naplib-python: Neural acoustic data processing and analysis tools in python.

Recently, the computational neuroscience community has pushed for more transparent and reproducible methods across the field. In the interest of unifying the domain of auditory neuroscience, naplib-python provides an intuitive and general data structure for handling all neural recordings and stimuli, as well as extensive preprocessing, feature extraction, and analysis tools which operate on that data structure. The package removes many of the complications associated with this domain, such as varying trial durations and multi-modal stimuli, and provides a general-purpose analysis framework that interfaces easily with existing toolboxes used in the field.

naplib-python: Neural Acoustic Data Processing and Analysis Tools in Python.

Recently, the computational neuroscience community has pushed for more transparent and reproducible methods across the field. In the interest of unifying the domain of auditory neuroscience, naplib-python provides an intuitive and general data structure for handling all neural recordings and stimuli, as well as extensive preprocessing, feature extraction, and analysis tools which operate on that data structure. The package removes many of the complications associated with this domain, such as varying trial durations and multi-modal stimuli, and provides a general-purpose analysis framework that interfaces easily with existing toolboxes used in the field.

Joint, distributed and hierarchically organized encoding of linguistic features in the human auditory cortex.

The precise role of the human auditory cortex in representing speech sounds and transforming them to meaning is not yet fully understood. Here we used intracranial recordings from the auditory cortex of neurosurgical patients as they listened to natural speech. We found an explicit, temporally ordered and anatomically distributed neural encoding of multiple linguistic features, including phonetic, prelexical phonotactics, word frequency, and lexical-phonological and lexical-semantic information. Grouping neural sites on the basis of their encoded linguistic features revealed a hierarchical pattern, with distinct representations of prelexical and postlexical features distributed across various auditory areas. While sites with longer response latencies and greater distance from the primary auditory cortex encoded higher-level linguistic features, the encoding of lower-level features was preserved and not discarded. Our study reveals a cumulative mapping of sound to meaning and provides empirical evidence for validating neurolinguistic and psycholinguistic models of spoken word recognition that preserve the acoustic variations in speech.

Deep neural networks effectively model neural adaptation to changing background noise and suggest nonlinear noise filtering methods in auditory cortex.

The human auditory system displays a robust capacity to adapt to sudden changes in background noise, allowing for continuous speech comprehension despite changes in background environments. However, despite comprehensive studies characterizing this ability, the computations that underly this process are not well understood. The first step towards understanding a complex system is to propose a suitable model, but the classical and easily interpreted model for the auditory system, the spectro-temporal receptive field (STRF), cannot match the nonlinear neural dynamics involved in noise adaptation. Here, we utilize a deep neural network (DNN) to model neural adaptation to noise, illustrating its effectiveness at reproducing the complex dynamics at the levels of both individual electrodes and the cortical population. By closely inspecting the model's STRF-like computations over time, we find that the model alters both the gain and shape of its receptive field when adapting to a sudden noise change. We show that the DNN model's gain changes allow it to perform adaptive gain control, while the spectro-temporal change creates noise filtering by altering the inhibitory region of the model's receptive field. Further, we find that models of electrodes in nonprimary auditory cortex also exhibit noise filtering changes in their excitatory regions, suggesting differences in noise filtering mechanisms along the cortical hierarchy. These findings demonstrate the capability of deep neural networks to model complex neural adaptation and offer new hypotheses about the computations the auditory cortex performs to enable noise-robust speech perception in real-world, dynamic environments.

Understanding Adaptive, Multiscale Temporal Integration In Deep Speech Recognition Systems.

Natural signals such as speech are hierarchically structured across many different timescales, spanning tens (e.g., phonemes) to hundreds (e.g., words) of milliseconds, each of which is highly variable and context-dependent. While deep neural networks (DNNs) excel at recognizing complex patterns from natural signals, relatively little is known about how DNNs flexibly integrate across multiple timescales. Here, we show how a recently developed method for studying temporal integration in biological neural systems - the temporal context invariance (TCI) paradigm - can be used to understand temporal integration in DNNs. The method is simple: we measure responses to a large number of stimulus segments presented in two different contexts and estimate the smallest segment duration needed to achieve a context invariant response. We applied our method to understand how the popular DeepSpeech2 model learns to integrate across time in speech. We find that nearly all of the model units, even in recurrent layers, have a compact integration window within which stimuli substantially alter the response and outside of which stimuli have little effect. We show that training causes these integration windows to shrink at early layers and expand at higher layers, creating a hierarchy of integration windows across the network. Moreover, by measuring integration windows for time-stretched/compressed speech, we reveal a transition point, midway through the trained network, where integration windows become yoked to the duration of stimulus structures (e.g., phonemes or words) rather than absolute time. Similar phenomena were observed in a purely recurrent and purely convolutional network although structure-yoked integration was more prominent in the recurrent network. These findings suggest that deep speech recognition systems use a common motif to encode the hierarchical structure of speech: integrating across short, time-yoked windows at early layers and long, structure-yoked windows at later layers. Our method provides a straightforward and general-purpose toolkit for understanding temporal integration in black-box machine learning models.

Estimating and interpreting nonlinear receptive field of sensory neural responses with deep neural network models.

Our understanding of nonlinear stimulus transformations by neural circuits is hindered by the lack of comprehensive yet interpretable computational modeling frameworks. Here, we propose a data-driven approach based on deep neural networks to directly model arbitrarily nonlinear stimulus-response mappings. Reformulating the exact function of a trained neural network as a collection of stimulus-dependent linear functions enables a locally linear receptive field interpretation of the neural network. Predicting the neural responses recorded invasively from the auditory cortex of neurosurgical patients as they listened to speech, this approach significantly improves the prediction accuracy of auditory cortical responses, particularly in nonprimary areas. Moreover, interpreting the functions learned by neural networks uncovered three distinct types of nonlinear transformations of speech that varied considerably from primary to nonprimary auditory regions. The ability of this framework to capture arbitrary stimulus-response mappings while maintaining model interpretability leads to a better understanding of cortical processing of sensory signals.