Recursive Estimation of User Intent from Noninvasive Electroencephalography using Discriminative Models

We study the problem of inferring user intent from noninvasive electroencephalography (EEG) to restore communication for people with severe speech and physical impairments (SSPI). The focus of this work is improving the estimation of posterior symbol probabilities in a typing task. At each iteration of the typing procedure, a subset of symbols is chosen for the next query based on the current probability estimate. Evidence about the user's response is collected from event-related potentials (ERP) in order to update symbol probabilities, until one symbol exceeds a predefined confidence threshold. We provide a graphical model describing this task, and derive a recursive Bayesian update rule based on a discriminative probability over label vectors for each query, which we approximate using a neural network classifier. We evaluate the proposed method in a simulated typing task and show that it outperforms previous approaches based on generative modeling.Comment: 5 pages, 2 figure

Stabilizing Subject Transfer in EEG Classification with Divergence Estimation

Classification models for electroencephalogram (EEG) data show a large decrease in performance when evaluated on unseen test sub jects. We reduce this performance decrease using new regularization techniques during model training. We propose several graphical models to describe an EEG classification task. From each model, we identify statistical relationships that should hold true in an idealized training scenario (with infinite data and a globally-optimal model) but that may not hold in practice. We design regularization penalties to enforce these relationships in two stages. First, we identify suitable proxy quantities (divergences such as Mutual Information and Wasserstein-1) that can be used to measure statistical independence and dependence relationships. Second, we provide algorithms to efficiently estimate these quantities during training using secondary neural network models. We conduct extensive computational experiments using a large benchmark EEG dataset, comparing our proposed techniques with a baseline method that uses an adversarial classifier. We find our proposed methods significantly increase balanced accuracy on test subjects and decrease overfitting. The proposed methods exhibit a larger benefit over a greater range of hyperparameters than the baseline method, with only a small computational cost at training time. These benefits are largest when used for a fixed training period, though there is still a significant benefit for a subset of hyperparameters when our techniques are used in conjunction with early stopping regularization.Comment: 16 pages, 5 figure

Fast and Expressive Gesture Recognition using a Combination-Homomorphic Electromyogram Encoder

We study the task of gesture recognition from electromyography (EMG), with the goal of enabling expressive human-computer interaction at high accuracy, while minimizing the time required for new subjects to provide calibration data. To fulfill these goals, we define combination gestures consisting of a direction component and a modifier component. New subjects only demonstrate the single component gestures and we seek to extrapolate from these to all possible single or combination gestures. We extrapolate to unseen combination gestures by combining the feature vectors of real single gestures to produce synthetic training data. This strategy allows us to provide a large and flexible gesture vocabulary, while not requiring new subjects to demonstrate combinatorially many example gestures. We pre-train an encoder and a combination operator using self-supervision, so that we can produce useful synthetic training data for unseen test subjects. To evaluate the proposed method, we collect a real-world EMG dataset, and measure the effect of augmented supervision against two baselines: a partially-supervised model trained with only single gesture data from the unseen subject, and a fully-supervised model trained with real single and real combination gesture data from the unseen subject. We find that the proposed method provides a dramatic improvement over the partially-supervised model, and achieves a useful classification accuracy that in some cases approaches the performance of the fully-supervised model.Comment: 24 pages, 7 figures, 6 tables V2: add link to code, fix bibliograph

User Training with Error Augmentation for Electromyogram-based Gesture Classification

We designed and tested a system for real-time control of a user interface by extracting surface electromyographic (sEMG) activity from eight electrodes in a wrist-band configuration. sEMG data were streamed into a machine-learning algorithm that classified hand gestures in real-time. After an initial model calibration, participants were presented with one of three types of feedback during a human-learning stage: veridical feedback, in which predicted probabilities from the gesture classification algorithm were displayed without alteration, modified feedback, in which we applied a hidden augmentation of error to these probabilities, and no feedback. User performance was then evaluated in a series of minigames, in which subjects were required to use eight gestures to manipulate their game avatar to complete a task. Experimental results indicated that, relative to baseline, the modified feedback condition led to significantly improved accuracy and improved gesture class separation. These findings suggest that real-time feedback in a gamified user interface with manipulation of feedback may enable intuitive, rapid, and accurate task acquisition for sEMG-based gesture recognition applications.Comment: 10 pages, 10 figure

