Quality-on-Demand Compression of EEG Signals for Telemedicine Applications Using Neural Network Predictors

A telemedicine system using communication and information technology to deliver medical signals such as ECG, EEG for long distance medical services has become reality. In either the urgent treatment or ordinary healthcare, it is necessary to compress these signals for the efficient use of bandwidth. This paper discusses a quality on demand compression of EEG signals using neural network predictors for telemedicine applications. The objective is to obtain a greater compression gains at a low bit rate while preserving the clinical information content. A two-stage compression scheme with a predictor and an entropy encoder is used. The residue signals obtained after prediction is first thresholded using various levels of thresholds and are further quantized and then encoded using an arithmetic encoder. Three neural network models, single-layer and multi-layer perceptrons and Elman network are used and the results are compared with linear predictors such as FIR filters and AR modeling. The fidelity of the reconstructed EEG signal is assessed quantitatively using parameters such as PRD, SNR, cross correlation and power spectral density. It is found from the results that the quality of the reconstructed signal is preserved at a low PRD thereby yielding better compression results compared to results obtained using lossless scheme

VLSI Implementation of an Efficient Lossless EEG Compression Design for Wireless Body Area Network

Data transmission of electroencephalography (EEG) signals over Wireless Body Area Network (WBAN) is currently a widely used system that comes together with challenges in terms of efficiency and effectivity. In this study, an effective Very-Large-Scale Integration (VLSI) circuit design of lossless EEG compression circuit is proposed to increase both efficiency and effectivity of EEG signal transmission over WBAN. The proposed design was realized based on a novel lossless compression algorithm which consists of an adaptive fuzzy predictor, a voting-based scheme and a tri-stage entropy encoder. The tri-stage entropy encoder is composed of a two-stage Huffman and Golomb-Rice encoders with static coding table using basic comparator and multiplexer components. A pipelining technique was incorporated to enhance the performance of the proposed design. The proposed design was fabricated using a 0.18 μm CMOS technology containing 8405 gates with 2.58 mW simulated power consumption under an operating condition of 100 MHz clock speed. The CHB-MIT Scalp EEG Database was used to test the performance of the proposed technique in terms of compression rate which yielded an average value of 2.35 for 23 channels. Compared with previously proposed hardware-oriented lossless EEG compression designs, this work provided a 14.6% increase in compression rate with a 37.3% reduction in hardware cost while maintaining a low system complexity

Optimal Resource Allocation Using Deep Learning-Based Adaptive Compression For Mhealth Applications

In the last few years the number of patients with chronic diseases that require constant monitoring increases rapidly; which motivates the researchers to develop scalable remote health applications. Nevertheless, transmitting big real-time data through a dynamic network limited by the bandwidth, end-to-end delay and transmission energy; will be an obstacle against having an efficient transmission of the data. The problem can be resolved by applying data reduction techniques on the vital signs at the transmitter side and reconstructing the data at the receiver side (i.e. the m-Health center). However, a new problem will be introduced which is the ability to receive the vital signs at the server side with an acceptable distortion rate (i.e. deformation of vital signs because of inefficient data reduction). In this thesis, we integrate efficient data reduction with wireless networking to deliver an adaptive compression with an acceptable distortion, while reacting to the wireless network dynamics such as channel fading and user mobility. A Deep Learning (DL) approach was used to implement an adaptive compression technique to compress and reconstruct the vital signs in general and specifically the Electroencephalogram Signal (EEG) with the minimum distortion. Then, a resource allocation framework was introduced to minimize the transmission energy along with the distortion of the reconstructed signa

A High-Performance Lossless Compression Scheme for EEG Signals Using Wavelet Transform and Neural Network Predictors

Developments of new classes of efficient compression algorithms, software systems, and hardware for data intensive applications in today's digital health care systems provide timely and meaningful solutions in response to exponentially growing patient information data complexity and associated analysis requirements. Of the different 1D medical signals, electroencephalography (EEG) data is of great importance to the neurologist for detecting brain-related disorders. The volume of digitized EEG data generated and preserved for future reference exceeds the capacity of recent developments in digital storage and communication media and hence there is a need for an efficient compression system. This paper presents a new and efficient high performance lossless EEG compression using wavelet transform and neural network predictors. The coefficients generated from the EEG signal by integer wavelet transform are used to train the neural network predictors. The error residues are further encoded using a combinational entropy encoder, Lempel-Ziv-arithmetic encoder. Also a new context-based error modeling is also investigated to improve the compression efficiency. A compression ratio of 2.99 (with compression efficiency of 67%) is achieved with the proposed scheme with less encoding time thereby providing diagnostic reliability for lossless transmission as well as recovery of EEG signals for telemedicine applications

A Deep Learning Approach for Vital Signs Compression and Energy Efficient Delivery in mhealth Systems

