Sequence Compression Research Articles

Work and heat integration: An emerging research area

The extension from Heat Integration (HI) and design of Heat Exchanger Networks (HENs) to including heating and cooling effects from pressure changing equipment has been referred to as Work and Heat Integration and design of Work and Heat Exchange Networks (WHENs). This is an emerging research area of Process Synthesis, however, WHENs is a considerably more complex design task than HENs. A key challenge is the fact that temperature changes (related to heat) and pressure changes (related to work) of process streams are interacting. Changes in inlet temperatures to compressors and expanders resulting from heat integration will influence work consumption and production. Likewise, pressure changes by compression and expansion will change the temperatures of process streams, thus affecting heat integration.As a result, Composite and Grand Composite Curves will change shape due to pressure changes in the process. The thermodynamic path of process streams from supply (pressure, temperature) to target state is not known and depends on the sequence of heating, cooling, compression and expansion. This paper introduces a definition and describes the development of WHENs. Future research challenges related to methodology development and industrial applications will be addressed. The potential of WHENs will be indicated through examples in literature.

Design and Analysis of an Improved Nucleotide Sequences Compression Algorithm Using Look up Table (LUT)

DNA (deoxyribonucleic acid), is the hereditary material in humans and almost all other organisms. Nearly every cell in a person’s body has the same DNA. The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). With continuous technology development and growth of sequencing data, large amount of biological data is generated. This large amount of generated data causes difficulty to store, analyse and process DNA sequences. So there is a wide need of reducing the size, for this reason, DNA Compression is employed to reduce the size of DNA sequence. Therefore there is a huge need of compressing the DNA sequence. In this paper, we have proposed an efficient and fast DNA sequence compression algorithm based on differential direct coding and variable look up table (LUT).

Microstructural evolution in the low strain amplitude multi-axial compression (LSA-MAC) after equal channel equal pressing (ECAP) of aluminum

Low strain amplitude multi-axial compression (LSA-MAC) increases the work hardening capacity and uniform ductility of Aluminum after Severe Plastic Deformation (SPD) through Equal Channel Angular Pressing (ECAP). The mechanisms associated with this processing after ECAP are analyzed. LSA-MAC after 1 ECAP pass in Aluminum softens the material and is connected to the stabilization of the dislocation structures induced by ECAP into a configuration displaying an increased fraction of High Angle Grain Boundaries (HAGB). This occurs for a lower total imposed strain than that through a sequence of high strain ECAP passes or high strain amplitude multi-axial compression (HAS-MAC).

Incremental Relaying for Time-Varying Fading Channels With Thresholds at Relay and Destination

Incremental relaying is a spectral-efficient relaying approach which introduces itself as one of the possible solutions to the spectrum scarcity problem for future generations of cellular communications systems. In this paper, we study threshold amplify-and-forward incremental relaying for correlated fading channels, i.e., fading channels for which the channel gain amplitude varies during the time interval of a block transmission; however, the variation occurs in a correlating fashion. From this aspect, these channels are different from both block-fading and fast-fading channels. Due to the correlating nature of the channels, it is possible to compress channel state information (CSI) sequences and employ the compressed CSI sequences as side information to carefully select the bits transmitted by the relay. This idea is already employed in previous works to increase the spectral efficiency; however, those works consider block-fading channels and also assume maximal ratio combining (MRC) at receiver. In case of MRC, explicit expressions for the end-to-end signal-to-noise ratio (SNR) exist, which enable packet error rate analysis by aid of Moment Generating Functions of the SNR. However, to apply MRC, the receiver requires all channel gains (including source-relay channel gain). In case of correlated channels, communicating all real-valued channel gains, requires a large overhead. This fact renders applicability of MRC for correlated channels. We apply the more practical Equal-Gain Combining method. We derive series approximations for symbol error rate, given M-QAM and MPSK modulations, and assuming Nakagami- $m$ fading channels. We also analyze the spectral efficiency by assuming Markov models for the channels. We compare the spectral efficiency in case of correlated and fast-fading channels and show that, unlike fast-fading channels, correlated fading channels allow for a spectrally efficient scheme.

