Residue–Residue Contact Can Be a Potential Feature for the Prediction of Lysine Crotonylation Sites

Lysine crotonylation (Kcr) is involved in plenty of activities in the human body. Various technologies have been developed for Kcr prediction. Sequence-based features are typically adopted in existing methods, in which only linearly neighboring amino acid composition was considered. However, modified Kcr sites are neighbored by not only the linear-neighboring amino acid but also those spatially surrounding residues around the target site. In this paper, we have used residue–residue contact as a new feature for Kcr prediction, in which features encoded with not only linearly surrounding residues but also those spatially nearby the target site. Then, the spatial-surrounding residue was used as a new scheme for feature encoding for the first time, named residue–residue composition (RRC) and residue–residue pair composition (RRPC), which were used in supervised learning classification for Kcr prediction. As the result suggests, RRC and RRPC have achieved the best performance of RRC at an accuracy of 0.77 and an area under curve (AUC) value of 0.78, RRPC at an accuracy of 0.74, and an AUC value of 0.80. In order to show that the spatial feature is of a competitively high significance as other sequence-based features, feature selection was carried on those sequence-based features together with feature RRPC. In addition, different ranges of the surrounding amino acid compositions’ radii were used for comparison of the performance. After result assessment, RRC and RRPC features have shown competitively outstanding performance as others or in some cases even around 0.20 higher in accuracy or 0.3 higher in AUC values compared with sequence-based features.

A Computer Vision-Based Yoga Pose Grading Approach Using Contrastive Skeleton Feature Representations

The main objective of yoga pose grading is to assess the input yoga pose and compare it to a standard pose in order to provide a quantitative evaluation as a grade. In this paper, a computer vision-based yoga pose grading approach is proposed using contrastive skeleton feature representations. First, the proposed approach extracts human body skeleton keypoints from the input yoga pose image and then feeds their coordinates into a pose feature encoder, which is trained using contrastive triplet examples; finally, a comparison of similar encoded pose features is made. Furthermore, to tackle the inherent challenge of composing contrastive examples in pose feature encoding, this paper proposes a new strategy to use both a coarse triplet example—comprised of an anchor, a positive example from the same category, and a negative example from a different category, and a fine triplet example—comprised of an anchor, a positive example, and a negative example from the same category with different pose qualities. Extensive experiments are conducted using two benchmark datasets to demonstrate the superior performance of the proposed approach.

AFGL-Net: Attentive Fusion of Global and Local Deep Features for Building Façades Parsing

In this paper, we propose a deep learning framework, namely AFGL-Net to achieve building façade parsing, i.e., obtaining the semantics of small components of building façade, such as windows and doors. To this end, we present an autoencoder embedding position and direction encoding for local feature encoding. The autoencoder enhances the local feature aggregation and augments the representation of skeleton features of windows and doors. We also integrate the Transformer into AFGL-Net to infer the geometric shapes and structural arrangements of façade components and capture the global contextual features. These global features can help recognize inapparent windows/doors from the façade points corrupted with noise, outliers, occlusions, and irregularities. The attention-based feature fusion mechanism is finally employed to obtain more informative features by simultaneously considering local geometric details and the global contexts. The proposed AFGL-Net is comprehensively evaluated on Dublin and RueMonge2014 benchmarks, achieving 67.02% and 59.80% mIoU, respectively. We also demonstrate the superiority of the proposed AFGL-Net by comparing with the state-of-the-art methods and various ablation studies.

Leaf Spot Attention Networks Based on Spot Feature Encoding for Leaf Disease Identification and Detection

This study proposes a new attention-enhanced YOLO model that incorporates a leaf spot attention mechanism based on regions-of-interest (ROI) feature extraction into the YOLO framework for leaf disease detection. Inspired by a previous study, which revealed that leaf spot attention based on the ROI-aware feature extraction can improve leaf disease recognition accuracy significantly and outperform state-of-the-art deep learning models, this study extends the leaf spot attention model to leaf disease detection. The primary idea is that spot areas indicating leaf diseases appear only in leaves, whereas the background area does not contain useful information regarding leaf diseases. To increase the discriminative power of the feature extractor that is required in the object detection framework, it is essential to extract informative and discriminative features from the spot and leaf areas. To realize this, a new ROI-aware feature extractor, that is, a spot feature extractor was designed. To divide the leaf image into spot, leaf, and background areas, the leaf segmentation module was first pretrained, and then spot feature encoding was applied to encode spot information. Next, the ROI-aware feature extractor was connected to an ROI-aware feature fusion layer to model the leaf spot attention mechanism, and to be joined with the YOLO detection subnetwork. The experimental results confirm that the proposed ROI-aware feature extractor can improve leaf disease detection by boosting the discriminative power of the spot features. In addition, the proposed attention-enhanced YOLO model outperforms conventional state-of-the-art object detection models.

A Feature Encoding Approach and a Cloud Computing Architecture to Map Fishing Activities

Monitoring fish stocks and fleets’ activities is key for Marine Spatial Planning. In recent years Vessel Monitoring System and Automatic Identification System have been developed for vessels longer than 12 and 15m in length, respectively, while small scale vessels (< 12m in length) remain untracked and largely unregulated, even though they account for 83% of all fishing activity in the Mediterranean Sea. In this paper we present an architecture that makes use of a low-cost LoRa/cellular network to acquire and process positioning data from small scale vessels, and a feature encoding approach that can be easily extended to process and map small scale fisheries. The feature encoding method uses a Markov chain to model transitions between successive behavioural states (e.g., fishing, steaming) of each vessel and classify its activity. The approach is evaluated using k-fold and Leave One Boat Out cross-validations and, in both cases, it results in significant improvements in the classification of fishing activities. The use of a such low-cost and open source technology coupled to artificial intelligence could open up potential for more integrated and transparent platforms to inform coastal resource and fisheries management, and cross-border marine spatial planning. It enables a new monitoring strategy that could effectively include small-scale fleets and support the design of new policies oriented to the optimal use of marine resources.

Machine learning based disease prediction from genotype data

Using results from genome-wide association studies for understanding complex traits is a current challenge. Here we review how genotype data can be used with different machine learning (ML) methods to predict phenotype occurrence and severity from genotype data. We discuss common feature encoding schemes and how studies handle the often small number of samples compared to the huge number of variants. We compare which ML methods are being applied, including recent results using deep neural networks. Further, we review the application of methods for feature explanation and interpretation.