An adaptive recovery method in compressed sensing of extracellular neural recording

ABSTRACT: A novel adaptive recovery method in the emerging compressed sensing theory is described and applied to extracellular neural recordings in order to reduce data rate in wireless neural recording systems. To strike a balance between high compression ratio and high spike reconstruction quality, a novel method that employs a group-sparsity recovery algorithm, prior information about the input neural signal, learning prior supports of spikes, and a matched wavelet technique is introduced. Our simulation results, using four different sets of real extracellular recordings from four distinct neural sources, show that our proposed method is effective, viable, and outperforms the state-of-the-art compressed sensing-based methods, in particular, when the number of the measurement is two times of the sparsity

Advances in Microelectronics for Implantable Medical Devices

Implantable medical devices provide therapy to treat numerous health conditions as well as monitoring and diagnosis. Over the years, the development of these devices has seen remarkable progress thanks to tremendous advances in microelectronics, electrode technology, packaging and signal processing techniques. Many of today’s implantable devices use wireless technology to supply power and provide communication. There are many challenges when creating an implantable device. Issues such as reliable and fast bidirectional data communication, efficient power delivery to the implantable circuits, low noise and low power for the recording part of the system, and delivery of safe stimulation to avoid tissue and electrode damage are some of the challenges faced by the microelectronics circuit designer. This paper provides a review of advances in microelectronics over the last decade or so for implantable medical devices and systems. The focus is on neural recording and stimulation circuits suitable for fabrication in modern silicon process technologies and biotelemetry methods for power and data transfer, with particular emphasis on methods employing radio frequency inductive coupling. The paper concludes by highlighting some of the issues that will drive future research in the field

Adaptive Markov Random Fields for Structured Compressive Sensing

Compressive sensing (CS) has underpinned recent developments in data compression and signal acquisition systems. The goal of CS is to recover a high dimensional sparse signal from a few measurements. Recent progress in CS has attempted to further reduce the measurements by employing signal structures. This thesis presents a novel structured sparsity model, namely, adaptive Markov random field (MRF) to effectively extract the signal structures. The adaptive MRF achieves two desirable properties: flexibility—the ability to represent a wide range of structures—and adaptability—being adaptive to any structures. However, most existing work can only achieve one of these two properties. Previous MRF-based methods offer high flexibility but cannot adapt to new signal structures, while the data-adaptive based methods assume limited signal structures. Therefore, the contribution of this thesis is the novel and efficient signal recovery methods for CS. We propose to leverage the adaptability of the MRF by refining the MRF parameters based on a point estimate of the latent sparse signal, and then the sparse signal is estimated based on the resulting MRF. This method is termed Two-step-Adaptive MRF. To maximize the adaptability, we also propose a new sparse signal estimation method that estimates the sparse signal, support, and noise parameters jointly. The point estimation of the latent sparse signals underpins the performance of MRF parameter estimation, but it cannot depict the statistical uncertainty of the latent sparse signals, which can lead to inaccurate parameter estimations, and thus limit the ultimate signal recovery performance. Therefore, we reformulate the parameter estimation problem to offer better generalization over the latent sparse signals. We propose to obtain the MRF parameters from given measurements by solving a maximum marginal likelihood (MML) problem. The resulting MML problem allows the MRF parameters to be estimated from measurements directly in one step; thus, we term this method One-step-Adaptive MRF. To solve the MML problem efficiently, we propose to approximate the MRF model with the product of two simpler distributions which enables closed-form solutions for all unknown variables with low computational cost. Extensive experiments on three real-world datasets demonstrate the promising performance of Two-steps-Adaptive MRF. One-step-Adaptive MRF further improves over the state-of-the-art methods. Motivated by this, we apply One-step-Adaptive MRF to collaborative-representation based classifications (CRCs) to extract the underlying information that can help identify the class label of the corresponding query sample. CRCs have offered state-of-the-art performance in wearable sensor-based human activity recognition when training samples are limited. Existing work is based on the shortest Euclidean distance to a query sample, which can be susceptible to noise and correlation in the training samples. To improve robustness, we employ the adaptive MRF to extract the underlying structure of a representation vector directly from the query sample to improve discriminative power, because the underlying structure is unique to its corresponding query sample and independent of the quality of the training samples. The adaptive MRF can be customized to further reduce to the correlation in the training samples. Extensive experiments on two real-world datasets demonstrate the promising performance of the proposed method.Thesis (Ph.D.) -- University of Adelaide, School of Computer Science, 201