Multiple abdominal burst patterns observed during tracheobronchial coughing in anesthetized cats

The cough motor pattern is classically defined as a neuromechanical sequence of inspiration, compression, and expulsion. This definition is most applicable to single coughs. However, humans routinely produce multiple expulsions per each inspiratory effort during single or repetitive coughing. The functional significance of this coughing pattern is not fully understood, but it could represent a mechanism to facilitate the stairstep movement of particulates and mucus up the airway tree against gravity in humans. This repetitive expulsion pattern following single inspiratory cough efforts has not been reported in animal models of coughing. In the anesthetized cat, repetitive coughing can be produced by either mechanical or chemical stimulation of airway afferents. We hypothesized that expulsive cough motor patterns consistent with those seen in humans could be observed in the anesthetized cat. Further, we have previously observed that thoracotomy depresses cough excitability, presumably though a decrease in pulmonary volume‐related feedback. We also hypothesized that thoracotomy would reduce the occurrence of coughs in which multiple expiratory bursts were observed. We investigated the cough patterns of 9 cats pre‐ (n=5) and post‐thoracotomy (n=4) for multiple abdominal bursting patterns during cough. Thoracotomized animals were artificially ventilated at a positive end expiratory pressure of 5 cmH2O. Electromyograms (EMGs) were recorded from the diaphragm, thyroarytenoid, and internal oblique muscles. Repetitive coughing was produced by mechanical stimulation of the intrathoracic airway. The percentage of cough epochs that contained at least one cough with a multiple bursting pattern was similar for closed (CC, 44±18%) and open chested (OC, 42±11%) animals. These patterns consisted of double abdominal bursts (71%), three abdominal bursts (23%) and four bursts (5%). Corresponding abdominal bursts had similar amplitudes in both CC and OC animals. In OC animals, the amplitude of the second abdominal burst (CC − 45±11 to 31±7%, p=n.s.; OC − 43±4 to 28±5, p<0.05) was significantly lower than the first. Thoracotomy prolonged E2 duration for coughs with only 1 expiratory burst (CC 1±0.2s; OC 2±0.4 s, p < 0.05), but not for multiple expiratory bursts (CC 0.6±0.1 s; OC 0.9±0.4 s). The time between multiple abdominal bursts (CC 232±16 msec; OC 233±32 msec) was not different after thoracotomy. In some animals, small amplitude bursts in thyroarytenoid EMGs occurred out of phase with multiple abdominal bursting, consistent with adductor/abdominal oscillations. We conclude that the anesthetized cat is capable of expressing multiple abdominal bursting following a single inspiratory effort during tracheobronchial coughing. Our results support the existence of multiple oscillatory patterns during repetitive tracheobronchial coughing in the cat. This pattern may be analogous to that exhibited by awake humans.Support or Funding InformationSupported by NIH HL 103415 and 1OT20D001983.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

An enhanced performance for H.265/SHVC based on combined AEGBM3D filter and back-propagation neural network

This paper deals with the latest video coding standard H265 SHVC, a scalable extension to High Efficiency Video Coding (HEVC). HEVC introduces new coding tools compared to its predecessor and is backward compatible with all types of electronic gadgets. The gadgets with different display capabilities cannot be offered the same quality video due to the constraints in transmission bandwidth is a major problem. One solution to this problem will be the compression of the video sequence which is focused in this paper to preserve or increase PSNR while reducing bit-rate besides a novel method implemented in SHVC encoder. The novel method undergoes a combined AEGBM3D (adaptive edge guided block-matching and 3D) filtering and back-propagation technique. The technique includes an AEGBM3D filter which avoids spatial redundancy and de-noise frames; hence enhancement in PSNR is achieved. The obtained PSNR of the video is compared with the set threshold PSNR to maintain PSNR above the threshold by repeated AEGBM3D filtering. The BP technique based on the neural network machine learning approach continually restrains the output if the input block does not contain a feature they were trained to recognize. This frequent control over the output produces few bits; hence reduction in bit-rate is achieved. The simulation results show that the proposed technique delivers an average increment of 0.16 and 0.25dB in PSNR and an average decrement of 28 and 37% in bit-rate for 1.5 and 2 times spatial ratios respectively, compared with the existing methods.

Modified HuffBit Compress Algorithm - An Application of R.

