1149 Publications

SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases

Fuqing Wu, Amy Xiao, R. Bonneau, et al.

Current estimates of COVID-19 prevalence are largely based on symptomatic, clinically diagnosed cases. The existence of a large number of undiagnosed infections hampers population-wide investigation of viral circulation. Here, we quantify the SARS-CoV-2 concentration and track its dynamics in wastewater at a major urban wastewater treatment facility in Massachusetts, between early January and May 2020. SARS-CoV-2 was first detected in wastewater on March 3. SARS-CoV-2 RNA concentrations in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 4–10 days earlier in wastewater than in clinical data. We inferred viral shedding dynamics by modeling wastewater viral load as a convolution of back-dated new clinical cases with the average population-level viral shedding function. The inferred viral shedding function showed an early peak, likely before symptom onset and clinical diagnosis, consistent with emerging clinical and experimental evidence. This finding suggests that SARS-CoV-2 concentrations in wastewater may be primarily driven by viral shedding early in infection. This work shows that longitudinal wastewater analysis can be used to identify trends in disease transmission in advance of clinical case reporting, and infer early viral shedding dynamics for newly infected individuals, which are difficult to capture in clinical investigations.

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Robust regression with compositional covariates

Many high-throughput sequencing data sets in biology are compositional in nature. A prominent example is microbiome profiling data, including targeted amplicon-based and metagenomic sequencing data. These profiling data comprises surveys of microbial communities in their natural habitat and sparse proportional (or compositional) read counts that represent operational taxonomic units or genes. When paired measurements of other covariates, including physicochemical properties of the habitat or phenotypic variables of the host, are available, inference of parsimonious and robust statistical relationships between the microbial abundance data and the covariate measurements is often an important first step in exploratory data analysis. To this end, we propose a sparse robust statistical regression framework that considers compositional and non-compositional measurements as predictors and identifies outliers in continuous response variables. Our model extends the seminal log-contrast model of Aitchison and Bacon-Shone (1984) by a mean shift formulation for capturing outliers, sparsity-promoting convex and non-convex penalties for parsimonious model selection, and data-driven robust initialization procedures adapted to the compositional setting. We show, in theory and simulations, the ability of our approach to jointly select a sparse set of predictive microbial features and identify outliers in the response. We illustrate the viability of our method by robustly predicting human body mass indices from American Gut Project amplicon data and non-compositional covariate data. We believe that the robust estimators introduced here and available in the R package RobRegCC can serve as a practical tool for reliable statistical regression analysis of compositional data, including microbiome survey data.

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Motile dislocations knead odd crystals into whorls

Ephraim S. Bililign, Florencio Balboa Usabiaga,, M. Shelley, et al.

The competition between thermal fluctuations and potential forces governs the stability of matter in equilibrium, in particular the proliferation and annihilation of topological defects. However, driving matter out of equilibrium allows for a new class of forces that are neither attractive nor repulsive, but rather transverse. The possibility of activating transverse forces raises the question of how they affect basic principles of material self-organization and control. Here we show that transverse forces organize colloidal spinners into odd elastic crystals crisscrossed by motile dislocations. These motile topological defects organize into a polycrystal made of grains with tunable length scale and rotation rate. The self-kneading dynamics drive super-diffusive mass transport, which can be controlled over orders of magnitude by varying the spinning rate. Simulations of both a minimal model and fully resolved hydrodynamics establish the generic nature of this crystal whorl state. Using a continuum theory, we show that both odd and Hall stresses can destabilize odd elastic crystals, giving rise to a generic state of crystalline active matter. Adding rotations to a material’s constituents has far-reaching consequences for continuous control of structures and transport at all scales.

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December 16, 2021

Bidirectional communication in oogenesis: a dynamic conversation in mice and Drosophila

Caroline A. Doherty , Farners Amargant , S. Shvartsman, et al.

In most animals, the oocyte is the largest cell by volume. The oocyte undergoes a period of large-scale growth during its development, prior to fertilization. At first glance, tissues that support the development of the oocyte in different organisms have diverse cellular characteristics that would seem to prohibit functional comparisons. However, these tissues often act with a common goal of establishing dynamic forms of two-way communication with the oocyte. We propose that this bidirectional communication between oocytes and support cells is a universal phenomenon that can be directly compared across species. Specifically, we highlight fruit fly and mouse oogenesis to demonstrate that similarities and differences in these systems should be used to inform and design future experiments in both models.

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December 15, 2021

Computational mechanisms of distributed value representations and mixed learning strategies

S. Farashahi, A. Soltani

Learning appropriate representations of the reward environment is challenging in the real world where there are many options, each with multiple attributes or features. Despite existence of alternative solutions for this challenge, neural mechanisms underlying emergence and adoption of value representations and learning strategies remain unknown. To address this, we measure learning and choice during a multi-dimensional probabilistic learning task in humans and trained recurrent neural networks (RNNs) to capture our experimental observations. We find that human participants estimate stimulus-outcome associations by learning and combining estimates of reward probabilities associated with the informative feature followed by those of informative conjunctions. Through analyzing representations, connectivity, and lesioning of the RNNs, we demonstrate this mixed learning strategy relies on a distributed neural code and opponency between excitatory and inhibitory neurons through value-dependent disinhibition. Together, our results suggest computational and neural mechanisms underlying emergence of complex learning strategies in naturalistic settings.

