MProtoNet: A Case-Based Interpretable Model for Brain Tumor Classification with 3D Multi-parametric Magnetic Resonance Imaging

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.Comment: 15 pages, 5 figures, 1 table; accepted for oral presentation at MIDL 2023 (https://openreview.net/forum?id=6Wbj3QCo4U4); camera-ready versio

Transformer Convolutional Neural Networks for Automated Artifact Detection in Scalp EEG

It is well known that electroencephalograms (EEGs) often contain artifacts due to muscle activity, eye blinks, and various other causes. Detecting such artifacts is an essential first step toward a correct interpretation of EEGs. Although much effort has been devoted to semi-automated and automated artifact detection in EEG, the problem of artifact detection remains challenging. In this paper, we propose a convolutional neural network (CNN) enhanced by transformers using belief matching (BM) loss for automated detection of five types of artifacts: chewing, electrode pop, eye movement, muscle, and shiver. Specifically, we apply these five detectors at individual EEG channels to distinguish artifacts from background EEG. Next, for each of these five types of artifacts, we combine the output of these channel-wise detectors to detect artifacts in multi-channel EEG segments. These segment-level classifiers can detect specific artifacts with a balanced accuracy (BAC) of 0.947, 0.735, 0.826, 0.857, and 0.655 for chewing, electrode pop, eye movement, muscle, and shiver artifacts, respectively. Finally, we combine the outputs of the five segment-level detectors to perform a combined binary classification (any artifact vs. background). The resulting detector achieves a sensitivity (SEN) of 60.4%, 51.8%, and 35.5%, at a specificity (SPE) of 95%, 97%, and 99%, respectively. This artifact detection module can reject artifact segments while only removing a small fraction of the background EEG, leading to a cleaner EEG for further analysis.Comment: This is an extension to a paper presented at the 2022 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC) Scottish Event Campus, Glasgow, UK, July 11-15, 202

An Empirical Study on the Language Modal in Visual Question Answering

Generalization beyond in-domain experience to out-of-distribution data is of paramount significance in the AI domain. Of late, state-of-the-art Visual Question Answering (VQA) models have shown impressive performance on in-domain data, partially due to the language priors bias which, however, hinders the generalization ability in practice. This paper attempts to provide new insights into the influence of language modality on VQA performance from an empirical study perspective. To achieve this, we conducted a series of experiments on six models. The results of these experiments revealed that, 1) apart from prior bias caused by question types, there is a notable influence of postfix-related bias in inducing biases, and 2) training VQA models with word-sequence-related variant questions demonstrated improved performance on the out-of-distribution benchmark, and the LXMERT even achieved a 10-point gain without adopting any debiasing methods. We delved into the underlying reasons behind these experimental results and put forward some simple proposals to reduce the models' dependency on language priors. The experimental results demonstrated the effectiveness of our proposed method in improving performance on the out-of-distribution benchmark, VQA-CPv2. We hope this study can inspire novel insights for future research on designing bias-reduction approaches.Comment: Accepted by IJCAI202

Few-shot Multi-domain Knowledge Rearming for Context-aware Defence against Advanced Persistent Threats

Advanced persistent threats (APTs) have novel features such as multi-stage penetration, highly-tailored intention, and evasive tactics. APTs defense requires fusing multi-dimensional Cyber threat intelligence data to identify attack intentions and conducts efficient knowledge discovery strategies by data-driven machine learning to recognize entity relationships. However, data-driven machine learning lacks generalization ability on fresh or unknown samples, reducing the accuracy and practicality of the defense model. Besides, the private deployment of these APT defense models on heterogeneous environments and various network devices requires significant investment in context awareness (such as known attack entities, continuous network states, and current security strategies). In this paper, we propose a few-shot multi-domain knowledge rearming (FMKR) scheme for context-aware defense against APTs. By completing multiple small tasks that are generated from different network domains with meta-learning, the FMKR firstly trains a model with good discrimination and generalization ability for fresh and unknown APT attacks. In each FMKR task, both threat intelligence and local entities are fused into the support/query sets in meta-learning to identify possible attack stages. Secondly, to rearm current security strategies, an finetuning-based deployment mechanism is proposed to transfer learned knowledge into the student model, while minimizing the defense cost. Compared to multiple model replacement strategies, the FMKR provides a faster response to attack behaviors while consuming less scheduling cost. Based on the feedback from multiple real users of the Industrial Internet of Things (IIoT) over 2 months, we demonstrate that the proposed scheme can improve the defense satisfaction rate.Comment: It has been accepted by IEEE SmartNet