COMPRESSION OF WEARABLE BODY SENSOR NETWORK DATA USING IMPROVED TWO-THRESHOLD-TWO-DIVISOR DATA CHUNKING ALGORITHM

Compression plays a significant role in Body Sensor Networks (BSN) data since the sensors in BSNs have limited battery power and memory. Also, data needs to be transmitted fast and in a lossless manner to provide near real-time feedback. The paper evaluates lossless data compression algorithms like Run Length Encoding (RLE), Lempel Zev Welch (LZW) and Huffman on data from wearable devices and compares them in terms of Compression Ratio, Compression Factor, Savings Percentage and Compression Time. It also evaluates a data deduplication technique used for Low Bandwidth File Systems (LBFS) named Two Thresholds Two Divisors (TTTD) algorithm to determine if it could be used for BSN data. By changing the parameters and running the algorithm multiple times on the data, it arrives at a set of values that give \u3e50 compression ratio on BSN data. This is the first value of the paper. Based on these performance evaluation results of TTTD and various classical compression algorithms, it proposes a technique to combine multiple algorithms in sequence. Upon comparison of the performance, it has been found that the new algorithm, TTTD-H, which does TTTD and Huffman in sequence, improves the Savings Percentage by 23 percent over TTTD, and 31 percent over Huffman when executed independently. Compression Factor improved by 142 percent over TTTD, 52 percent over LZW, 178 percent over Huffman for a file of 3.5 MB. These significant results are the second important value of the project

A Simple Method to Simultaneously Detect and Identify Spikes from Raw Extracellular Recordings

The ability to track when and which neurons fire in the vicinity of an electrode, in an efficient and reliable manner can revolutionize the neuroscience field. The current bottleneck lies in spike sorting algorithms; existing methods for detecting and discriminating the activity of multiple neurons rely on inefficient, multi-step processing of extracellular recordings. In this work, we show that a single-step processing of raw (unfiltered) extracellular signals is sufficient for both the detection and identification of active neurons, thus greatly simplifying and optimizing the spike sorting approach. The efficiency and reliability of our method is demonstrated in both real and simulated data

2022 Review of Data-Driven Plasma Science

Data-driven science and technology offer transformative tools and methods to science. This review article highlights the latest development and progress in the interdisciplinary field of data-driven plasma science (DDPS), i.e., plasma science whose progress is driven strongly by data and data analyses. Plasma is considered to be the most ubiquitous form of observable matter in the universe. Data associated with plasmas can, therefore, cover extremely large spatial and temporal scales, and often provide essential information for other scientific disciplines. Thanks to the latest technological developments, plasma experiments, observations, and computation now produce a large amount of data that can no longer be analyzed or interpreted manually. This trend now necessitates a highly sophisticated use of high-performance computers for data analyses, making artificial intelligence and machine learning vital components of DDPS. This article contains seven primary sections, in addition to the introduction and summary. Following an overview of fundamental data-driven science, five other sections cover widely studied topics of plasma science and technologies, i.e., basic plasma physics and laboratory experiments, magnetic confinement fusion, inertial confinement fusion and high-energy-density physics, space and astronomical plasmas, and plasma technologies for industrial and other applications. The final section before the summary discusses plasma-related databases that could significantly contribute to DDPS. Each primary section starts with a brief introduction to the topic, discusses the state-of-the-art developments in the use of data and/or data-scientific approaches, and presents the summary and outlook. Despite the recent impressive signs of progress, the DDPS is still in its infancy. This article attempts to offer a broad perspective on the development of this field and identify where further innovations are required

