Computing With Residue Numbers in High-Dimensional Representation.

We introduce residue hyperdimensional computing, a computing framework that unifies residue number systems with an algebra defined over random, high-dimensional vectors. We show how residue numbers can be represented as high-dimensional vectors in a manner that allows algebraic operations to be performed with component-wise, parallelizable operations on the vector elements. The resulting framework, when combined with an efficient method for factorizing high-dimensional vectors, can represent and operate on numerical values over a large dynamic range using resources that scale only logarithmically with the range, a vast improvement over previous methods.

Time-asymmetric fluctuation theorem and efficient free-energy estimation.

The free-energy difference ΔF between two high-dimensional systems is notoriously difficult to compute but very important for many applications such as drug discovery. We demonstrate that an unconventional definition of work introduced by Vaikuntanathan and Jarzynski (2008) satisfies a microscopic fluctuation theorem that relates path ensembles that are driven by protocols unequal under time reversal. It has been shown before that counterdiabatic protocols-those having additional forcing that enforces the system to remain in instantaneous equilibrium, also known as escorted dynamics or engineered swift equilibration-yield zero-variance work measurements for this definition.

Spatial maps in piriform cortex during olfactory navigation.

Odors are a fundamental part of the sensory environment used by animals to inform behaviors such as foraging and navigation. Primary olfactory (piriform) cortex is thought to be dedicated to encoding odor identity. Here, using neural ensemble recordings in freely moving rats performing a novel odor-cued spatial choice task, we show that posterior piriform cortex neurons also carry a robust spatial map of the environment.

Beyond Linear Response: Equivalence between Thermodynamic Geometry and Optimal Transport.

A fundamental result of thermodynamic geometry is that the optimal, minimal-work protocol that drives a nonequilibrium system between two thermodynamic states in the slow-driving limit is given by a geodesic of the friction tensor, a Riemannian metric defined on control space. For overdamped dynamics in arbitrary dimensions, we demonstrate that thermodynamic geometry is equivalent to L^{2} optimal transport geometry defined on the space of equilibrium distributions corresponding to the control parameters. We show that obtaining optimal protocols past the slow-driving or linear response regime is computationally tractable as the sum of a friction tensor geodesic and a counterdiabatic term related to the Fisher information metric.

Binding in hippocampal-entorhinal circuits enables compositionality in cognitive maps.

We propose a normative model for spatial representation in the hippocampal formation that combines optimality principles, such as maximizing coding range and spatial information per neuron, with an algebraic framework for computing in distributed representation. Spatial position is encoded in a residue number system, with individual residues represented by high-dimensional, complex-valued vectors. These are composed into a single vector representing position by a similarity-preserving, conjunctive vector-binding operation.

Bayesian inference of structured latent spaces from neural population activity with the orthogonal stochastic linear mixing model.

The brain produces diverse functions, from perceiving sounds to producing arm reaches, through the collective activity of populations of many neurons. Determining if and how the features of these exogenous variables (e.g.

Data-driven distillation and precision prognosis in traumatic brain injury with interpretable machine learning.

Traumatic brain injury (TBI) affects how the brain functions in the short and long term. Resulting patient outcomes across physical, cognitive, and psychological domains are complex and often difficult to predict. Major challenges to developing personalized treatment for TBI include distilling large quantities of complex data and increasing the precision with which patient outcome prediction (prognoses) can be rendered.

Computing with Residue Numbers in High-Dimensional Representation.

We introduce , a computing framework that unifies residue number systems with an algebra defined over random, high-dimensional vectors. We show how residue numbers can be represented as high-dimensional vectors in a manner that allows algebraic operations to be performed with component-wise, parallelizable operations on the vector elements. The resulting framework, when combined with an efficient method for factorizing high-dimensional vectors, can represent and operate on numerical values over a large dynamic range using vastly fewer resources than previous methods, and it exhibits impressive robustness to noise.

Learning Energy-Based Models in High-Dimensional Spaces with Multiscale Denoising-Score Matching.

Energy-based models (EBMs) assign an unnormalized log probability to data samples. This functionality has a variety of applications, such as sample synthesis, data denoising, sample restoration, outlier detection, Bayesian reasoning and many more. But, the training of EBMs using standard maximum likelihood is extremely slow because it requires sampling from the model distribution.

Early selection of task-relevant features through population gating.

Brains can gracefully weed out irrelevant stimuli to guide behavior. This feat is believed to rely on a progressive selection of task-relevant stimuli across the cortical hierarchy, but the specific across-area interactions enabling stimulus selection are still unclear. Here, we propose that population gating, occurring within primary auditory cortex (A1) but controlled by top-down inputs from prelimbic region of medial prefrontal cortex (mPFC), can support across-area stimulus selection.

