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2020 Vol. 42, No. 6
Molecular data storage has great potential as durable and high-density data-storage media, which will deal with the growing gap between produced information and the data storage ability. With storing data in molecular form, DNA can provide alternative substrates for storage to overcome the physical limits for existing medias. This review provides an overview of the history, process and the current status of the DNA data storage, and presents the problems of current data storage technology.
With the arrival of the post-moore era, the development of traditional silicon-based computers has been on the verge of the limit, which pushes people to develop new computing technology to meet the needs of science and technology and life. Due to its superior parallel computing capability and outstanding data storage capability, DNA computing becomes an important branch of new computer technologies and a hot research field. The booming DNA nanotechnology has provided a new development platform for DNA computing. In this review, a brief introduction to DNA nanotechnology is given firstly, and then the development of DNA computing which is based on DNA logic gate, DNA cascade circuit and intelligent DNA molecular machine is dicussed and prospected.
DNA storage is a new kind of technique to store information by the biological molecules DNA. Compared with traditional electronic storage medium, DNA storage has the advantages such as massive storage capacity, high storage density and low energy consumption. The developments in DNA synthetic and sequencing technique, and the exponential requirement for big data storage have pushed the research of DNA storage achieving great progress on storage capacity, storage density and reliability. The development history of DNA storage, its general workflow, and the development in DNA database, documental storage and in vivo storage are introduced. Finally, the challenge of DNA storage and its potential future research direction are pointed out.
Due to the natural characteristics of specificity, high parallelism and miniaturization of DNA molecules, it exhibits strong parallel computing power and data storage capability in information processing. In this study, restriction endonuclease with specific recognition function are introduced into DNA strand displacement as the input of the DNA circuit. The YES gate, NOT gate and AND gate are designed by controlling the generation and removal of the toehold. The logic model is simulated by Visual DSD, and the design is verified by PolyacrylAmide Gel Electrophoresis(PAGE) experiments. Compared with previous molecular logic gates, this design has a quick response, simple operation, and good scalability, which provides the possibility for the design of large-scale circuits.
Drug recommendation research based on personalized markers can help to achieve personalized medicine and promote the development of precision medicine. In this paper, a method for calculating the weight of drugs on personalized markers is proposed, which first uses gene expression profile data and protein network information to filter out personalized network markers based on gene two-dimensional Gaussian distribution and then uses the importance degree of genes and the drugs side effect data to calculate the weight of drugs. This method is applied to lung adenocarcinoma, kidney renal clear cell carcinoma and uterine corpus endometrial carcinoma. Through the iterative process, a list of important drug recommendations for each disease sample is got. The results show that there are some differences in the recommended drug list and the ordering importance of drugs in different cases of the same kind of cancer, which indicates the importance and necessity of personalized drugs in the treatment of diseases. By querying the relationship between drugs from the drug database, many of the drug combinations screened by this method have a positive effect on the treatment of specific diseases, which further proves the accuracy of the drug recommendation methods based on personalized network markers. This study will effectively promote the development of precision medicine.
Alternative splicing is closely related to the occurrence and development of a variety of complex diseases, the emergence of various diseases including tumors is often accompanied by the occurrence of alternative splicing disorders. The existing analysis of breast cancer subtypes is mainly based on single splicing isoform, and the difference in the overall distribution of splicing isoforms caused by alternative splicing disorders among subtypes is not considered. Therefore, a prediction method of breast cancer subtypes based on alternative splicing disorders is proposed, which mainly uses Jensen-Shannon(JS) divergence to find genes with large differences in alternative splicing disorders between subtypes, then constructes Back Propagation(BP) neural network model to classify breast cancer subtypes. The results show that this method could not only effectively detect tumor heterogeneous molecules, but also had good identification results in the classification of breast cancer subtypes, with an average F1-score of 0.89, and could provide personalized drug recommendations for patients with breast cancer subtypes. This study will effectively promote the development of breast cancer subtypes based on alternative splicing disorders.