Structured Dictionary Learning and its applications in Neural Recording

Widely utilized in the field of neuroscience, implantable neural recording devices could capture neuron activities with an acquisition rate on the order of megabytes per second. In order to efficiently transmit neural signals through wireless channels, these devices require compression methods that reduce power consumption. Although recent Compressed Sensing (CS) approaches have successfully demonstrated their power, their full potential is yet to be explored, particularly towards exploring a more efficient representation of the neural signals. As a promising solution, sparse representation not only provides better signal compression for bandwidth/storage efficiency, but also leads to faster processing algorithms as well as more effective signal separation for classification purpose. However, current sparsity‐based approaches for neural recording are limited due to several critical drawbacks: (i) the lack of an efficient data‐driven representation to fully capture the characteristics of specific neural signal; (ii) most existing methods do not fully explore the prior knowledge of neural signals (e.g., labels), while such information is often known; and (iii) the capability to encode discriminative information into the representation to promote classification. Using neural recording as a case study, this dissertation presents new theoretical ideas and mathematical frameworks on structured dictionary learning with applications in compression and classification. Start with a single task setup, we provide theoretical proofs to show the benefits of using structured sparsity in dictionary learning. Then we provide various novel models for the representation of a single measurement, as well as multiple measurements where signals exhibit both with‐in class similarity as well as with‐in class difference. Under the assumption that the label information of the neural signal is known, the proposed models minimize the data fidelity term together with the structured sparsity terms to drive for more discriminative representation. We demonstrate that this is particularly essential in neural recording since it can further improve the compression ratio, classification accuracy and help deal with non‐ideal scenarios such as co-occurrences of neuron firings. Fast and efficient algorithms based on Bayesian inference and alternative direction method are proposed. Extensive experiments are conducted on both neural recording applications as well as some other classification task, such as image classification

Extending BIM for air quality monitoring

As we spend more than 90% of our time inside buildings, indoor environmental quality is a major concern for healthy living. Recent studies show that almost 80% of people in European countries and the United States suffer from SBS (Sick Building Syndrome), which affects physical health, productivity and psychological well-being. In this context, environmental quality monitoring provides stakeholders with crucial information about indoor living conditions, thus facilitating building management along its lifecycle, from design, construction and commissioning to usage, maintenance and end-of-life. However, currently available modelling tools for building management remain limited to static models and lack integration capacities to efficiently exploit environmental quality monitoring data. In order to overcome these limitations, we designed and implemented a generic software architecture that relies on accessible Building Information Model (BIM) attributes to add a dynamic layer that integrates environmental quality data coming from deployed sensors. Merging sensor data with BIM allows creation of a digital twin for the monitored building where live information about environmental quality enables evaluation through numerical simulation. Our solution allows accessing and displaying live sensor data, thus providing advanced functionality to the end-user and other systems in the building. In order to preserve genericity and separation of concerns, our solution stores sensor data in a separate database available through an application programming interface (API), which decouples BIM models from sensor data. Our proof-of-concept experiments were conducted with a cultural heritage building located in Bled, Slovenia. We demonstrated that it is possible to display live information regarding environmental quality (temperature, relative humidity, CO2, particle matter, light) using Revit as an example, thus enabling end-users to follow the conditions of their living environment and take appropriate measures to improve its quality.Pages 244-250

Compressed Sensing Beyond the IID and Static Domains: Theory, Algorithms and Applications

Sparsity is a ubiquitous feature of many real world signals such as natural images and neural spiking activities. Conventional compressed sensing utilizes sparsity to recover low dimensional signal structures in high ambient dimensions using few measurements, where i.i.d measurements are at disposal. However real world scenarios typically exhibit non i.i.d and dynamic structures and are confined by physical constraints, preventing applicability of the theoretical guarantees of compressed sensing and limiting its applications. In this thesis we develop new theory, algorithms and applications for non i.i.d and dynamic compressed sensing by considering such constraints. In the first part of this thesis we derive new optimal sampling-complexity tradeoffs for two commonly used processes used to model dependent temporal structures: the autoregressive processes and self-exciting generalized linear models. Our theoretical results successfully recovered the temporal dependencies in neural activities, financial data and traffic data. Next, we develop a new framework for studying temporal dynamics by introducing compressible state-space models, which simultaneously utilize spatial and temporal sparsity. We develop a fast algorithm for optimal inference on such models and prove its optimal recovery guarantees. Our algorithm shows significant improvement in detecting sparse events in biological applications such as spindle detection and calcium deconvolution. Finally, we develop a sparse Poisson image reconstruction technique and the first compressive two-photon microscope which uses lines of excitation across the sample at multiple angles. We recovered diffraction-limited images from relatively few incoherently multiplexed measurements, at a rate of 1.5 billion voxels per second