Yuanyuan Wei

Yuanyuan Wei, Roger Tam, Xiaoying Tang

Recent applications of deep convolutional neural networks in medical imaging raise concerns about their interpretability. While most explainable deep learning applications use post hoc methods (such as GradCAM) to generate feature attribution maps, there is a new type of case-based reasoning models, namely ProtoPNet and its variants, which identify prototypes during training and compare input image patches with those prototypes. We propose the first medical prototype network (MProtoNet) to extend ProtoPNet to brain tumor classification with 3D multi-parametric magnetic resonance imaging (mpMRI) data. To address different requirements between 2D natural images and 3D mpMRIs especially in terms of localizing attention regions, a new attention module with soft masking and online-CAM loss is introduced. Soft masking helps sharpen attention maps, while online-CAM loss directly utilizes image-level labels when training the attention module. MProtoNet achieves statistically significant improvements in interpretability metrics of both correctness and localization coherence (with a best activation precision of $0.713\pm0.058$) without human-annotated labels during training, when compared with GradCAM and several ProtoPNet variants. The source code is available at https://github.com/aywi/mprotonet.

Yuanyuan Wei, Julian Jang-Jaccard, Wen Xu et al.

Anomaly detection for indoor air quality (IAQ) data has become an important area of research as the quality of air is closely related to human health and well-being. However, traditional statistics and shallow machine learning-based approaches in anomaly detection in the IAQ area could not detect anomalies involving the observation of correlations across several data points (i.e., often referred to as long-term dependences). We propose a hybrid deep learning model that combines LSTM with Autoencoder for anomaly detection tasks in IAQ to address this issue. In our approach, the LSTM network is comprised of multiple LSTM cells that work with each other to learn the long-term dependences of the data in a time-series sequence. Autoencoder identifies the optimal threshold based on the reconstruction loss rates evaluated on every data across all time-series sequences. Our experimental results, based on the Dunedin CO2 time-series dataset obtained through a real-world deployment of the schools in New Zealand, demonstrate a very high and robust accuracy rate (99.50%) that outperforms other similar models.

Yuanyuan Wei, Julian Jang-Jaccard, Fariza Sabrina et al.

A Distributed Denial-of-service (DDoS) attack is a malicious attempt to disrupt the regular traffic of a targeted server, service, or network by sending a flood of traffic to overwhelm the target or its surrounding infrastructure. As technology improves, new attacks have been developed by hackers. Traditional statistical and shallow machine learning techniques can detect superficial anomalies based on shallow data and feature selection, however, these approaches cannot detect unseen DDoS attacks. In this context, we propose a reconstruction-based anomaly detection model named LSTM-Autoencoder (LSTM-AE) which combines two deep learning-based models for detecting DDoS attack anomalies. The proposed structure of long short-term memory (LSTM) networks provides units that work with each other to learn the long short-term correlation of data within a time series sequence. Autoencoders are used to identify the optimal threshold based on the reconstruction error rates evaluated on each sample across all time-series sequences. As such, a combination model LSTM-AE can not only learn delicate sub-pattern differences in attacks and benign traffic flows, but also minimize reconstructed benign traffic to obtain a lower range reconstruction error, with attacks presenting a larger reconstruction error. In this research, we trained and evaluated our proposed LSTM-AE model on reflection-based DDoS attacks (DNS, LDAP, and SNMP). The results of our experiments demonstrate that our method performs better than other state-of-the-art methods, especially for LDAP attacks, with an accuracy of over 99.

Yuanyuan Wei, Julian Jang-Jaccard, Amardeep Singh et al.

DDoS attacks involve overwhelming a target system with a large number of requests or traffic from multiple sources, disrupting the normal traffic of a targeted server, service, or network. Distinguishing between legitimate traffic and malicious traffic is a challenging task. It is possible to classify legitimate traffic and malicious traffic and analysis the network traffic by using machine learning and deep learning techniques. However, an inter-model explanation implemented to classify a traffic flow whether is benign or malicious is an important investigation of the inner working theory of the model to increase the trustworthiness of the model. Explainable Artificial Intelligence (XAI) can explain the decision-making of the machine learning models that can be classified and identify DDoS traffic. In this context, we proposed a framework that can not only classify legitimate traffic and malicious traffic of DDoS attacks but also use SHAP to explain the decision-making of the classifier model. To address this concern, we first adopt feature selection techniques to select the top 20 important features based on feature importance techniques (e.g., XGB-based SHAP feature importance). Following that, the Multi-layer Perceptron Network (MLP) part of our proposed model uses the optimized features of the DDoS attack dataset as inputs to classify legitimate and malicious traffic. We perform extensive experiments with all features and selected features. The evaluation results show that the model performance with selected features achieves above 99\% accuracy. Finally, to provide interpretability, XAI can be adopted to explain the model performance between the prediction results and features based on global and local explanations by SHAP, which can better explain the results achieved by our proposed framework.