STAGE: Span Tagging and Greedy Inference Scheme for Aspect Sentiment Triplet Extraction

Aspect Sentiment Triplet Extraction (ASTE) has become an emerging task in sentiment analysis research, aiming to extract triplets of the aspect term, its corresponding opinion term, and its associated sentiment polarity from a given sentence. Recently, many neural networks based models with different tagging schemes have been proposed, but almost all of them have their limitations: heavily relying on 1) prior assumption that each word is only associated with a single role (e.g., aspect term, or opinion term, etc. ) and 2) word-level interactions and treating each opinion/aspect as a set of independent words. Hence, they perform poorly on the complex ASTE task, such as a word associated with multiple roles or an aspect/opinion term with multiple words. Hence, we propose a novel approach, Span TAgging and Greedy infErence (STAGE), to extract sentiment triplets in span-level, where each span may consist of multiple words and play different roles simultaneously. To this end, this paper formulates the ASTE task as a multi-class span classification problem. Specifically, STAGE generates more accurate aspect sentiment triplet extractions via exploring span-level information and constraints, which consists of two components, namely, span tagging scheme and greedy inference strategy. The former tag all possible candidate spans based on a newly-defined tagging set. The latter retrieves the aspect/opinion term with the maximum length from the candidate sentiment snippet to output sentiment triplets. Furthermore, we propose a simple but effective model based on the STAGE, which outperforms the state-of-the-arts by a large margin on four widely-used datasets. Moreover, our STAGE can be easily generalized to other pair/triplet extraction tasks, which also demonstrates the superiority of the proposed scheme STAGE.Comment: Accepted by AAAI 202

Deciphering of interactions between platinated DNA and HMGB1 by hydrogen/deuterium exchange mass spectrometry

A high mobility group box 1 (HMGB1) protein has been reported to recognize both 1,2-intrastrand crosslinked DNA by cisplatin (1,2-cis-Pt-DNA) and monofunctional platinated DNA using trans-[PtCl2(NH3)(thiazole)] (1-trans-PtTz-DNA). However, the molecular basis of recognition between the trans-PtTz-DNA and HMGB1 remains unclear. In the present work, we described a hydrogen/deuterium exchange mass spectrometry (HDX-MS) method in combination with docking simulation to decipher the interactions of platinated DNA with domain A of HMGB1. The global deuterium uptake results indicated that 1-trans-PtTz-DNA bound to HMGB1a slightly tighter than the 1,2-cis-Pt-DNA. The local deuterium uptake at the peptide level revealed that the helices I and II, and loop 1 of HMGB1a were involved in the interactions with both platinated DNA adducts. However, docking simulation disclosed different H-bonding networks and distinct DNA-backbone orientations in the two Pt-DNA-HMGB1a complexes. Moreover, the Phe37 residue of HMGB1a was shown to play a key role in the recognition between HMGB1a and the platinated DNAs. In the cis-Pt-DNA-HMGB1a complex, the phenyl ring of Phe37 intercalates into a hydrophobic notch created by the two platinated guanines, while in the trans-PtTz-DNA-HMGB1a complex the phenyl ring appears to intercalate into a hydrophobic crevice formed by the platinated guanine and the opposite adenine in the complementary strand, forming a penta-layer π–π stacking associated with the adjacent thymine and the thiazole ligand. This work demonstrates that HDX-MS associated with docking simulation is a powerful tool to elucidate the interactions between platinated DNAs and proteins