The essence of NAND gate is the superposition of AND gate and NOT gate. The AND gate operation is performed first, and then the NOT gate is performed. It is the basis of the DNA computer. In order to realize the computing of NAND gate, a NAND gate computational model is established based on the DNA origami template. The inputs of the logic value are completed by the Hybridization Chain Reaction (HCR) on the DNA origami template. The input strands first react with the AND gate region and then react with the NOT gate region. The result of the reaction is shown by dynamically separation of the gold nanoparticles on the DNA origami template. The simulation of the model through Visual DSD shows that the system has the advantages of high feasibility.
It is important to design high-quality DNA sequences set, which can improve the reliability and efficiency of DNA computing. DNA sequence design problem is an multiobjective optimization problem that needs to satisfy multiple conflict objectives which are thermodynamic constraint, similarity constraint and GC content constraint simultaneously. A MultiObjective Evolutionary Strategy (MOES) is proposed to solve the DNA sequence design problem. The random base mutation operator is designed for exploration and exploitation the search space. The fitness function is improved for obtaining balanced similarity and H-measure objective functions. Some state-of-the-art approaches are chosen to evaluate the effectivity of proposed algorithm. The experiment results show that the proposed multiobjective evolution strategy algorithm obtains very promising DNA sequences and outperforms previous approaches.
In recent years, with the rapid development of DNA nanotechnology, fluorescence biosensors based on DNA as aptamer are studied and constructed by a large number of scholars in order to realize the sensitive and rapid detection of target materials. As a new branch of DNA nanotechnology, fluorescence biosensors based on DNA aptamer have great application. The fluorescence biosensors based on DNA aptamers are summarized. The realization of fluorescence signal contains fluorescent dyes and non-fluorescent dye labeled. Enhancement of fluorescence signals involve enzyme-assisted, chain replacement reaction and both of all mediated target circulation and signals amplification strategy. On this basis, the fluorescence biosensor based on DNA aptamer is prospected and some suggestions are put forward.
The security of digital image transmission and storage has become a hotspot of information security research. An image encryption algorithm based on variable step length Josephus traversing and DNA dynamic coding is proposed. Firstly, through the thorough analysis of Joseph traversing, the random sequence generated by chaotic map is taken as the variable step length of Joseph traversing, and the pixel position is permutated. Secondly, according to the random sequence generated by chaotic map, the DNA coding rules of pixel points transformation are selected, and the image is dynamically encoded into DNA strand, and the DNA sequence is calculated based on the principle of complementary base pairing. Because the DNA coding rules of the pixels transformation are dynamic, the hidden danger caused by the lack of DNA coding rules is well solved, and the security of the algorithm is improved. Finally, the permutation and diffusion characteristics of the algorithm are further enhanced by ciphertext feedback and chaotic system iteration. Experiment and security analysis results show that the algorithm not only has large key space and strong sensitivity to keys, but also can effectively resist attacks such as statistical analysis and brutal analysis.
Alternative splicing is an important mechanism of protein diversity in a wide range of organisms, which plays an important role in the fine regulation of cell proliferation, differentiation, development, apoptosis and a series of important biological processes. In recent years, it is found that the occurrence of multiple complex diseases is often accompanied by the disordered expression of splicing isoforms. In order to study the difference of splicing isoforms on the whole distribution, a differential analysis method of Alternative Splicing (AS) based on the median value by Jensen-Shannon (JS) divergence is proposed in this paper. The results show the method can finds plenty of genes with significant differences in the overall distribution of splicing isoforms. These genes are not only concentrated in some cancer related pathways, but also in some signaling pathways based on alternative splicing regulation, cell division process and protein function. In addition, compared with the gene-level differential analysis, the genes with significant difference in alternative splicing also have better performance in survival analysis. In conclusion, the proposed method will lay a foundation for further revealing the mechanism of alternative splicing in cancer.