The databases of genomic sequences are growing at an explicative rate because of the increasing growth of living organisms. Compressing deoxyribonucleic acid (DNA) sequences is a momentous task as the databases are getting closest to its threshold. Various compression algorithms are developed for DNA sequence compression. An efficient DNA compression algorithm that works on both repetitive and non-repetitive sequences known as “HuffBit Compress” is based on the concept of Extended Binary Tree. In this paper, here is proposed and developed a modified version of “HuffBit Compress” algorithm to compress and decompress DNA sequences using the R language which will always give the Best Case of the compression ratio but it uses extra 6 bits to compress than best case of “HuffBit Compress” algorithm and can be named as the “Modified HuffBit Compress Algorithm”. The algorithm makes an extended binary tree based on the Huffman Codes and the maximum occurring bases (A, C, G, T). Experimenting with 6 sequences the proposed algorithm gives approximately 16.18 % improvement in compression ration over the “HuffBit Compress” algorithm and 11.12 % improvement in compression ration over the “2-Bits Encoding Method”.

Injectivity on distribution of elements in the compressed sequences derived from primitive sequences over ℤ p e $\mathbb {Z}_{p^{e}}$

Let p ≥ 3 be a prime, e ≥ 2 an integer and $\mathbb {Z}_{p^{e}}$ the residue ring modulo pe. Let σ(x) be a primitive polynomial of degree n over $\mathbb {Z}_{p^{e}}$ and let G′(σ(x), pe) be the set of primitive linear recurring sequences over $\mathbb {Z}_{p^{e}}$ generated by σ(x). A compressing mapping $\varphi :\mathbb {Z}_{p^{e}}\rightarrow \mathscr {A}$ naturally induces a mapping $\widehat {\varphi }$ on G ′(σ(x), pe), i.e., $\widehat {\varphi }$ maps a sequence (…,si− 1,si,si+ 1,… ) to (…,φ(si− 1),φ(si),φ(si+ 1),… ). For any pair of sequences in $\{\widehat {\varphi }(\underline {s}):\underline {s}\in G^{\prime }_{~}(\sigma (x),p^{e})\}$ , it is desirable to determine whether (at least) one element of $\mathscr {A}$ is distributed differently in them. For $\emptyset \neq D\subseteq \mathscr {A}$ , $\widehat {\varphi }$ is said to be injective on G ′(σ(x), pe) w.r.t. D-uniformity if for any two distinct sequences $\underline {u},\underline {v}\in G^{\prime }_{~}(\sigma (x),p^{e})$ , the distribution of at least one element of D in $\widehat {\varphi }(\underline {u})$ differs from that in $\widehat {\varphi }(\underline {v})$ . A sufficient condition on φ is given to ensure that $\widehat {\varphi }$ is injective on G ′(σ(x), pe) w.r.t. D-uniformity. If $\left (\left ((x^{p^{n}-1}-1)^{2}\bmod \sigma (x)\right ) \bmod p^{3}\right ) \notin p^{2}\mathbb {Z}_{p}$ , then an equivalent condition on φ is obtained to decide whether $\widehat {\varphi }$ is injective on G ′(σ(x), pe) w.r.t. D-uniformity. Furthermore, quantitative estimation suggests that almost all mappings on $\mathbb {Z}_{p^{e}}$ induce injective mappings on G ′(σ(x), pe) as p and e increase.

Construction of employee training program evaluation system of three exponential forecast based on sliding window

One construction method for employee training program evaluation system of three exponential forecast based on sliding window has been proposed to improve the effectiveness of construction process for employee training program evaluation system. Firstly, construct employee training program evaluation forecast model with gray model and set up regression forecast objective function; secondly, construct sliding window by setting segmentation points and make real-time segmentation for gray model data by combining three smoothness exponential algorithm, attain real-time statistical feature of data, construct the function relation between sequence error forecast and compression ratio, make use of error forecast sequence to make segmentation point judgment and improve robustness of test. Lastly, the effectiveness of the algorithm has been verified through simulation experiment.

Analiza performansi objektivnih mera procene kvaliteta slika i videa sa potpunim referenciranjem

This paper presents the performance evaluation of image and video quality assessment metrics on two publicly available datasets with subjective quality ratings. In addition to the performance analysis at the global level - at the level of complete datasets, the paper presents the objective measures performance evaluation on subsets of signals inside them. The image dataset contains five subsets created by using different types of JPEG compression, while the video dataset contains six subsets of sequences - four created by compression of original sequences, and two subsets are with video signal transmission characteristic degradations. To determine the success of objective measures, i.e. comparison of subjective and objective quality scores, there were used measures accepted by the International Telecommunication Union - ITU (linear correlation coefficient, rank-order correlation coefficient, mean absolute error, root mean squared error and outlier ratio). It was shown that objective quality measures can reach a high level of agreement with the results of subjective tests on subsets of datasets. Objective measures performances depend on the type of degradation which significantly affects the performance at the complete dataset level. The difference in performances is more pronounced on video sequences due to considerable visual differences in sequences created by using compression, packet losses and additive Gaussian noise. Therefore, we can say that a universal objective measure, i.e. measure that is useful for different types of signal degradation, for different degradation levels, and for different applications currently does not exist.

