Research on ecological risk assessment and risk level prediction in the central urban area of Chongqing, China.

Complex geological conditions, coupled with urban expansion, resource consumption, and rapid economic development, make the ecological environment of Chongqing's central urban area more vulnerable. To enhance the carrying capacity of resources and the environment in this region, it is significant to scientifically assess the trend of ecological risk changes in Chongqing. The article developed an ecological risk assessment index system for Chongqing, utilizing the "pressure-state-response" framework. The entropy weight method (EWM) is employed to assign weights to each variable, subsequently establishing a grey weighted clustering evaluation model (GWCEM). We evaluated the ecological risks of nine central urban areas in Chongqing from 2005 to 2021 and projected the ecological risk levels and changes from 2022 to 2025. Our research indicates that the comprehensive ranking of influencing factors of ecological risk in Chongqing follows this order: response factor > pressure factor > state factor. Throughout the study period, we observed a decrease in the ecological risk values of Ba'nan, Shapingba, Jiulongpo, Nan'an and Yubei Districts by more than 50%. These decline rates are accelerating and regional differences in ecological risk levels are diminishing. From 2022 to 2025, except Shapingba, Jiangbei, Yuzhong, and Nan'an District which consistently maintained a "low-risk" level, the ecological risk levels of all other areas continue to decrease, aligning with a "low-risk" classification by 2025. Based on the results of ecological risk assessment and ecological risk level prediction, corresponding recommendations are proposed for ecological environment protection and ecological risk management in the central urban area of Chongqing.

INFLECT: an R-package for cytometry cluster evaluation using marker modality.

BACKGROUND: Current methods of high-dimensional unsupervised clustering of mass cytometry data lack means to monitor and evaluate clustering results. Whether unsupervised clustering is correct is typically evaluated by agreement with dimensionality reduction techniques or based on benchmarking with manually classified cells. The ambiguity and lack of reproducibility of sequential gating has been replaced with ambiguity in interpretation of clustering results. On the other hand, spurious overclustering of data leads to loss of statistical power. We have developed INFLECT, an R-package designed to give insight in clustering results and provide an optimal number of clusters. In our approach, a mass cytometry dataset is overclustered intentionally to ensure the smallest phenotypically different subsets are captured using FlowSOM. A range of metacluster number endpoints are generated and evaluated using marker interquartile range and distribution unimodality checks. The fraction of marker distributions that pass these checks is taken as a measure of clustering success. The fraction of unimodal distributions within metaclusters is plotted against the number of generated metaclusters and reaches a plateau of diminishing returns. The inflection point at which this occurs gives an optimal point of capturing cellular heterogeneity versus statistical power. RESULTS: We applied INFLECT to four publically available mass cytometry datasets of different size and number of markers. The unimodality score consistently reached a plateau, with an inflection point dependent on dataset size and number of dimensions. We tested both ConsenusClusterPlus metaclustering and hierarchical clustering. While hierarchical clustering is less computationally expensive and thus faster, it achieved similar results to ConsensusClusterPlus. The four datasets consisted of labeled data and we compared INFLECT metaclustering to published results. INFLECT identified a higher optimal number of metaclusters for all datasets. We illustrated the underlying heterogeneity within labels, showing that these labels encompass distinct types of cells. CONCLUSION: INFLECT addresses a knowledge gap in high-dimensional cytometry analysis, namely assessing clustering results. This is done through monitoring marker distributions for interquartile range and unimodality across a range of metacluster numbers. The inflection point is the optimal trade-off between cellular heterogeneity and statistical power, applied in this work for FlowSOM clustering on mass cytometry datasets.

A clustering effectiveness measurement model based on merging similar clusters.

This article presents a clustering effectiveness measurement model based on merging similar clusters to address the problems experienced by the affinity propagation (AP) algorithm in the clustering process, such as excessive local clustering, low accuracy, and invalid clustering evaluation results that occur due to the lack of variety in some internal evaluation indices when the proportion of clusters is very high. First, depending upon the "rough clustering" process of the AP clustering algorithm, similar clusters are merged according to the relationship between the similarity between any two clusters and the average inter-cluster similarity in the entire sample set to decrease the maximum number of clusters Kmax. Then, a new scheme is proposed to calculate intra-cluster compactness, inter-cluster relative density, and inter-cluster overlap coefficient. On the basis of this new method, several internal evaluation indices based on intra-cluster cohesion and inter-cluster dispersion are designed. Results of experiments show that the proposed model can perform clustering and classification correctly and provide accurate ranges for clustering using public UCI and NSL-KDD datasets, and it is significantly superior to the three improved clustering algorithms compared with it in terms of intrusion detection indices such as detection rate and false positive rate (FPR).

Feature selection based on unsupervised clustering evaluation for predicting neoadjuvant chemoradiation response for patients with locally advanced rectal cancer.

Accurate response prediction allows for personalized cancer treatment of locally advanced rectal cancer (LARC) with neoadjuvant chemoradiation. In this work, we designed a convolutional neural network (CNN) feature extractor with switchable 3D and 2D convolutional kernels to extract deep learning features for response prediction. Compared with radiomics features, convolutional kernels may adaptively extract local or global image features from multi-modal MR sequences without the need of feature predefinition. We then developed an unsupervised clustering based evaluation method to improve the feature selection operation in the feature space formed by the combination of CNN features and radiomics features. While normal process of feature selection generally includes the operations of classifier training and classification execution, the process needs to be repeated many times after new feature combinations were found to evaluate the model performance, which incurs a significant time cost. To address this issue, we proposed a cost effective process to use a constructed unsupervised clustering analysis indicator to replace the classifier training process by indirectly evaluating the quality of new found feature combinations in feature selection process. We evaluated the proposed method using 43 LARC patients underwent neoadjuvant chemoradiation. Our prediction model achieved accuracy, area-under-curve (AUC), sensitivity and specificity of 0.852, 0.871, 0.868, and 0.735 respectively. Compared with traditional radiomics methods, the prediction models (AUC = 0.846) based on deep learning-based feature sets are significantly better than traditional radiomics methods (AUC = 0.714). The experiments also showed following findings: (1) the features with higher predictive power are mainly from high-order abstract features extracted by CNN on ADC images and T2 images; (2) both ADC_Radiomics and ADC_CNN features are more advantageous for predicting treatment responses than the radiomics and CNN features extracted from T2 images; (3) 3D CNN features are more effective than 2D CNN features in the treatment response prediction. The proposed unsupervised clustering indicator is feasible with low computational cost, which facilitates the discovery of valuable solutions by highlighting the correlation and complementarity between different types of features.

A close-up comparison of the misclassification error distance and the adjusted Rand index for external clustering evaluation.

The misclassification error distance and the adjusted Rand index are two of the most common criteria used to evaluate the performance of clustering algorithms. This paper provides an in-depth comparison of the two criteria, with the aim of better understand exactly what they measure, their properties and their differences. Starting from their population origins, the investigation includes many data analysis examples and the study of particular cases in great detail. An exhaustive simulation study provides insight into the criteria distributions and reveals some previous misconceptions.