The research content of DNA computing is various and complex. The construction of DNA complex logic circuit belongs to an important research branch of DNA computing, in which the construction of logic gate belongs to the basic research of DNA complex logic circuit construction. The design of a simpler logic gate is used to provide a reference for researchers to build complex circuits and save valuable time for basic research. In order to solve the above problems, the idea of enable control end and DNA strand displacement technique are used to design three kinds of DNA combinatorial logic gates: AND-OR gate, NAND-NOR gate and XOR-XNOR gate. The results show that the three kinds of combinatorial logic gates can realize six kinds of logic operation functions, and the multi-stage combinatorial molecular logic circuits are successfully constructed by using the combinatorial logic gates, which provides more solutions for DNA calculation. It promotes the development of DNA computer.
As a new subject born at the end of the 20th century, biological computing has become a hot spot of frontier scientific research. Similar to the electronic computer, the construction of biological computer needs a variety of molecular logic gates, and the introduction of Graphene Oxide(GO), heavy metal ion heavy metal particles and other substances with biochemical characteristics into the design of molecular logic gates is expected to put forward new ideas for research. In addition, molecular logic gates should be realized at the level of biological experiments, which requires the study of controllability and controllable range of various conditions of biological experiments. Based on this idea, several logic gates are designed based on graphene oxide and metal ions. The feasibility is verified by simulation experiment, electrophoresis experiment, orthogonal experiment, fluorescence experiment, etc. At the same time, the controllability and controllable range of the experiment are further researched. On the one hand, the feasibility of the designed logic gate is proved, on the other hand, it be found that can be applied to actual samples.
Accurately predicting the synergistic and antagonistic relationship of drugs is helpful to the safety of drug use and the development of drug combination. A method for predicting drug synergy and antagonistic is proposed, which based on the Drug-Drug Interaction Network (DDINet) and its topological structure. From the result of feature selection, it can be seen that the feature constructed based on the interaction between the drug and its common neighbor node shows an obvious difference in the distribution of positive and negative samples, which can effectively reflect the drug synergy or antagonism. In the classification results using different feature classifiers, the optimal Area Under the Curve (AUC) and classification accuracy value reache 0.9687 and 0.9187 respectively. In the prediction results of synergy and antagonism, the prediction accuracy also reache above 0.45 and 0.75. This shows that the method based on network topology can effectively classify and predict the synergistic and antagonistic effects of drugs. Compared with the traditional methods based on similarity features of drug function, structure, target gene, etc, this method is simple and efficient to calculate, and can effectively promote the development of combination drugs.
Considering the dynamic resource allocation and energy management problem in the 5G Heterogeneous Cloud Radio Access Networks(H-CRANs) architecture for hybrid energy supply, a dynamic network resource allocation and energy management algorithm based on deep reinforcement learning is proposed. Firstly, due to the volatility of renewable energy and the randomness of user data service arrival, taking into account the stability of the system, the sustainability of energy and the Quality of Service(QoS) requirements of users, the resource allocation and energy management issues in the H-CRANs network as a Constrained infinite time Markov Decision Process (CMDP) are modeled with the goal of maximizing the average net profit of service providers. Then, the Lagrange multiplier method is used to transform the proposed CMDP problem into an unconstrained Markov Decision Process (MDP) problem. Finally, because the action space and the state space are both continuous value sets, the deep reinforcement learning is used to solve the above MDP problem. The simulation results show that the proposed algorithm can effectively guarantee the QoS and energy sustainability of the system, while improving the average net income of the service provider and reducing energy consumption.