Stress and Strain Rate Effects on Incipient Spall in Tantalum

Spall fracture is a high-rate tensile damage phenomenon associated with impulsive and shock-load events. Typically, the material undergoes a sequence of compression followed by release into high rate (on the order of 104 s-1 and up) tension, causing voids to nucleate and grow, which can then coalesce into a crack and the material fails. We present a series of experiments on high purity, well characterized tantalum samples subjected to shock-loading via gas-gun plate impact. Through careful selection of the flyer-plate velocity and material we have independent control over the peak compressive stress and the tensile strain rate in the sample. At all times, the spall damage remains incipient, i.e. in the early stages of void formation and the material does not fully fracture. Velocimetry was used on the rear of the sample to record the wave-profiles and determine spall strength. Soft recovery and sectioning of the samples allowed the internal damage to be observed, quantifying the damage amount, distribution, and relationship to microstructural features with both optical and electron based microscopy.

High performance angiogram sequence compression using 2D bi-orthogonal multi wavelet and hybrid speck-deflate algorithm

Fast communication of medical information is a big challenge for today’s researchers. Either bandwidth or information needs to be sacrificed in order to communicate the entire information within a short time with minimal bandwidth. Compression of medical information before transmission helps us to communicate the entire information within short time with minimal cost. This paper concentrates on reducing the transmission bandwidth by compressing the entire medical information using a Hybrid algorithm which uses 2D Bi-orthogonal multi-wavelet transform and SPECK – Deflate encoder. The algorithm is studied with the standard test dataset GRUSELAMBIX. The real time data was analyzed to ensure the perseverance of the diagnostic information. 2D Bi-orthogonal multi-wavelet transform was applied on each frame on the DICOM file and the co-efficients are encoded using SPECK encoder followed by the deflate compression algorithm. To preserve the original diagnostic information, motion estimation and compensation was not applied on the medical videos. The qualitative performance of this algorithm is evaluated using Compression Ratio, PSNR, MSE, UIQIand SSIM. The Mean opinion Score from experts and non-experts was obtained on the real time data to evaluate the quantitative performance. The proposed algorithm revealed a better compression ratio than the traditional compression algorithm.

Parallel Fractal Compression Method for Big Video Data

With the development of technologies such as multimedia technology and information technology, a great deal of video data is generated every day. However, storing and transmitting big video data requires a large quantity of storage space and network bandwidth because of its large scale. Therefore, the compression method of big video data has become a challenging research topic at present. Performance of existing content‐based video sequence compression method is difficult to be effectively improved. Therefore, in this paper, we present a fractal‐based parallel compression method without content for big video data. First of all, in order to reduce computational complexity, a video sequence is divided into several fragments according to the spatial and temporal similarity. Secondly, domain and range blocks are classified based on the color similarity feature to reduce computational complexity in each video fragment. Meanwhile, a fractal compression method is deployed in a SIMD parallel environment to reduce compression time and improve the compression ratio. Finally, experimental results show that the proposed method not only improves the quality of the recovered image but also improves the compression speed by compared with existing compression algorithms.

On Empirical Cumulant Generating Functions of Code Lengths for Individual Sequences

We consider the problem of lossless compression of individual sequences using finite-state (FS) machines, from the perspective of the best achievable empirical cumulant generating function (CGF) of the code length, i.e., the normalized logarithm of the empirical average of the exponentiated code length. Since the probabilistic CGF is minimized in terms of the Renyi entropy of the source, one of the motivations of this paper is to derive an individual-sequence analogue of the Renyi entropy, in the same way that the FS compressibility is the individual-sequence counterpart of the Shannon entropy. We consider the CGF of the code-length both from the perspective of fixed-to-variable length coding and the perspective of variable-to-variable (V-V) length coding, where the latter turns out to yield a better result, that coincides with the FS compressibility. We also extend our results to compression with side information, available at both the encoder and decoder. In this case, the V-V version no longer coincides with the FS compressibility, but results in a different complexity measure.

