MLFLHMDA: predicting human microbe-disease association based on multi-view latent feature learning

IntroductionA growing body of research indicates that microorganisms play a crucial role in human health. Imbalances in microbial communities are closely linked to human diseases, and identifying potential relationships between microbes and diseases can help elucidate the pathogenesis of diseases. However, traditional methods based on biological or clinical experiments are costly, so the use of computational models to predict potential microbe-disease associations is of great importance.MethodsIn this paper, we present a novel computational model called MLFLHMDA, which is based on a Multi-View Latent Feature Learning approach to predict Human potential Microbe-Disease Associations. Specifically, we compute Gaussian interaction profile kernel similarity between diseases and microbes based on the known microbe-disease associations from the Human Microbe-Disease Association Database and perform a preprocessing step on the resulting microbe-disease association matrix, namely, weighting K nearest known neighbors (WKNKN) to reduce the sparsity of the microbe-disease association matrix. To obtain unobserved associations in the microbe and disease views, we extract different latent features based on the geometrical structure of microbes and diseases, and project multi-modal latent features into a common subspace. Next, we introduce graph regularization to preserve the local manifold structure of Gaussian interaction profile kernel similarity and add Lp,q-norms to the projection matrix to ensure the interpretability and sparsity of the model.ResultsThe AUC values for global leave-one-out cross-validation and 5-fold cross validation implemented by MLFLHMDA are 0.9165 and 0.8942+/−0.0041, respectively, which perform better than other existing methods. In addition, case studies of different diseases have demonstrated the superiority of the predictive power of MLFLHMDA. The source code of our model and the data are available on https://github.com/LiangzheZhang/MLFLHMDA_master

PolyMaX: General Dense Prediction with Mask Transformer

Dense prediction tasks, such as semantic segmentation, depth estimation, and surface normal prediction, can be easily formulated as per-pixel classification (discrete outputs) or regression (continuous outputs). This per-pixel prediction paradigm has remained popular due to the prevalence of fully convolutional networks. However, on the recent frontier of segmentation task, the community has been witnessing a shift of paradigm from per-pixel prediction to cluster-prediction with the emergence of transformer architectures, particularly the mask transformers, which directly predicts a label for a mask instead of a pixel. Despite this shift, methods based on the per-pixel prediction paradigm still dominate the benchmarks on the other dense prediction tasks that require continuous outputs, such as depth estimation and surface normal prediction. Motivated by the success of DORN and AdaBins in depth estimation, achieved by discretizing the continuous output space, we propose to generalize the cluster-prediction based method to general dense prediction tasks. This allows us to unify dense prediction tasks with the mask transformer framework. Remarkably, the resulting model PolyMaX demonstrates state-of-the-art performance on three benchmarks of NYUD-v2 dataset. We hope our simple yet effective design can inspire more research on exploiting mask transformers for more dense prediction tasks. Code and model will be made available.Comment: WACV 202

SnapNETS: Automatic Segmentation of Network Sequences with Node Labels

Given a sequence of snapshots of flu propagating over a population network, can we find a segmentation when the patterns of the disease spread change, possibly due to interventions? In this paper, we study the problem of segmenting graph sequences with labeled nodes. Memes on the Twitter network, diseases over a contact network, movie-cascades over a social network, etc. are all graph sequences with labeled nodes. Most related work is on plain graphs (and hence ignore the label dynamics) or fix parameters or require much feature engineering. Instead, we propose SnapNETS, to automatically find segmentations of such graph sequences, with different characteristics of nodes of each label in adjacent segments. It satisfies all the desired properties (being parameter-free, comprehensive and scalable) by leveraging a principled, multi-level, flexible framework which maps the problem to a path optimization problem over a weighted DAG. Extensive experiments on several diverse real datasets show that it finds cut points matching ground-truth or meaningful external signals outperforming non-trivial baselines. We also show that SnapNETS scales near-linearly with the size of the input

Meta-Learning for Few-Shot Plant Disease Detection

Plant diseases can harm crop growth, and the crop production has a deep impact on food. Although the existing works adopt Convolutional Neural Networks (CNNs) to detect plant diseases such as Apple Scab and Squash Powdery mildew, those methods have limitations as they rely on a large amount of manually labeled data. Collecting enough labeled data is not often the case in practice because: plant pathogens are variable and farm environments make collecting data difficulty. Methods based on deep learning suffer from low accuracy and confidence when facing few-shot samples. In this paper, we propose local feature matching conditional neural adaptive processes (LFM-CNAPS) based on meta-learning that aims at detecting plant diseases of unseen categories with only a few annotated examples, and visualize input regions that are ‘important’ for predictions. To train our network, we contribute Miniplantdisease-Dataset that contains 26 plant species and 60 plant diseases. Comprehensive experiments demonstrate that our proposed LFM-CNAPS method outperforms the existing methods