Vector Symbolic Architectures as a Computing Framework for Emerging Hardware.

This article reviews recent progress in the development of the computing framework (also known as Hyperdimensional Computing). This framework is well suited for implementation in stochastic, emerging hardware and it naturally expresses the types of cognitive operations required for Artificial Intelligence (AI). We demonstrate in this article that the field-like algebraic structure of Vector Symbolic Architectures offers simple but powerful operations on high-dimensional vectors that can support all data structures and manipulations relevant to modern computing.

Efficient optimization with higher-order ising machines.

A prominent approach to solving combinatorial optimization problems on parallel hardware is Ising machines, i.e., hardware implementations of networks of interacting binary spin variables.

Resolving Non-identifiability Mitigates Bias in Models of Neural Tuning and Functional Coupling.

In the brain, all neurons are driven by the activity of other neurons, some of which maybe simultaneously recorded, but most are not. As such, models of neuronal activity need to account for simultaneously recorded neurons and the influences of unmeasured neurons. This can be done through inclusion of model terms for observed external variables (e.

DL-TODA: A Deep Learning Tool for Omics Data Analysis.

Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species.

Efficient Decoding of Compositional Structure in Holistic Representations.

We investigate the task of retrieving information from compositional distributed representations formed by hyperdimensional computing/vector symbolic architectures and present novel techniques that achieve new information rate bounds. First, we provide an overview of the decoding techniques that can be used to approach the retrieval task. The techniques are categorized into four groups.

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms.

On separating long- and short-term memories in hyperdimensional computing.

Operations on high-dimensional, fixed-width vectors can be used to distribute information from several vectors over a single vector of the same width. For example, a set of key-value pairs can be encoded into a single vector with multiplication and addition of the corresponding key and value vectors: the keys are bound to their values with component-wise multiplication, and the key-value pairs are combined into a single superposition vector with component-wise addition. The superposition vector is, thus, a memory which can then be queried for the value of any of the keys, but the result of the query is approximate.

Perspectives for self-driving labs in synthetic biology.

Self-driving labs (SDLs) combine fully automated experiments with artificial intelligence (AI) that decides the next set of experiments. Taken to their ultimate expression, SDLs could usher a new paradigm of scientific research, where the world is probed, interpreted, and explained by machines for human benefit. While there are functioning SDLs in the fields of chemistry and materials science, we contend that synthetic biology provides a unique opportunity since the genome provides a single target for affecting the incredibly wide repertoire of biological cell behavior.

Limited-control optimal protocols arbitrarily far from equilibrium.

Recent studies have explored finite-time dissipation-minimizing protocols for stochastic thermodynamic systems driven arbitrarily far from equilibrium, when granted full external control to drive the system. However, in both simulation and experimental contexts, systems often may only be controlled with a limited set of degrees of freedom. Here, going beyond slow- and fast-driving approximations employed in previous studies, we obtain exact finite-time optimal protocols for this limited-control setting.

Multiple bumps can enhance robustness to noise in continuous attractor networks.

A central function of continuous attractor networks is encoding coordinates and accurately updating their values through path integration. To do so, these networks produce localized bumps of activity that move coherently in response to velocity inputs. In the brain, continuous attractors are believed to underlie grid cells and head direction cells, which maintain periodic representations of position and orientation, respectively.

The Neurodata Without Borders ecosystem for neurophysiological data science.

The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data must be findable, accessible, interoperable, and reusable (FAIR). This requires a standard language for data and metadata that can coevolve with neuroscience.

High-fidelity eye, head, body, and world tracking with a wearable device.

We describe the design and performance of a high-fidelity wearable head-, body-, and eye-tracking system that offers significant improvement over previous such devices. This device's sensors include a binocular eye tracker, an RGB-D scene camera, a high-frame-rate scene camera, and two visual odometry sensors, for a total of ten cameras, which we synchronize and record from with a data rate of over 700 MB/s. The sensors are operated by a mini-PC optimized for fast data collection, and powered by a small battery pack.

Learning and Inference in Sparse Coding Models With Langevin Dynamics.

We describe a stochastic, dynamical system capable of inference and learning in a probabilistic latent variable model. The most challenging problem in such models-sampling the posterior distribution over latent variables-is proposed to be solved by harnessing natural sources of stochasticity inherent in electronic and neural systems. We demonstrate this idea for a sparse coding model by deriving a continuous-time equation for inferring its latent variables via Langevin dynamics.

Scaling and Benchmarking an Evolutionary Algorithm for Constructing Biophysical Neuronal Models.

Single neuron models are fundamental for computational modeling of the brain's neuronal networks, and understanding how ion channel dynamics mediate neural function. A challenge in defining such models is determining biophysically realistic channel distributions. Here, we present an efficient, highly parallel evolutionary algorithm for developing such models, named .