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Neural optimal feedback control with local learning rules

A major problem in motor control is understanding how the brain plans and executes proper movements in the face of delayed and noisy stimuli. A prominent framework for addressing such control problems is Optimal Feedback Control (OFC). OFC generates control actions that optimize behaviorally relevant criteria by integrating noisy sensory stimuli and the predictions of an internal model using the Kalman filter or its extensions. However, a satisfactory neural model of Kalman filtering and control is lacking because existing proposals have the following limitations: not considering the delay of sensory feedback, training in alternating phases, and requiring knowledge of the noise covariance matrices, as well as that of systems dynamics. Moreover, the majority of these studies considered Kalman filtering in isolation, and not jointly with control. To address these shortcomings, we introduce a novel online algorithm which combines adaptive Kalman filtering with a model free control approach (i.e., policy gradient algorithm). We implement this algorithm in a biologically plausible neural network with local synaptic plasticity rules. This network performs system identification and Kalman filtering, without the need for multiple phases with distinct update rules or the knowledge of the noise covariances. It can perform state estimation with delayed sensory feedback, with the help of an internal model. It learns the control policy without requiring any knowledge of the dynamics, thus avoiding the need for weight transport. In this way, our implementation of OFC solves the credit assignment problem needed to produce the appropriate sensory-motor control in the presence of stimulus delay.

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Bridging the Gap: Point Clouds for Merging Neurons in Connectomics

J. Berman, D. Chklovskii, J. Wu

In the field of Connectomics, a primary problem is that of 3D neuron segmentation. Although deep learning-based methods have achieved remarkable accuracy, errors still exist, especially in regions with image defects. One common type of defect is that of consecutive missing image sections. Here, data is lost along some axis, and the resulting neuron segmentations are split across the gap. To address this problem, we propose a novel method based on point cloud representations of neurons. We formulate the problem as a classification problem and train CurveNet, a state-of-the-art point cloud classification model, to identify which neurons should be merged. We show that our method not only performs strongly but also scales reasonably to gaps well beyond what other methods have attempted to address. Additionally, our point cloud representations are highly efficient in terms of data, maintaining high performance with an amount of data that would be unfeasible for other methods. We believe that this is an indicator of the viability of using point cloud representations for other proofreading tasks.

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A Normative and Biologically Plausible Algorithm for Independent Component Analysis

The brain effortlessly solves blind source separation (BSS) problems, but the algorithm it uses remains elusive. In signal processing, linear BSS problems are often solved by Independent Component Analysis (ICA). To serve as a model of a biological circuit, the ICA neural network (NN) must satisfy at least the following requirements: 1. The algorithm must operate in the online setting where data samples are streamed one at a time, and the NN computes the sources on the fly without storing any significant fraction of the data in memory. 2. The synaptic weight update is local, i.e., it depends only on the biophysical variables present in the vicinity of a synapse. Here, we propose a novel objective function for ICA from which we derive a biologically plausible NN, including both the neural architecture and the synaptic learning rules. Interestingly, our algorithm relies on modulating synaptic plasticity by the total activity of the output neurons. In the brain, this could be accomplished by neuromodulators, extracellular calcium, local field potential, or nitric oxide.

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A Similarity-preserving Neural Network Trained on Transformed Images Recapitulates Salient Features of the Fly Motion Detection Circuit

Learning to detect content-independent transformations from data is one of the central problems in biological and artificial intelligence. An example of such problem is unsupervised learning of a visual motion detector from pairs of consecutive video frames. Rao and Ruderman formulated this problem in terms of learning infinitesimal transformation operators (Lie group generators) via minimizing image reconstruction error. Unfortunately, it is difficult to map their model onto a biologically plausible neural network (NN) with local learning rules. Here we propose a biologically plausible model of motion detection. We also adopt the transformation-operator approach but, instead of reconstruction-error minimization, start with a similarity-preserving objective function. An online algorithm that optimizes such an objective function naturally maps onto an NN with biologically plausible learning rules. The trained NN recapitulates major features of the well-studied motion detector in the fly. In particular, it is consistent with the experimental observation that local motion detectors combine information from at least three adjacent pixels, something that contradicts the celebrated Hassenstein-Reichardt model.

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Adaptive Denoising via GainTuning

E. P. Simoncelli, Sreyas Mohan

Deep convolutional neural networks (CNNs) for image denoising are usually trained on large datasets. These models achieve the current state of the art, but they have difficulties generalizing when applied to data that deviate from the training distribution. Recent work has shown that it is possible to train denoisers on a single noisy image. These models adapt to the features of the test image, but their performance is limited by the small amount of information used to train them. Here we propose “GainTuning”, in which CNN models pre trained on large datasets are adaptively and selectively adjusted for individual test images. To avoid overfitting, GainTuning optimizes a single multiplicative scaling parameter (the “Gain”) of each channel in the convolutional layers of the CNN. We show that GainTuning improves state-of-the-art CNNs on standard image-denoising benchmarks, boosting their denoising performance on nearly every image in a held-out test set. These adaptive improvements are even more substantial for test images differing systematically from the training data, either in noise level or image type. We illustrate the potential of adaptive denoising in a scientific application, in which a CNN is trained on synthetic data, and tested on real transmission-electronmicroscope images. In contrast to the existing methodology, GainTuning is able to faithfully reconstruct the structure of catalytic nanoparticles from these data at extremely low signal-to-noise ratios.

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