DRE-Net: A Dynamic Radius-Encoding Neural Network with an Incremental Training Strategy for Interactive Segmentation of Remote Sensing Images

Semantic segmentation of remote sensing (RS) images, which is a fundamental research topic, classifies each pixel in an image. It plays an essential role in many downstream RS areas, such as land-cover mapping, road extraction, traffic monitoring, and so on. Recently, although deep-learning-based methods have shown their dominance in automatic semantic segmentation of RS imagery, the performance of these existing methods has relied heavily on large amounts of high-quality training data, which are usually hard to obtain in practice. Moreover, human-in-the-loop semantic segmentation of RS imagery cannot be completely replaced by automatic segmentation models, since automatic models are prone to error in some complex scenarios. To address these issues, in this paper, we propose an improved, smart, and interactive segmentation model, DRE-Net, for RS images. The proposed model facilitates humans’ performance of segmentation by simply clicking a mouse. Firstly, a dynamic radius-encoding (DRE) algorithm is designed to distinguish the purpose of each click, such as a click for the selection of a segmentation outline or for fine-tuning. Secondly, we propose an incremental training strategy to cause the proposed model not only to converge quickly, but also to obtain refined segmentation results. Finally, we conducted comprehensive experiments on the Potsdam and Vaihingen datasets and achieved 9.75% and 7.03% improvements in NoC95 compared to the state-of-the-art results, respectively. In addition, our DRE-Net can improve the convergence and generalization of a network with a fast inference speed

DRE-Net: A Dynamic Radius-Encoding Neural Network with an Incremental Training Strategy for Interactive Segmentation of Remote Sensing Images

Semantic segmentation of remote sensing (RS) images, which is a fundamental research topic, classifies each pixel in an image. It plays an essential role in many downstream RS areas, such as land-cover mapping, road extraction, traffic monitoring, and so on. Recently, although deep-learning-based methods have shown their dominance in automatic semantic segmentation of RS imagery, the performance of these existing methods has relied heavily on large amounts of high-quality training data, which are usually hard to obtain in practice. Moreover, human-in-the-loop semantic segmentation of RS imagery cannot be completely replaced by automatic segmentation models, since automatic models are prone to error in some complex scenarios. To address these issues, in this paper, we propose an improved, smart, and interactive segmentation model, DRE-Net, for RS images. The proposed model facilitates humans’ performance of segmentation by simply clicking a mouse. Firstly, a dynamic radius-encoding (DRE) algorithm is designed to distinguish the purpose of each click, such as a click for the selection of a segmentation outline or for fine-tuning. Secondly, we propose an incremental training strategy to cause the proposed model not only to converge quickly, but also to obtain refined segmentation results. Finally, we conducted comprehensive experiments on the Potsdam and Vaihingen datasets and achieved 9.75% and 7.03% improvements in NoC95 compared to the state-of-the-art results, respectively. In addition, our DRE-Net can improve the convergence and generalization of a network with a fast inference speed

Towards Optimizing Garlic Combine Harvester Design with Logistic Regression

In this paper, a garlic combine harvester machine was designed and some influential parameters of the machine were optimized. The working parts of the machine mainly consisted of a reel, a reciprocating cutter, a seedling conveyor, a profiling depth-stop device, a digging shovel and a lifting chain. Each part had unique structural parameters and motion parameters, as different parameters would deeply affect the performance of the machine. A logistical regression algorithm was utilized to analyze the working speed of the reel, the digging depth of the reciprocating cutter and the lifting speed of the lifting chain. This paper also discussed the influence of these three functions on the damage rate based on the collected data when harvesting garlic. Specifically, each function was tested 60 times for collecting data. The experimental results showed that the order of influence of the three functions on the damage rate was the digging depth, working speed and lifting speed. Moreover, the lowest damage rate was 0.18% when the digging depth was 100 mm, the working speed was 1.05 km·h−1 and the lifting speed was 0.69 m·s−1. A validation test was taken out based on the three functions of the analysis results, and the damage rate was 0.83%, which was close to the analysis results, and proved that the analysis results were accurate and meaningful. The research results are beneficial to the development and application of the garlic combine harvester