ACRES: efficient query answering on large compressed sequences

With the advances in next generation sequencing, the amount of genomic sequence data being produced continues to grow at an exponential rate. It is estimated that the entire genome of each individual human, each containing about 3 billion letters, could be made available in the next a few years. An increasingly pressing issue in genomics and medicine is how to efficiently store and query these massive amounts of sequence data. Recently a lossless compression technique has been proposed to drastically reduce the storage space of genomic sequences, taking advantage of the fact that any two genomes from the same species are highly similar and therefore only their differences need to be encoded. In this paper we study how to efficiently answer queries on the compressed sequences without first decompressing them. We study three important types of queries, including retrieving a subsequence, finding subsequences matching a given pattern, and finding subsequences similar to a pattern. We propose an index structure, filtering techniques, and efficient algorithms for answering these queries. We further demonstrate the utility of these algorithms using a real dataset.

Chroma Subsampling Influence on the Perceived Video Quality for Compressed Sequences in High Resolutions

This paper deals with the influence of chroma subsampling on perceived video quality measured by subjective metrics. The evaluation was done for two most used video codecs H.264/AVC and H.265/HEVC. Eight types of video sequences with Full HD and Ultra HD resolutions depending on content were tested. The experimental results showed that observers did not see the difference between unsubsampled and subsampled sequences, so using subsampled videos is preferable even 50 % of the amount of data can be saved. Also, the minimum bitrates to achieve the good and fair quality by each codec and resolution were determined.

Clustering-Based Compression for Population DNA Sequences.

Due to the advancement of DNA sequencing techniques, the number of sequenced individual genomes has experienced an exponential growth. Thus, effective compression of this kind of sequences is highly desired. In this work, we present a novel compression algorithm called Reference-based Compression algorithm using the concept of Clustering (RCC). The rationale behind RCC is based on the observation about the existence of substructures within the population sequences. To utilize these substructures, k-means clustering is employed to partition sequences into clusters for better compression. A reference sequence is then constructed for each cluster so that sequences in that cluster can be compressed by referring to this reference sequence. The reference sequence of each cluster is also compressed with reference to a sequence which is derived from all the reference sequences. Experiments show that RCC can further reduce the compressed size by up to 91.0 percent when compared with state-of-the-art compression approaches. There is a compromise between compressed size and processing time. The current implementation in Matlab has time complexity in a factor of thousands higher than the existing algorithms implemented in C/C++. Further investigation is required to improve processing time in future.

Adaptive Dictionary-based Compression of Protein Sequences

Adaptive Dictionary-based Compression of Protein Sequences

Chest compression using the foot or hand method: a prospective, randomized, controlled manikin study with school children.

Maintaining a chest compression depth of 5 cm or more as specified by resuscitation guidelines is difficult. Historical studies have shown an advantage of the foot method (FM) over the hand method (HM) in participants weighing less than 50 kg. Because of the fact that the importance of chest compression is increasing from guideline to guideline, the FM technique had not been evaluated conclusively and worldwide resuscitation is taught to school children, we investigated whether school children achieved a higher quality of chest compression with the FM than with the HM. A total of 105 school children, aged 12 to 15 years, were randomized to an FM or an HM resuscitation group. After a 3 min training video, 5 min of practice, and a 5 min latent time, the participants performed a 2 min sequence of chest compressions, which was recorded on a PC and evaluated later. The mean percentage of correct chest compression depth (primary endpoint) was low in both groups (HM 45%, FM 47%, P=0.76). This was also found for those weighing less than 50 kg and at least 50 kg in both groups (FM 23%, HM 34%, P=0.2; FM 62%, HM 56%, P=0.57). However, the HM group was better in frequency (98 vs. 86% in FM, P=0.03) and complete decompression (99 vs. 91% in FM, P≤0.001). The FM of applying chest compression did not result in a more accurately delivered compression depth compared with the HM for children and adolescents, irrespective of body weight.

3D Reconstruction and 3D Point Cloud Compression

3D reconstruction and 3D Point Cloud Compression of image sequences is an important application in computer graphics and image processing, especially in biomedical engineering. Based on the introduction of the basic principle of 3D reconstruction, this paper presents a simple and easy implementation process of 3D reconstruction, and focuses on the key technologies of point cloud acquisition, finally, the future research directions of 3D Point Cloud Compression is discussed.