Multi-Scale Heterogeneity-Aware Hypergraph Representation for Histopathology Whole Slide Images

Survival prediction is a complex ordinal regression task that aims to predict the survival coefficient ranking among a cohort of patients, typically achieved by analyzing patients' whole slide images. Existing deep learning approaches mainly adopt multiple instance learning or graph neural networks under weak supervision. Most of them are unable to uncover the diverse interactions between different types of biological entities(\textit{e.g.}, cell cluster and tissue block) across multiple scales, while such interactions are crucial for patient survival prediction. In light of this, we propose a novel multi-scale heterogeneity-aware hypergraph representation framework. Specifically, our framework first constructs a multi-scale heterogeneity-aware hypergraph and assigns each node with its biological entity type. It then mines diverse interactions between nodes on the graph structure to obtain a global representation. Experimental results demonstrate that our method outperforms state-of-the-art approaches on three benchmark datasets. Code is publicly available at \href{https://github.com/Hanminghao/H2GT}{https://github.com/Hanminghao/H2GT}.Comment: 9 pages, 6 figures, accepted by ICME202

Faster Diffusion Action Segmentation

Temporal Action Segmentation (TAS) is an essential task in video analysis, aiming to segment and classify continuous frames into distinct action segments. However, the ambiguous boundaries between actions pose a significant challenge for high-precision segmentation. Recent advances in diffusion models have demonstrated substantial success in TAS tasks due to their stable training process and high-quality generation capabilities. However, the heavy sampling steps required by diffusion models pose a substantial computational burden, limiting their practicality in real-time applications. Additionally, most related works utilize Transformer-based encoder architectures. Although these architectures excel at capturing long-range dependencies, they incur high computational costs and face feature-smoothing issues when processing long video sequences. To address these challenges, we propose EffiDiffAct, an efficient and high-performance TAS algorithm. Specifically, we develop a lightweight temporal feature encoder that reduces computational overhead and mitigates the rank collapse phenomenon associated with traditional self-attention mechanisms. Furthermore, we introduce an adaptive skip strategy that allows for dynamic adjustment of timestep lengths based on computed similarity metrics during inference, thereby further enhancing computational efficiency. Comprehensive experiments on the 50Salads, Breakfast, and GTEA datasets demonstrated the effectiveness of the proposed algorithm.Comment: 25 pages, 6 figure

Towards Context-Aware Emotion Recognition Debiasing from a Causal Demystification Perspective via De-confounded Training

Understanding emotions from diverse contexts has received widespread attention in computer vision communities. The core philosophy of Context-Aware Emotion Recognition (CAER) is to provide valuable semantic cues for recognizing the emotions of target persons by leveraging rich contextual information. Current approaches invariably focus on designing sophisticated structures to extract perceptually critical representations from contexts. Nevertheless, a long-neglected dilemma is that a severe context bias in existing datasets results in an unbalanced distribution of emotional states among different contexts, causing biased visual representation learning. From a causal demystification perspective, the harmful bias is identified as a confounder that misleads existing models to learn spurious correlations based on likelihood estimation, limiting the models\u27 performance. To address the issue, we embrace causal inference to disentangle the models from the impact of such bias, and formulate the causalities among variables in the CAER task via a customized causal graph. Subsequently, we present a Contextual Causal Intervention Module (CCIM) to de-confound the confounder, which is built upon backdoor adjustment theory to facilitate seeking approximate causal effects during model training. As a plug-and-play component, CCIM can easily integrate with existing approaches and bring significant improvements. Systematic experiments on three datasets demonstrate the effectiveness of our CCIM.TPAMI 202

DASES: a database of alternative splicing for esophageal squamous cell carcinoma

Esophageal carcinoma ranks as the sixth leading cause of cancer-related mortality globally, with esophageal squamous cell carcinoma (ESCC) being particularly prevalent among Asian populations. Alternative splicing (AS) plays a pivotal role in ESCC development and progression by generating diverse transcript isoforms. However, the current landscape lacks a specialized database focusing on alternative splicing events (ASEs) derived from a large number of ESCC cases. Additionally, most existing AS databases overlook the contribution of long non-coding RNAs (lncRNAs) in ESCC molecular mechanisms, predominantly focusing on mRNA-based ASE identification. To address these limitations, we deployed DASES (http://www.hxdsjzx.cn/DASES). Employing a combination of publicly available and in-house ESCC RNA-seq datasets, our extensive analysis of 346 samples, with 93% being paired tumor and adjacent non-tumor tissues, led to the identification of 257 novel lncRNAs in esophageal squamous cell carcinoma. Leveraging a paired comparison of tumor and adjacent normal tissues, DASES identified 59,094 ASEs that may be associated with ESCC. DASES fills a critical gap by providing comprehensive insights into ASEs in ESCC, encompassing lncRNAs and mRNA, thus facilitating a deeper understanding of ESCC molecular mechanisms and serving as a valuable resource for ESCC research communities

