Zhi Wang

Zijie Fang, Yihan Liu, Yifeng Wang et al.

Biomarker detection is an indispensable part in the diagnosis and treatment of low-grade glioma (LGG). However, current LGG biomarker detection methods rely on expensive and complex molecular genetic testing, for which professionals are required to analyze the results, and intra-rater variability is often reported. To overcome these challenges, we propose an interpretable deep learning pipeline, a Multi-Biomarker Histomorphology Discoverer (Multi-Beholder) model based on the multiple instance learning (MIL) framework, to predict the status of five biomarkers in LGG using only hematoxylin and eosin-stained whole slide images and slide-level biomarker status labels. Specifically, by incorporating the one-class classification into the MIL framework, accurate instance pseudo-labeling is realized for instance-level supervision, which greatly complements the slide-level labels and improves the biomarker prediction performance. Multi-Beholder demonstrates superior prediction performance and generalizability for five LGG biomarkers (AUROC=0.6469-0.9735) in two cohorts (n=607) with diverse races and scanning protocols. Moreover, the excellent interpretability of Multi-Beholder allows for discovering the quantitative and qualitative correlations between biomarker status and histomorphology characteristics. Our pipeline not only provides a novel approach for biomarker prediction, enhancing the applicability of molecular treatments for LGG patients but also facilitates the discovery of new mechanisms in molecular functionality and LGG progression.

David Tschan, Zhi Wang, Dominik Strebel et al.

Urban heat islands (UHIs) are often accentuated during heat waves (HWs) and pose a public health risk. Mitigating UHIs requires urban planners to first estimate how urban heat is influenced by different land use types (LUTs) and drivers across scales - from synoptic-scale climatic background processes to small-scale urban- and scale-bridging features. This study proposes to classify these drivers into driving (D), urban (U), and local (L) features, respectively. To increase interpretability and enhance computation efficiency, a LUT-distinguishing machine learning approach is proposed as a fast emulator for Weather Research and Forecasting model (WRF) coupled to the Noah land surface model (LSM) to predict ground- (TSK) and 2-meter air temperature (T2). Using random forest regression (RFR) with extreme gradient boosting (XGB) trained on WRF output over Zurich, Switzerland, during heatwave (HW) periods in 2017 and 2019, this study proposes LUT-based (LB) models that categorize features by scales and practical controllability, allowing optional categorical weighting. This approach enables category-specific feature ranking and sensitivity estimation of T2 and TSK to most important small-scale drivers - most notably surface emissivity, albedo, and leaf area index (LAI). Models employing the LB framework are statistically significantly more accurate than models that do not, with higher performance when more HW data is included in training. With RFR-XGB robustly performing optimal with unit weights, the method substantially increase interpretability. Despite the needs to reduce uncertainties and test the method on other cities, the proposed approach offers urban planners a direct framework for feasibility-centered UHI mitigation assessment.

Xueying Tang, Susu Zhang, Zhi Wang et al.

Process data refer to data recorded in the log files of computer-based items. These data, represented as timestamped action sequences, keep track of respondents' response processes of solving the items. Process data analysis aims at enhancing educational assessment accuracy and serving other assessment purposes by utilizing the rich information contained in response processes. The R package ProcData presented in this article is designed to provide tools for processing, describing, and analyzing process data. We define an S3 class "proc" for organizing process data and extend generic methods summary and print for class "proc". Two feature extraction methods for process data are implemented in the package for compressing information in the irregular response processes into regular numeric vectors. ProcData also provides functions for fitting and making predictions from a neural-network-based sequence model. These functions call relevant functions in package keras for constructing and training neural networks. In addition, several response process generators and a real dataset of response processes of the climate control item in the 2012 Programme for International Student Assessment are included in the package.