Shufeng Kong, Xingru Yang, Yuanyuan Wei et al.

Traditional Chinese Medicine (TCM) is a holistic medical system with millennia of accumulated clinical experience, playing a vital role in global healthcare-particularly across East Asia. However, the implicit reasoning, diverse textual forms, and lack of standardization in TCM pose major challenges for computational modeling and evaluation. Large Language Models (LLMs) have demonstrated remarkable potential in processing natural language across diverse domains, including general medicine. Yet, their systematic evaluation in the TCM domain remains underdeveloped. Existing benchmarks either focus narrowly on factual question answering or lack domain-specific tasks and clinical realism. To fill this gap, we introduce MTCMB-a Multi-Task Benchmark for Evaluating LLMs on TCM Knowledge, Reasoning, and Safety. Developed in collaboration with certified TCM experts, MTCMB comprises 12 sub-datasets spanning five major categories: knowledge QA, language understanding, diagnostic reasoning, prescription generation, and safety evaluation. The benchmark integrates real-world case records, national licensing exams, and classical texts, providing an authentic and comprehensive testbed for TCM-capable models. Preliminary results indicate that current LLMs perform well on foundational knowledge but fall short in clinical reasoning, prescription planning, and safety compliance. These findings highlight the urgent need for domain-aligned benchmarks like MTCMB to guide the development of more competent and trustworthy medical AI systems. All datasets, code, and evaluation tools are publicly available at: https://github.com/Wayyuanyuan/MTCMB.

Shufeng Kong, Zijie Wang, Nuan Cui et al.

Automated interpretation of medical images demands robust modeling of complex visual-semantic relationships while addressing annotation scarcity, label imbalance, and clinical plausibility constraints. We introduce MIRNet (Medical Image Reasoner Network), a novel framework that integrates self-supervised pre-training with constrained graph-based reasoning. Tongue image diagnosis is a particularly challenging domain that requires fine-grained visual and semantic understanding. Our approach leverages self-supervised masked autoencoder (MAE) to learn transferable visual representations from unlabeled data; employs graph attention networks (GAT) to model label correlations through expert-defined structured graphs; enforces clinical priors via constraint-aware optimization using KL divergence and regularization losses; and mitigates imbalance using asymmetric loss (ASL) and boosting ensembles. To address annotation scarcity, we also introduce TongueAtlas-4K, a comprehensive expert-curated benchmark comprising 4,000 images annotated with 22 diagnostic labels--representing the largest public dataset in tongue analysis. Validation shows our method achieves state-of-the-art performance. While optimized for tongue diagnosis, the framework readily generalizes to broader diagnostic medical imaging tasks.

Xian-Xian Liu, Yuanyuan Wei, Mingkun Xu et al.

Early detection of gastric cancer, a leading cause of cancer-related mortality worldwide, remains hampered by the limitations of current diagnostic technologies, leading to high rates of misdiagnosis and missed diagnoses. To address these challenges, we propose an integrated system that synergizes advanced hardware and software technologies to balance speed-accuracy. Our study introduces the One Class Twin Cross Learning (OCT-X) algorithm. Leveraging a novel fast double-threshold grid search strategy (FDT-GS) and a patch-based deep fully convolutional network, OCT-X maximizes diagnostic accuracy through real-time data processing and seamless lesion surveillance. The hardware component includes an all-in-one point-of-care testing (POCT) device with high-resolution imaging sensors, real-time data processing, and wireless connectivity, facilitated by the NI CompactDAQ and LabVIEW software. Our integrated system achieved an unprecedented diagnostic accuracy of 99.70%, significantly outperforming existing models by up to 4.47%, and demonstrated a 10% improvement in multirate adaptability. These findings underscore the potential of OCT-X as well as the integrated system in clinical diagnostics, offering a path toward more accurate, efficient, and less invasive early gastric cancer detection. Future research will explore broader applications, further advancing oncological diagnostics. Code is available at https://github.com/liu37972/Multirate-Location-on-OCT-X-Learning.git.

Xian-Xian Liu, Mingkun Xu, Yuanyuan Wei et al.

