does not require user-annotated images for learning. Using FLLIT, we carried out high-throughput and high-resolution analysis of gait and tremor features in Drosophila neurodegeneration mutants for the first time. We found that fly models of PD and SCA3 exhibited markedly different walking gait and tremor signatures, which recapitulated characteristics of the respective human diseases. Selective expression of mutant SCA3 in dopaminergic neurons led to a gait signature that more closely resembled those of PD flies. This suggests that the behavioral phenotype depends on the neurons affected rather than the specific nature of the mutation. Different mutations produced tremors in distinct leg pairs, indicating that different motor circuits were affected. Using this approach, fly models can be used to dissect the neurogenetic mechanisms that underlie movement disorders.

The original author list did not accurately reflect the contributions of the following colleagues.

Pose estimation, tracking, and action recognition of articulated objects from depth images are important and challenging problems, which are normally considered separately. In this paper, a unified paradigm based on Lie group theory is proposed, which enables us to collectively address these related problems. Our approach is also applicable to a wide range of articulated objects. Empirically it is evaluated on lab animals including mouse and fish, as well as on human hand. On these applications, it is shown to deliver competitive results compared to the state-of-the-arts, and non-trivial baselines including convolutional neural networks and regression forest methods. Moreover, new sets of annotated depth data of articulated objects are created which, together with our code, are made publicly available.

Sensory input is often ambiguous, leading to uncertain interpretations of the external world. Estimates of perceptual uncertainty might be useful in guiding behavior, but it remains unclear whether humans explicitly represent uncertainty in naturalistic settings, and whether any such representations are normatively correct. Progress has been hindered by the absence of stimulus-computable models that estimate uncertainty. We developed a class of task-optimized models that generate probability distributions over perceptual estimates. To assess whether human uncertainty representations align with the model's, we compared human confidence judgments, which might indirectly reflect uncertainty representations, to confidence judgments extracted from the model's uncertainty. In both sound localization and pitch perception, human confidence varied systematically, being lower for stimuli that produced more variable estimates across trials. Human confidence tracked model confidence across conditions, suggesting that human uncertainty representations accurately reflect the actual uncertainty of perceptual estimation. The modeling framework is extensible to other perceptual domains.

Following prolonged swimming, Caenorhabditis elegans cycle between active swimming bouts and inactive quiescent bouts. Swimming is exercise for C. elegans and here we suggest that inactive bouts are a recovery state akin to fatigue. Previously, analysis of exercise-induced quiescent (EIQ) bouts relied on laborious manual observation, as existing automated analysis methods for C. elegans swimming either cannot analyze EIQ bouts or fail to accurately track animal posture during these bouts. It is known that cGMP-dependent kinase (PKG) activity plays a conserved role in sleep, rest, and arousal. Using C. elegans EGL-4 PKG, we first validate a novel learning-based computer vision approach to automatically analyze C. elegans locomotory behavior and distinguish between activity and inactivity during swimming for long periods of time. We find that C. elegans EGL-4 PKG function predicts EIQ first bout timing, fractional quiescence, bout number, and bout duration, suggesting that previously described pathways are engaged during EIQ bouts. However, EIQ bouts are likely not sleep as animals are feeding during the majority of EIQ bouts. We find that genetic perturbation of neurons required for other C. elegans sleep states also does not alter EIQ dynamics. Additionally, we find that EIQ onset is sensitive to age and DAF-16 FOXO function. In summary, we have validated a new behavioral analysis software that enabled a quantitative and detailed assessment of swimming behavior, including EIQ. We found novel EIQ defects in aged animals and animals with mutations in a gene involved in stress tolerance. We anticipate that further use of this software will facilitate the analysis of genes and pathways critical for fatigue and other C. elegans behaviors.