Lossless data compression system is prone to bit error and causes error spread during communication transmission, which affects its application to file system and wireless communication. For the lossless data compression algorithm Lempel-Ziv-Welch (LZW), which is widely used in the field of general coding, analyzes and utilizes the redundancy of LZW compressed data, carries the check code by selecting part of the codeword and dynamically adjusting the length of its corresponding compressed string. A lossless data compression method Carrier-LZW(CLZW) with error correction capability is proposed. This method does not need additional data, does not change the data specification and coding rules, and is compatible with the standard LZW algorithm. The experimental results show that the file compressed by this method can still be decompressed by the standard LZW decoder. In the range of error correction capability, the method can effectively correct the error of LZW compressed data.
Due to the popularity of vehicle applications and the increase of the number of vehicles, the physical resources of roadside infrastructure are limited. When a large number of vehicles are connected to the vehicle networks, the energy consumption and latency are simultaneously increased. The framework for integrating the Content Delivery Network (CDN) and Mobile Edge Computing (MEC) can reduce the latency and energy consumption. In vehicle network, vehicle mobility poses a major challenge to the continuity of cloud services. Therefore, Mobility Management (MM) is proposed to deal with this problem. The Dynamic Channel Allocation algorithm with Overhead selection (ODCA) is used to avoid the ping-pong effect and reduces the handover time of vehicles between cells. The cooperative game algorithm based on RoadSide Unit (RSU) is used for virtual machine migration and a learning-based price control mechanism is developed to process vehicular computation resources efficiently. The simulation results show that the proposed algorithm can improve resource utilization and reduce overhead compared with the existing algorithms.
Since real-time processing scenarios for ever-increasing amount and type of streaming data caused by the development of the Internet of Things (IoT) keep increasing, and strategies based on empirical knowledge for checkpoint configuration are deficiencies, the strategy faces huge challenges, such as time-consuming, labor-intensive, causing system anomalies, etc. To address these challenges, regression algorithm-based prediction is proposed for checkpoint performance. Firstly, six kinds of features, which have a huge influence on the performance, are analyzed, and then feature vectors of the training set are input into the regression algorithms for training, finally, test sets are used for the checkpoint performance prediction. Compared with other machine learning algorithms, the experimental results illustrat that the Random Forest (RF) has lower errors, higher accuracy and faster execution on CPU intensive benchmark, memory intensive benchmark and network intensive benchmark.
In virtualized network slicing scenario, one anomaly Physical Node (PN) or Physical Link (PL) in substrate networks will cause performance degradation of multiple network slices. For new measurements are achieved in each period, two online anomaly detection algorithms to monitor the working states of substrate networks in real time are designed. An online One-Class Support Vector Machine (OCSVM) algorithm is first proposed in this paper to detect the working states of PNs. Without requiring any labeled data, the model parameters of OCSVM can be updated based on the new measurements of Virtual Nodes (VNs) in each iteration. Then, an online Canonical Correlation Analysis (CCA) based PL anomaly detection algorithm is proposed according to the natural correlation of measurements between neighboring VNs of virtual links. With a small amount of labeled data, the algorithm can accurately analyze the working states of PLs. The simulation results verify the effectiveness and robustness of the proposed online anomaly detection algorithms for the virtualized network slicing.
In order to meet the demand of the substantial increase of wireless data traffic, the resource optimization of the Heterogeneous Cloud Radio Access Network (H-CRAN) is still an important problem that needs to be solved urgently. In this paper, under the H-CRAN downlink scenario, a wireless resource allocation algorithm based on Deep Reinforcement Learning (DRL) is proposed. Firstly, a stochastic optimization model for maximizing the total network throughput is established to jointly optimize the congestion control, the user association, subcarrier allocation and the power allocation under the constraint of queue stability. Secondly, considering the complexity of scheduling problem, the DRL algorithm uses neural network as nonlinear approximate function to solve the dimensional disaster problem efficiently. Finally, considering the complexity and dynamic variability of the wireless network environment, the Transfer Learning(TL) algorithm is introduced to make use of the small sample learning characteristics of TL so that the DRL algorithm can obtain the optimal resource allocation strategy in the case of insufficient samples. In addition, TL further accelerates the convergence rate of DRL algorithm by transferring the weight parameters of DRL model. Simulation results show that the proposed algorithm can effectively increase network throughput and improve network stability.