Timely and precise classification and segmentation of gastric bleeding in endoscopic imagery are pivotal for the rapid diagnosis and intervention of gastric complications, which is critical in life-saving medical procedures. Traditional methods grapple with the challenge posed by the indistinguishable intensity values of bleeding tissues adjacent to other gastric structures. Our study seeks to revolutionize this domain by introducing a novel deep learning model, the Dual Spatial Kernelized Constrained Fuzzy C-Means (Deep DuS-KFCM) clustering algorithm. This Hybrid Neuro-Fuzzy system synergizes Neural Networks with Fuzzy Logic to offer a highly precise and efficient identification of bleeding regions. Implementing a two-fold coarse-to-fine strategy for segmentation, this model initially employs the Spatial Kernelized Fuzzy C-Means (SKFCM) algorithm enhanced with spatial intensity profiles and subsequently harnesses the state-of-the-art DeepLabv3+ with ResNet50 architecture to refine the segmentation output. Through extensive experiments across mainstream gastric bleeding and red spots datasets, our Deep DuS-KFCM model demonstrated unprecedented accuracy rates of 87.95%, coupled with a specificity of 96.33%, outperforming contemporary segmentation methods. The findings underscore the model's robustness against noise and its outstanding segmentation capabilities, particularly for identifying subtle bleeding symptoms, thereby presenting a significant leap forward in medical image processing.

Yuanyuan Wei, Yucheng Wu, Fuyang Qu et al.

Accurate molecular quantification is essential for advancing research and diagnostics in fields such as infectious diseases, cancer biology, and genetic disorders. Droplet digital PCR (ddPCR) has emerged as a gold standard for achieving absolute quantification. While computational ddPCR technologies have advanced significantly, achieving automatic interpretation and consistent adaptability across diverse operational environments remains a challenge. To address these limitations, we introduce the intelligent interpretable droplet digital PCR (I2ddPCR) assay, a comprehensive framework integrating front-end predictive models (for droplet segmentation and classification) with GPT-4o multimodal large language model (MLLM, for context-aware explanations and recommendations) to automate and enhance ddPCR image analysis. This approach surpasses the state-of-the-art models, affording 99.05% accuracy in processing complex ddPCR images containing over 300 droplets per image with varying signal-to-noise ratios (SNRs). By combining specialized neural networks and large language models, the I2ddPCR assay offers a robust and adaptable solution for absolute molecular quantification, achieving a sensitivity capable of detecting low-abundance targets as low as 90.32 copies/μL. Furthermore, it improves model's transparency through detailed explanation and troubleshooting guidance, empowering users to make informed decisions. This innovative framework has the potential to benefit molecular diagnostics, disease research, and clinical applications, especially in resource-constrained settings.

Yimeng Zhang, Harold Rockwell, Sicheng Dai et al.

Feedforward CNN models have proven themselves in recent years as state-of-the-art models for predicting single-neuron responses to natural images in early visual cortical neurons. In this paper, we extend these models with recurrent convolutional layers, reflecting the well-known massive recurrence in the cortex, and show robust increases in predictive performance over feedforward models across thousands of hyperparameter combinations in three datasets of macaque V1 and V2 single-neuron responses. We propose the recurrent circuit can be conceptualized as a form of ensemble computing, with each iteration generating more effective feedforward paths of various path lengths to allow a combination of solutions in the final approximation. The statistics of the paths in the ensemble provide insights to the differential performance increases among our recurrent models. We also assess whether the recurrent circuits learned for neural response prediction can be related to cortical circuits. We find that the hidden units in the recurrent circuits of the appropriate models, when trained on long-duration wide-field image presentations, exhibit similar temporal response dynamics and classical contextual modulations as observed in V1 neurons. This work provides insights to the computational rationale of recurrent circuits and suggests that neural response prediction could be useful for characterizing the recurrent neural circuits in the visual cortex.

Yuanyuan Wei, Julian Jang-Jaccard, Fariza Sabrina et al.

Outlier detection is a technique in data mining that aims to detect unusual or unexpected records in the dataset. Existing outlier detection algorithms have different pros and cons and exhibit different sensitivity to noisy data such as extreme values. In this paper, we propose a novel cluster-based outlier detection algorithm named MSD-Kmeans that combines the statistical method of Mean and Standard Deviation (MSD) and the machine learning clustering algorithm K-means to detect outliers more accurately with the better control of extreme values. There are two phases in this combination method of MSD-Kmeans: (1) applying MSD algorithm to eliminate as many noisy data to minimize the interference on clusters, and (2) applying K-means algorithm to obtain local optimal clusters. We evaluate our algorithm and demonstrate its effectiveness in the context of detecting possible overcharging of taxi fares, as greedy dishonest drivers may attempt to charge high fares by detouring. We compare the performance indicators of MSD-Kmeans with those of other outlier detection algorithms, such as MSD, K-means, Z-score, MIQR and LOF, and prove that the proposed MSD-Kmeans algorithm achieves the highest measure of precision, accuracy, and F-measure. We conclude that MSD-Kmeans can be used for effective and efficient outlier detection on data of varying quality on IoT devices.