Target enrichment sequencing techniques are gaining widespread use in the field of genomics, prized for their economic efficiency and swift processing times. However, their success depends on the performance of probes and the evenness of sequencing depth among each probe. To accurately predict probe coverage depth, a model called Deqformer is proposed in this study. Deqformer utilizes the oligonucleotides sequence of each probe, drawing inspiration from Watson-Crick base pairing and incorporating two BERT encoders to capture the underlying information from the forward and reverse probe strands, respectively. The encoded data are combined with a feed-forward network to make precise predictions of sequencing depth. The performance of Deqformer is evaluated on four different datasets: SNP panel with 38 200 probes, lncRNA panel with 2000 probes, synthetic panel with 5899 probes and HD-Marker panel for Yesso scallop with 11 000 probes. The SNP and synthetic panels achieve impressive factor 3 of accuracy (F3acc) of 96.24% and 99.66% in 5-fold cross-validation. F3acc rates of over 87.33% and 72.56% are obtained when training on the SNP panel and evaluating performance on the lncRNA and HD-Marker datasets, respectively. Our analysis reveals that Deqformer effectively captures hybridization patterns, making it robust for accurate predictions in various scenarios. Deqformer leads to a novel perspective for probe design pipeline, aiming to enhance efficiency and effectiveness in probe design tasks.

The LSTM network was proposed to overcome the difficulty in learning long-term dependence, and has made significant advancements in applications. With its success and drawbacks in mind, this paper raises the question - do RNN and LSTM have long memory? We answer it partially by proving that RNN and LSTM do not have long memory from a statistical perspective. A new definition for long memory networks is further introduced, and it requires the model weights to decay at a polynomial rate. To verify our theory, we convert RNN and LSTM into long memory networks by making a minimal modification, and their superiority is illustrated in modeling long-term dependence of various datasets.

Extracting fields from layer 7 protocols such as HTTP, known as L7 parsing, is the key to many critical network applications. However, existing L7 parsing techniques center around protocol specifications, thereby incurring large human efforts in specifying data format and high computational/memory costs that poorly scale with the explosive number of L7 protocols. To this end, this paper introduces a new framework namedcontent-based L7 parsing, where the content instead of the format becomes the first class citizen. Under this framework, users only need to label what content they are interested in, and the parser learns an extraction model from the users’ labeling behaviors. Since the parser is specification-independent, both the human effort and computational/memory costs can be dramatically reduced. To realize content-based L7 parsing, we propose REPLAY which builds on recurrent neural network (RNN) and addresses a series of technical challenges like large labeling overhead and slow parsing speed. We prototype REPLAY on GPUs, and show it can achieve a precision of 98% and a recall of 97%, with a throughput as high as 12Gbps for diverse extraction tasks.

Gene selection prior to classification has been an important topic in bioinformatics, since last decade. Small sample size and high dimensionality in microarray data pose great challenges for performing efficient classification. In this paper we propose efficient hybrid method (GTkernelPLS) with a combination of wrapper like technique coalitional game theory and kernel partial least square (kernelPLS) filter method. Experimental results on ten microarray data sets ensure that GTkernelPLS achieve higher accuracy than several state of the art feature selection methods, and it exhibits a reasonable execution time, even for the data sets having more than twenty thousand genes.

Local learning has been successfully applied to transductive classification problems. In this paper, it is generalized to multi-class classification of transductive learning problems owing to its good classification ability. Meanwhile, there is essentially no ordinal meaning in class label of multi-class classification, and it belongs to discrete nominal variable. However, common binary series class label representation has the equal distance from one class to another, and it does not reflect the sparse and density relationship among classes distribution, so a learning and adjustable nominal class label representation method is presented. Experimental results on a set of benchmark multi-class datasets show the superiority of our algorithm.

Most current semantic Web services (SWS) discovery approaches focus on the matchmaking of services in a specific description language while in practical application the advertised services are often heterogeneous and distributed. This paper proposes a metric space approach to resolve this problem in which all heterogeneous Web services are modeled as metric objects regardless of concrete description languages, and thereby the discovery problem can be treated as similarity search in metric space with a uniform criterion. In the matchmaking process, both the functional semantics and non-functional semantics of the Web services are integrated as selection conditions for similarity query. And two types of similarity queries: range query and an improved nearest neighbor query are combined to produce a sorted result set.