Considering the problems of low resource utilization and poor reliability of traditional network slice embedding, a Reliability-aware Network Slice (NS) Reconfiguration and Embedding (RNSRE) strategy is proposed. Firstly, a utility function of reliable embedding oriented reliability and available resources is established. Then, considering the resource requirements and the location constraints of Virtual Network Function (VNF), a method is proposed to quantify the reliability requirement of VNF. Based on the above works, the reliable network slice embedding problem is formulated as an integer linear programming which maximizes the profits of reliable VNF deployment while minimizing the consumption of link bandwidth resource. Finally, according to different types of network slices, a network slice reliable embedding algorithm based on neighborhood search and a network slice reconfiguration embedding algorithm based on key VNF backup are proposed. Simulation results show that the proposed algorithms improve the resources utilization and reduce the embedding cost while meeting the reliability of VNF.
Pedestrian detector performance is damaged because occlusion often leads to missed detection. In order to improve the detector's ability to detect pedestrian, a single-stage detector based on feature-guided attention mechanism is proposed. Firstly, a feature attention module is designed, which preserves the association between the feature channels while retaining spatial information, and guides the model to focus on visible region. Secondly, the attention module is used to fuse shallow and deep features, then high-level semantic features of pedestrians are extracted. Finally, pedestrian detection is treated as a high-level semantic feature detection problem. Pedestrian location and scale are obtained through heat map prediction, then the final prediction bounding box is generated. This way, the proposed method avoids the extra parameter settings of the traditional anchor-based method. Experiments show that the proposed method is superior to other comparison algorithms for the accuracy of occlusion target detection on CityPersons and Caltech pedestrian database. At the same time, the proposed method achieves a faster detection speed and a better balance between detection accuracy and speed.
Hilbert curve is an important method for high-dimensional reduction to one-dimensional. It has good characteristics of spatial aggregation and spatial continuity and is widely used in geographic information system, spatial databases and information retrieval. Existing Hilbert encoding or decoding algorithms do not consider the differences between input data, thus treating them equally. To this end, an efficient Hilbert coding algorithm Front-Zero-Free Hilbert Encoding(FZF-HE) and an efficient decoding algorithm Front-Zero-Free Hilbert Decoding(FZF-HD) are proposed. FZF-HE and FZF-HD can quickly identify the 0 s of the front part of input data before iterative calculation by combining efficient state views and first bit-1 detection algorithm, thus reducing the number of iterations and the complexity of the algorithm, and improving the encoding and decoding efficiency. The experimental results show that efficiencies of these two algorithms are slightly higher than existing algorithms for uniform distributed data, and are much higher than existing algorithms for skew distributed data.
With an increasing diversity in modern architectural design, the inner structure of buildings is much more complex than before, which makes the traditional fire emergency escape indication system fail to provide people with real-time instructions because of its inflexibility of changing direction. These failures always lead people to dangerous areas during a fire emergency, which is actual a threaten to people in buildings. A combined algorithm to find a path dynamically during a fire emergency based on Dijkstra and Ant Colony Optimization (ACO) algorithm is presented in this article. This new algorithm shortens the programming time by getting a globally optimal path based on Dijkstra algorithm and operates every single point with ACO algorithm in sequence to get a best path. The combined algorithm is tested by a simulation, in which it is proved effective in adjusting evacuation path depending on the point of ignition. The changeable real-time indication will extend the escaping time with people in a burning building, which is quite precious for saving lives.
