As an important post-translational modification, glutarylation plays a crucial role in a variety of cellular functions. Recently, diverse computational methods for glutarylation site identification have been proposed....
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As an important post-translational modification, glutarylation plays a crucial role in a variety of cellular functions. Recently, diverse computational methods for glutarylation site identification have been proposed. However, the class imbalance problem due to data noise and uncertainty of non-glutarylation sites remains a great challenge. In this article, we propose a novel semi-supervised learning algorithm, called WGAN-GP_Glu, for identifying reliable non-glutarylation lysine sites from those without glutarylation annotation. WGAN-GP_Glu method is a multi-module framework algorithm, which mainly includes a reliable negative sample selection module, a deep feature extraction module, and a glutarylation site prediction module. In reliable negative sample selection module, we design an improved method of Wasserstein GAN with Gradient Penalty (WGAN-GP), named ReliableWGAN-GP, including three parts, two generators G1, G2 and a discriminator D, which can select reliable non-glutarylation samples from a great number of unlabeled samples. Generator G1 is utilized to generate noise data from unlabeled samples. For generator G2, both the positive sample and the noise data are used as inputs to improve the discriminant capability of discriminator D. Then, convolutional neural network and bidirectional long short-term memory network combined with attention mechanism are utilized to extract deep features for glutarylation samples and reliable non-glutarylation samples. Finally, a glutarylation site prediction module based on the three-layer fully connected layer is designed to make class predictions for samples. The sensitivity, specificity, accuracy and Matthew correlation coefficient of WGAN-GP_Glu on the independent test data set reach 90.58 %, 95.82 %, 94.44 % and 0.8645, respectively, which surpassed the existing methods for glutarylation sites prediction. Therefore, WGAN-GP_Glu can serve as a powerful tool in identifying glutarylation sites and the ReliableWGAN-GP algo
Magnetic Particle Imaging (MPI) is an emerging technology utilized for mapping the spatial distribution of magnetic nanoparticles within biological tissues. The complexity of the physical behavior of nanoparticles pos...
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Continuous-flow microfluidic biochips (CFMBs) have become a hot research topic in recent years due to their ability to perform biochemical assays automatically and efficiently. For the first time, PathDriver+ takes th...
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Continuous-flow microfluidic biochips (CFMBs) have become a hot research topic in recent years due to their ability to perform biochemical assays automatically and efficiently. For the first time, PathDriver+ takes the requirements of the actual fluid transportation into account in the design process of CFMBs and implements the actual fluid transport and removal, and plans separate flow paths for each transport task, which have been neglected in previous work. However, PathDriver+ does not take full advantage of the flexibility of CFMBs routing because it only considers the optimization of flow channel length for the global routing in the mesh model, except for the detailed routing. In addition, PathDriver+ only considers the X architecture, while the existing work shows that the any-angle routing can utilize the routing resources more efficiently and shorten the flow channel length. To address the above issues, we propose a flow path-driven arbitrary angle routing algorithm, which can improve the utilization of routing resources and reduce the flow channel length while considering the actual fluid transportation requirements. The proposed algorithm constructs a search graph based on constrained Delaunay triangulation to improve the search efficiency of routing solutions while ensuring the routing quality. Then, a Dijkstra-based flow path routing method is used on the constructed search graph to generate a routing result with a short channel length quickly. In addition, in the routing process, channel reuse strategy and intersection optimization strategy are proposed for the flow path reuse and intersection number optimization problems, respectively, to further improve the quality of routing results. The experimental results show that compared with the latest work PathDriver+, the length of channels, the number of ports used, and the number of channel intersections are significantly reduced by 33.21%, 11.04%, and 44.79%, respectively, and the channel reuse rate is i
Sensor networks are widely used in many applications to collaboratively collect information from the physical environment. In these applications, the exploration of the relationship and linkage of sensing data within ...
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Sensor networks are widely used in many applications to collaboratively collect information from the physical environment. In these applications, the exploration of the relationship and linkage of sensing data within multiple regions can be naturally expressed by joining tuples in these regions. However, the highly distributed and resource-constraint nature of the network makes join a challenging query. In this paper, we address the problem of processing join query among different regions progressively and energy-efficiently in sensor networks. The proposed algorithm PEJA （Progressive Energy-efficient Join Algorithm） adopts an event-driven strategy to output the joining results as soon as possible, and alleviates the storage shortage problem in the in-network nodes. It also installs filters in the joining regions to prune unmatchable tuples in the early processing phase, saving lots of unnecessary transmissions. Extensive experiments on both synthetic and real world data sets indicate that the PEJA scheme outperforms other join algorithms, and it is effective in reducing the number of transmissions and the delay of query results during the join processing.
With the advancement of electronic design automation, continuous-flow microfluidic biochips have become one of the most promising platforms for biochemical experiments. This chip manipulates fluid samples in millilite...
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In this work, we address the challenging task of Generalized Referring Expression Comprehension (GREC). Compared to the classic Referring Expression Comprehension (REC) that focuses on single-target expressions, GREC ...
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Deep learning performance may decrease substantially with unseen heterogeneous data. While most unsupervised domain adaptation (UDA) methods seek to address this through image alignment, they often ignore uncertainty ...
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In recent years, multi-view multi-label learning (MVML) has gained popularity due to its close resemblance to real-world scenarios. However, the challenge of selecting informative features to ensure both performance a...
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Relation extraction (RE) poses significant challenges due to the complexity of identifying semantic relationships between overlapping entity pairs within sentences. Traditional kernel-based methods effectively leverag...
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Emerging cross-point memory can in-situ perform vector-matrix multiplication (VMM) for energy-efficient scientific computation. However, parasitic-capacitance-induced row charging and discharging latency is a major pe...
ISBN:
(纸本)9798350323481
Emerging cross-point memory can in-situ perform vector-matrix multiplication (VMM) for energy-efficient scientific computation. However, parasitic-capacitance-induced row charging and discharging latency is a major performance bottleneck of subarray VMM. We propose a memory-timing-compliant bulk VMM processing-using-memory design with row access and column access co-optimization from rethinking of read access commands and μ-op timing. We propose row-level-parallelism-adaptive timing termination mechanism to reduce tail latency of tRCD and tRP by exploiting row nonlinear charging and bulk-interleaved row-column-cooperative VMM access mechanism to reduce tRAS and overlap CL without increasing column ADC precision. Evaluations show that our design can achieve 5.03× performance speedup compared with an aggressive baseline.
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