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Incomplete knowledge of metabolic processes hinders the accuracy of GEnome-scale Metabolic models (GEMs), which in turn impedes advancements in systems biology and metabolic engineering. Existing gap-filling methods typically rely on phenotypic data to minimize the disparity between computational predictions and experimental results. However, there is still a lack of an automatic and precise gap-filling method for initial state GEMs before experimental data and annotated genomes become available. In this study, we introduce CLOSEgaps, a deep learning-driven tool that addresses the gap-filling issue by modeling it as a hyperedge prediction problem within GEMs. Specifically, CLOSEgaps maps metabolic networks as hypergraphs and learns their hyper-topology features to identify missing reactions and gaps by leveraging hypothetical reactions. This innovative approach allows for the characterization and curation of both known and hypothetical reactions within metabolic networks. Extensive results demonstrate that CLOSEgaps accurately gap-filling over 96% of artificially introduced gaps for various GEMs. Furthermore, CLOSEgaps enhances phenotypic predictions for 24 GEMs and also finds a notable improvement in producing four crucial metabolites (Lactate, Ethanol, Propionate, and Succinate) in two organisms. As a broadly applicable solution for any GEM, CLOSEgaps represents a promising model to automate the gap-filling process and uncover missing connections between reactions and observed metabolic phenotypes.

This paper focuses on the classification task of breast ultrasound images and researches on the reliability measurement of classification results. We proposed a dual-channel evaluation framework based on the proposed inference reliability and predictive reliability scores. For the inference reliability evaluation, human-aligned and doctor-agreed inference rationales based on the improved feature attribution algorithm SP-RISA are gracefully applied. Uncertainty quantification is used to evaluate the predictive reliability via the Test Time Enhancement. The effectiveness of this reliability evaluation framework has been verified on our breast ultrasound clinical dataset YBUS, and its robustness is verified on the public dataset BUSI. The expected calibration errors on both datasets are significantly lower than traditional evaluation methods, which proves the effectiveness of our proposed reliability measurement.

Automatic image segmentation technology is critical to the visual analysis. The autoencoder architecture has satisfying performance in various image segmentation tasks. However, autoencoders based on convolutional neural networks (CNN) seem to encounter a bottleneck in improving the accuracy of semantic segmentation. Increasing the inter-class distance between foreground and background is an inherent characteristic of the segmentation network. However, segmentation networks pay too much attention to the main visual difference between foreground and background, and ignores the detailed edge information, which leads to a reduction in the accuracy of edge segmentation. In this paper, we propose a light-weight end-to-end segmentation framework based on multi-task learning, termed Edge Attention autoencoder Network (EAA-Net), to improve edge segmentation ability. Our approach not only utilizes the segmentation network to obtain inter-class features, but also applies the reconstruction network to extract intra-class features among the foregrounds. We further design a intra-class and inter-class features fusion module -- I2 fusion module. The I2 fusion module is used to merge intra-class and inter-class features, and use a soft attention mechanism to remove invalid background information. Experimental results show that our method performs well in medical image segmentation tasks. EAA-Net is easy to implement and has small calculation cost.

Automatic segmentation of medical images based on multi-modality is an important topic for disease diagnosis. Although the convolutional neural network (CNN) has been proven to have excellent performance in image segmentation tasks, it is difficult to obtain global information. The lack of global information will seriously affect the accuracy of the segmentation results of the lesion area. In addition, there are visual representation differences between multimodal data of the same patient. These differences will affect the results of the automatic segmentation methods. To solve these problems, we propose a segmentation method suitable for multimodal medical images that can capture global information, named TranSiam. TranSiam is a 2D dual path network that extracts features of different modalities. In each path, we utilize convolution to extract detailed information in low level stage, and design a ICMT block to extract global information in high level stage. ICMT block embeds convolution in the transformer, which can extract global information while retaining spatial and detailed information. Furthermore, we design a novel fusion mechanism based on cross attention and selfattention, called TMM block, which can effectively fuse features between different modalities. On the BraTS 2019 and BraTS 2020 multimodal datasets, we have a significant improvement in accuracy over other popular methods.

The edit distance under the DCJ model can be computed in linear time for genomes with equal content or with Indels. But it becomes NP-Hard in the presence of duplications, a problem largely unsolved especially when Indels are considered. In this paper, we compare two mainstream methods to deal with duplications and associate them with Indels: one by deletion, namely DCJ-Indel-Exemplar distance; versus the other by gene matching, namely DCJ-Indel-Matching distance. We design branch-and-bound algorithms with set of optimization methods to compute exact distances for both. Furthermore, median problems are discussed in alignment with both of these distance methods, which are to find a median genome that minimizes distances between itself and three given genomes. Lin-Kernighan (LK) heuristic is leveraged and powered up by sub-graph decomposition and search space reduction technologies to handle median computation. A wide range of experiments are conducted on synthetic data sets and real data sets to show pros and cons of these two distance metrics per se, as well as putting them in the median computation scenario., Comment: 17 pages

Background: It is necessary and essential to discovery protein function from the novel primary sequences. Wet lab experimental procedures are not only time-consuming, but also costly, so predicting protein structure and function reliably based only on amino acid sequence has significant value. TATA-binding protein (TBP) is a kind of DNA binding protein, which plays a key role in the transcription regulation. Our study proposed an automatic approach for identifying TATA-binding proteins efficiently, accurately, and conveniently. This method would guide for the special protein identification with computational intelligence strategies. Results: Firstly, we proposed novel fingerprint features for TBP based on pseudo amino acid composition, physicochemical properties, and secondary structure. Secondly, hierarchical features dimensionality reduction strategies were employed to improve the performance furthermore. Currently, Pretata achieves 92.92% TATA- binding protein prediction accuracy, which is better than all other existing methods. Conclusions: The experiments demonstrate that our method could greatly improve the prediction accuracy and speed, thus allowing large-scale NGS data prediction to be practical. A web server is developed to facilitate the other researchers, which can be accessed at http://server.malab.cn/preTata/.