Source node location protection is critical to the Marine Wireless Sensor Networks (MWSNs), especially for unattended environment. However, due to most of the static deployment and the limitations in energy, storage and communication capabilities of the sensors, MWSNs are vulnerable to various location (and derivative) attacks. In this work, the node location privacy protection issues are studied from both aspects of attacks and defenses. First, a new two-phase location attack is proposed for two important types of nodes (including base station and source node). It can locate a base station node within few amounts of local wireless transmission monitoring, and then reversely traces the location of the source node. Different from existing methods, the proposed attack determines the node location based on the transmission direction, which can break through existing defenses. Then, to defend against such attack, a Hilbert-filling-curve-based Location-privacy Protection Scheme (HLPS) is designed for MWSNs. The theory analysis and confrontation experiment of attack and defense show that the proposed scheme owns capable of protecting the location privacy of the target node with moderate communication and computation overhead.
The lightweight block cipher algorithm PUFFIN based on substitution-permutation network structure is widely used in resource-constrained hardware environments. Differential fault attack is a more effective attack method for hardware cryptographic algorithms. The multi-bit fault model for PUFFIN algorithm is improved. By constructing the relationship between the output difference and the possible input values, the single input value of a single S-box can be determined by injecting 5 faults. The probability of successfully recovering the round key is 78.64%, and the initial key can be recovered.
In order to increase the classification speed of Aggregated Bit Vector (ABV) algorithm, an Improved Aggregated Bit Vector (IABV) algorithm is proposed, which is connection-oriented. Based on the characteristic that the packets which belong to the same connection have similar classification results, IABV establishes a Hash table-rule set two-level searching structure. It first searches in the Hash table to check the packet classification rule and then finds the matching rule in the rule set when the Hash table lookup fails. To avoid the accumulation of rules in the table, a collision handling mechanism is proposed. It judges whether to overwrite the Hash table entry which is collision according to the last hit time of the entry; Secondly, for the purpose of accelerate rule set searching, IABV divides each dimension into multiple intervals equally and employs array to index these intervals; Finally, the prefix in the rule is converted into range to reduce the complexity of the search structure, so that the time and memory consumption of the algorithm can be decreased. The experiment result shows that the performance of the algorithm can be improved by converting prefix into range and the time performance of IABV algorithm is significantly improved compared with the ABV algorithm under the same conditions.
In the view of the integrity verification problem of data sharing on the cloud platform, a Shared Data auditing scheme for efficient Revocation of group Members via multi-participation (SDRM) is proposed. First, through the Shamir secret sharing method, multiple group members participate in revoking the illegal group members, ensuring the equal rights between the group members. Second, this scheme combines with algebraic signature technology, the file identifier identifies the data owner’s upload data record and the normal group member’s access record, enabling the data owner to update efficiently all of its data. Finally, theoretical analysis and experimental verification of the correctness, safety and effectiveness of the scheme show that the scheme meets the requirement of efficient cancellation of group members, at the same time, as the number of data owners increases, the efficiency of updating data in this scheme is significantly higher than that of NPP.
Parameter estimation is essential for SAR imaging of moving targets. The existing algorithms mainly estimate the radial velocity and azimuth velocity of the moving target, but the normal velocity of the three-dimensional moving target can not be estimated. In this paper, a joint estimation algorithm of azimuth velocity and normal velocity is proposed by using an airborne multi-channel SAR system with L-shaped baseline. The algorithm extracts the moving target signal in Range-Doppler domain, and estimates the azimuth and normal velocity jointly using the phase differences between multiple SAR images. The algorithm does not rely on image registration, does not need to solve Doppler ambiguity. Therefore, the algorithm has high estimation accuracy and robustness, and has strong practical significance and application value.
A simulation model of total power microwave radiometer is developed for the microwave humidity and temperature sounder onboard the FY-3 satellite. The key components such as mixer, low noise amplifier, local oscillator, filter and detector are parametrically modeled. The model is studied from the aspect of signal processing, and dynamic range, sensitivity and linearity of the simulation system are evaluated and analyzed. The correctness of the simulation model is verified by comparing them with the test results of the actual system.