All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins

All-optical electrophysiology—spatially resolved simultaneous optical perturbation and measurement of membrane voltage—would open new vistas in neuroscience research. We evolved two archaerhodopsin-based voltage indicators, QuasAr1 and QuasAr2, which show improved brightness and voltage sensitivity, have microsecond response times and produce no photocurrent. We engineered a channelrhodopsin actuator, CheRiff, which shows high light sensitivity and rapid kinetics and is spectrally orthogonal to the QuasArs. A coexpression vector, Optopatch, enabled cross-talk–free genetically targeted all-optical electrophysiology. In cultured rat neurons, we combined Optopatch with patterned optical excitation to probe back-propagating action potentials (APs) in dendritic spines, synaptic transmission, subcellular microsecond-timescale details of AP propagation, and simultaneous firing of many neurons in a network. Optopatch measurements revealed homeostatic tuning of intrinsic excitability in human stem cell–derived neurons. In rat brain slices, Optopatch induced and reported APs and subthreshold events with high signal-to-noise ratios. The Optopatch platform enables high-throughput, spatially resolved electrophysiology without the use of conventional electrodes

Next-Generation Roadmap for Patient-Centered Genomics

In the era of precision medicine, understanding genetic variation has grown from a topic of research interest into a tangible source of therapeutic benefit for patients. As the list of confirmed links between genetic lesions and disease continues to grow, so does the list of actionable genetic diagnoses. The workup of a childhood-onset schizophrenia case provides a useful foil for discussion of current methods for genomic diagnostics, both to demonstrate some of the important available analyses, and to highlight areas of ongoing need. In brief, the stages of this case as pertains to the general diagnostic process are: clinical workup, sequencing and technical processing, analysis and interpretation of results, and follow-up research study. The patient in this case presented with command auditory hallucinations at age 6 and began empirical treatment for schizophrenia; he was subsequently found to have a novel de novo heterozygous missense mutation in ATP1A3 NM_152296.4 c.385G>A, predicted to cause the coding change p.V129M. This gene codes for a neuron-specific isoform of the alpha subunit of the sodium-potassium pump complex that helps establish transmembrane ion gradients necessary for neuronal function. The variant found in this case is now being replicated in a patient-derived iPS-neuron model to seek greater insight into the mechanism of disease and possible therapeutic opportunities. Generalizing from this case, researchers and clinicians hoping to replicate or improve upon this patient-centric genomics workflow can benefit from reviewing technical and infrastructural best practices. This case may also help illustrate some of the key difficulties in connecting genomic evidence with appropriate functional validation and other clinical markers to support well-informed decision-making

AutoTransfer: Subject Transfer Learning with Censored Representations on Biosignals Data

We provide a regularization framework for subject transfer learning in which we seek to train an encoder and classifier to minimize classification loss, subject to a penalty measuring independence between the latent representation and the subject label. We introduce three notions of independence and corresponding penalty terms using mutual information or divergence as a proxy for independence. For each penalty term, we provide several concrete estimation algorithms, using analytic methods as well as neural critic functions. We provide a hands-off strategy for applying this diverse family of regularization algorithms to a new dataset, which we call "AutoTransfer". We evaluate the performance of these individual regularization strategies and our AutoTransfer method on EEG, EMG, and ECoG datasets, showing that these approaches can improve subject transfer learning for challenging real-world datasets.Comment: 17 page extended version of International Engineering in Medicine and Biology Conference 2022 pape

Probabilistic program inference in network-based epidemiological simulations

Accurate epidemiological models require parameter estimates that account for mobility patterns and social network structure. We demonstrate the effectiveness of probabilistic programming for parameter inference in these models. We consider an agent-based simulation that represents mobility networks as degree-corrected stochastic block models, whose parameters we estimate from cell phone co-location data. We then use probabilistic program inference methods to approximate the distribution over disease transmission parameters conditioned on reported cases and deaths. Our experiments demonstrate that the resulting models improve the quality of fit in multiple geographies relative to baselines that do not model network topology.</jats:p

Additional file 14: Table S14. of Gene expression analysis in Fmr1KO mice identifies an immunological signature in brain tissue and mGluR5-related signaling in primary neuronal cultures

Enriched pathways in murine differentially expressed up-regulated genes in cortical and hippocampal cultures highlighted on human development (C0 and H0 clusters respectively). (XLSX 11 kb