Chimeric Antigen Receptor T Cells to Target cd79B in B-Ceall Lymphomas

BACKGROUND: Chimeric antigen receptor (CAR) T cells targeting CD19 mediate potent and durable effects in B-cell malignancies. However, antigen loss or downregulation is a frequent cause of resistance. Here, we report development of a novel CAR T-cell therapy product to target CD79b, a pan B-cell antigen, widely expressed in most B-cell lymphomas. METHODS: We generated a novel anti-CD79b monoclonal antibody by hybridoma method. The specificity of the antibody was determined by testing against isogenic cell lines with human CD79b knock-in or knock-out. A single-chain variable fragment derived from the monoclonal antibody was used to make a panel of CD79b-targeting CAR molecules containing various hinge, transmembrane, and co-stimulatory domains. These were lentivirally transduced into primary T cells and tested for antitumor activity in in vitro and in vivo B-cell lymphoma models. RESULTS: We found that the novel anti-CD79b monoclonal antibody was highly specific and bound only to human CD79b and no other cell surface protein. In testing the various CD79b-targeting CAR molecules, superior antitumor efficacy in vitro and in vivo was found for a CAR consisting CD8α hinge and transmembrane domains, an OX40 co-stimulatory domain, and a CD3ζ signaling domain. This CD79b CAR specifically recognized human CD79b-expressing lymphoma cell lines but not CD79b knock-out cell lines. CD79b CAR T cells, generated from T cells from either healthy donors or patients with lymphoma, proliferated, produced cytokines, degranulated, and exhibited robust cytotoxic activity in vitro against CD19 CONCLUSION: Our results indicated that this novel CD79b CAR T-cell therapy product has robust antitumor activity against B-cell lymphomas. These results supported initiation of a phase 1 clinical trial to evaluate this product in patients with relapsed or refractory B-cell lymphomas

EBBA: An Enhanced Binary Bat Algorithm Integrated with Chaos Theory and Lévy Flight for Feature Selection

Feature selection can efficiently improve classification accuracy and reduce the dimension of datasets. However, feature selection is a challenging and complex task that requires a high-performance optimization algorithm. In this paper, we propose an enhanced binary bat algorithm (EBBA) which is originated from the conventional binary bat algorithm (BBA) as the learning algorithm in a wrapper-based feature selection model. First, we model the feature selection problem and then transfer it as a fitness function. Then, we propose an EBBA for solving the feature selection problem. In EBBA, we introduce the Lévy flight-based global search method, population diversity boosting method and chaos-based loudness method to improve the BA and make it more applicable to feature selection problems. Finally, the simulations are conducted to evaluate the proposed EBBA and the simulation results demonstrate that the proposed EBBA outmatches other comparison benchmarks. Moreover, we also illustrate the effectiveness of the proposed improved factors by tests

EBBA: An Enhanced Binary Bat Algorithm Integrated with Chaos Theory and Lévy Flight for Feature Selection

Feature selection can efficiently improve classification accuracy and reduce the dimension of datasets. However, feature selection is a challenging and complex task that requires a high-performance optimization algorithm. In this paper, we propose an enhanced binary bat algorithm (EBBA) which is originated from the conventional binary bat algorithm (BBA) as the learning algorithm in a wrapper-based feature selection model. First, we model the feature selection problem and then transfer it as a fitness function. Then, we propose an EBBA for solving the feature selection problem. In EBBA, we introduce the Lévy flight-based global search method, population diversity boosting method and chaos-based loudness method to improve the BA and make it more applicable to feature selection problems. Finally, the simulations are conducted to evaluate the proposed EBBA and the simulation results demonstrate that the proposed EBBA outmatches other comparison benchmarks. Moreover, we also illustrate the effectiveness of the proposed improved factors by tests.</jats:p