Genetic models in Drosophila have made invaluable contributions to our understanding of the molecular mechanisms underlying neurodegeneration. In human patients, some neurodegenerative diseases lead to characteristic movement dysfunctions, such as abnormal gait and tremors. However, it is currently unknown whether similar movement defects occur in the respective fly models, which could be used to model and better understand the pathophysiology of movement disorders. To address this question, we developed a machine-learning image-analysis programme - Feature Learning-based LImb segmentation and Tracking (FLLIT) - that automatically tracks leg claw positions of freely moving flies recorded on high-speed video, generating a series of body and leg movement parameters. Of note, FLLIT requires no user input for learning. We used FLLIT to characterise fly models of Parkinson's Disease (PD) and Spinocerebellar ataxia 3 (SCA3). Between these models, walking gait and tremor characteristics differed markedly, and recapitulated signatures of the respective human diseases. Selective expression of mutant SCA3 in dopaminergic neurons led to phenotypes resembling that of PD flies, suggesting that the behavioural phenotype may depend on the circuits affected, rather than the specific nature of the mutation. Different mutations produced tremors in distinct leg pairs, indicating that different motor circuits are affected. Almost 190,000 video frames were tracked in this study, allowing, for the first time, high-throughput analysis of gait and tremor features in Drosophila mutants. As an efficient assay of mutant gait and tremor features in an important model system, FLLIT will enable the analysis of the neurogenetic mechanisms that underlie movement disorders.

Epidural electrical stimulation (EES) has shown promise as both a clinical therapy and research tool for studying nervous system function. However, available clinical EES paddles are limited to using a small number of contacts due to the burden of wires necessary to connect each contact to the therapeutic delivery device, limiting the treatment area or density of epidural electrode arrays. We aimed to eliminate this burden using advanced on-paddle electronics. We developed a smart EES paddle with a 60-electrode programmable array, addressable using an active electronic multiplexer embedded within the electrode paddle body. The electronics are sealed in novel, ultra-low profile hermetic packaging. We conducted extensive reliability testing on the novel array, including a battery of ISO 10993-1 biocompatibility tests and determination of the hermetic package leak rate. We then evaluated the EES device in vivo, placed on the epidural surface of the ovine lumbosacral spinal cord for 15 months. The active paddle array performed nominally when implanted in sheep for over 15 months and no device-related malfunctions were observed. The onboard multiplexer enabled bespoke electrode arrangements across, and within, experimental sessions. We identified stereotyped responses to stimulation in lower extremity musculature, and examined local field potential responses to EES using high-density recording bipoles. Finally, spatial electrode encoding enabled machine learning models to accurately perform EES parameter inference for unseen stimulation electrodes, reducing the need for extensive training data in future deep models. We report the development and chronic large animal in vivo evaluation of a high-density EES paddle array containing active electronics. Our results provide a foundation for more advanced computation and processing to be integrated directly into devices implanted at the neural interface, opening new avenues for the study of nervous system function and new therapies to treat neural injury and dysfunction.

The meteoric rise in the adoption of deep neural networks as computational models of vision has inspired efforts to \"align\" these models with humans. One dimension of interest for alignment includes behavioral choices, but moving beyond characterizing choice patterns to capturing temporal aspects of visual decision-making has been challenging. Here, we sketch a general-purpose methodology to construct computational accounts of reaction times from a stimulus-computable, task-optimized model. Specifically, we introduce a novel metric leveraging insights from subjective logic theory summarizing evidence accumulation in recurrent vision models. We demonstrate that our metric aligns with patterns of human reaction times for stimulus manipulations across four disparate visual decision-making tasks spanning perceptual grouping, mental simulation, and scene categorization. This work paves the way for exploring the temporal alignment of model and human visual strategies in the context of various other cognitive tasks toward generating testable hypotheses for neuroscience. Links to the code and data can be found on the project page: https://serre-lab.github.io/rnn_rts_site.

Primate vision depends on recurrent processing for reliable perception. A growing body of literature also suggests 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 standard 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 show that recurrent vision models trained with C-RBP to solve the large-scale Panoptic Segmentation MS-COCO challenge outperform the leading feedforward approach, with fewer free parameters. 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.

We present a novel approach for estimating the 2D pose of an articulated object with an application to automated video analysis of small laboratory animals. We have found that deformable part models developed for humans, exemplified by the flexible mixture of parts (FMP) model, typically fail on challenging animal poses. We argue that beyond encoding appearance and spatial relations, shape is needed to overcome the lack of distinctive landmarks on laboratory animal bodies. In our approach, a shape consistent FMP (scFMP) model computes promising pose candidates after a standard FMP model is used to rapidly discard false part detections. This \"cascaded\" approach combines the relative strengths of spatial-relations, appearance and shape representations and is shown to yield significant improvements over the original FMP model as well as a representative deep neural network baseline.