© 2013 IEEE. Due to the increasing number of chronic disease patients, continuous health monitoring has become the top priority for health-care providers and has posed a major stimulus for the development of scalable and energy efficient mobile health systems. Collected data in such systems are highly critical and can be affected by wireless network conditions, which in return, motivates the need for a preprocessing stage that optimizes data delivery in an adaptive manner with respect to network dynamics. We present in this paper adaptive single and multiple modality data compression schemes based on deep learning approach, which consider acquired data characteristics and network dynamics for providing energy efficient data delivery. Results indicate that: 1) the proposed adaptive single modality compression scheme outperforms conventional compression methods by 13.24% and 43.75% reductions in distortion and processing time, respectively; 2) the proposed adaptive multiple modality compression further decreases the distortion by 3.71% and 72.37% when compared with the proposed single modality scheme and conventional methods through leveraging inter-modality correlations; and 3) adaptive multiple modality compression demonstrates its efficiency in terms of energy consumption, computational complexity, and responding to different network states. Hence, our approach is suitable for mobile health applications (mHealth), where the smart preprocessing of vital signs can enhance energy consumption, reduce storage, and cut down transmission delays to the mHealth cloud.This work was supported by NPRP through the Qatar National Research Fund (a member of the Qatar Foundation) under Grant 7-684-1-127

Compression algorithms for biomedical signals and nanopore sequencing data

The massive generation of biological digital information creates various computing challenges such as its storage and transmission. For example, biomedical signals, such as electroencephalograms (EEG), are recorded by multiple sensors over long periods of time, resulting in large volumes of data. Another example is genome DNA sequencing data, where the amount of data generated globally is seeing explosive growth, leading to increasing needs for processing, storage, and transmission resources. In this thesis we investigate the use of data compression techniques for this problem, in two different scenarios where computational efficiency is crucial. First we study the compression of multi-channel biomedical signals. We present a new lossless data compressor for multi-channel signals, GSC, which achieves compression performance similar to the state of the art, while being more computationally efficient than other available alternatives. The compressor uses two novel integer-based implementations of the predictive coding and expert advice schemes for multi-channel signals. We also develop a version of GSC optimized for EEG data. This version manages to significantly lower compression times while attaining similar compression performance for that specic type of signal. In a second scenario we study the compression of DNA sequencing data produced by nanopore sequencing technologies. We present two novel lossless compression algorithms specifically tailored to nanopore FASTQ files. ENANO is a reference-free compressor, which mainly focuses on the compression of quality scores. It achieves state of the art compression performance, while being fast and with low memory consumption when compared to other popular FASTQ compression tools. On the other hand, RENANO is a reference-based compressor, which improves on ENANO, by providing a more efficient base call sequence compression component. For RENANO two algorithms are introduced, corresponding to the following scenarios: a reference genome is available without cost to both the compressor and the decompressor; and the reference genome is available only on the compressor side, and a compacted version of the reference is included in the compressed le. Both algorithms of RENANO significantly improve the compression performance of ENANO, with similar compression times, and higher memory requirements.La generación masiva de información digital biológica da lugar a múltiples desafíos informáticos, como su almacenamiento y transmisión. Por ejemplo, las señales biomédicas, como los electroencefalogramas (EEG), son generadas por múltiples sensores registrando medidas en simultaneo durante largos períodos de tiempo, generando grandes volúmenes de datos. Otro ejemplo son los datos de secuenciación de ADN, en donde la cantidad de datos a nivel mundial esta creciendo de forma explosiva, lo que da lugar a una gran necesidad de recursos de procesamiento, almacenamiento y transmisión. En esta tesis investigamos como aplicar técnicas de compresión de datos para atacar este problema, en dos escenarios diferentes donde la eficiencia computacional juega un rol importante. Primero estudiamos la compresión de señales biomédicas multicanal. Comenzamos presentando un nuevo compresor de datos sin perdida para señales multicanal, GSC, que logra obtener niveles de compresión en el estado del arte y que al mismo tiempo es mas eficiente computacionalmente que otras alternativas disponibles. El compresor utiliza dos nuevas implementaciones de los esquemas de codificación predictiva y de asesoramiento de expertos para señales multicanal, basadas en aritmética de enteros. También presentamos una versión de GSC optimizada para datos de EEG. Esta versión logra reducir significativamente los tiempos de compresión, sin deteriorar significativamente los niveles de compresión para datos de EEG. En un segundo escenario estudiamos la compresión de datos de secuenciación de ADN generados por tecnologías de secuenciación por nanoporos. En este sentido, presentamos dos nuevos algoritmos de compresión sin perdida, específicamente diseñados para archivos FASTQ generados por tecnología de nanoporos. ENANO es un compresor libre de referencia, enfocado principalmente en la compresión de los valores de calidad de las bases. ENANO alcanza niveles de compresión en el estado del arte, siendo a la vez mas eficiente computacionalmente que otras herramientas populares de compresión de archivos FASTQ. Por otro lado, RENANO es un compresor basado en la utilización de una referencia, que mejora el rendimiento de ENANO, a partir de un nuevo esquema de compresión de las secuencias de bases. Presentamos dos variantes de RENANO, correspondientes a los siguientes escenarios: (i) se tiene a disposición un genoma de referencia, tanto del lado del compresor como del descompresor, y (ii) se tiene un genoma de referencia disponible solo del lado del compresor, y se incluye una versión compacta de la referencia en el archivo comprimido. Ambas variantes de RENANO mejoran significativamente los niveles compresión de ENANO, alcanzando tiempos de compresión similares y un mayor consumo de memoria