Xiaoxiao Li

Sana Ayromlou, Purang Abolmaesumi, Teresa Tsang et al.

Standard deep learning-based classification approaches require collecting all samples from all classes in advance and are trained offline. This paradigm may not be practical in real-world clinical applications, where new classes are incrementally introduced through the addition of new data. Class incremental learning is a strategy allowing learning from such data. However, a major challenge is catastrophic forgetting, i.e., performance degradation on previous classes when adapting a trained model to new data. Prior methodologies to alleviate this challenge save a portion of training data require perpetual storage of such data that may introduce privacy issues. Here, we propose a novel data-free class incremental learning framework that first synthesizes data from the model trained on previous classes to generate a \ours. Subsequently, it updates the model by combining the synthesized data with new class data. Furthermore, we incorporate a cosine normalized Cross-entropy loss to mitigate the adverse effects of the imbalance, a margin loss to increase separation among previous classes and new ones, and an intra-domain contrastive loss to generalize the model trained on the synthesized data to real data. We compare our proposed framework with state-of-the-art methods in class incremental learning, where we demonstrate improvement in accuracy for the classification of 11,062 echocardiography cine series of patients.

Xinnan Dai, Caihua Shan, Jie Zheng et al.

Genes are fundamental for analyzing biological systems and many recent works proposed to utilize gene expression for various biological tasks by deep learning models. Despite their promising performance, it is hard for deep neural networks to provide biological insights for humans due to their black-box nature. Recently, some works integrated biological knowledge with neural networks to improve the transparency and performance of their models. However, these methods can only incorporate partial biological knowledge, leading to suboptimal performance. In this paper, we propose the Biological Factor Regulatory Neural Network (BFReg-NN), a generic framework to model relations among biological factors in cell systems. BFReg-NN starts from gene expression data and is capable of merging most existing biological knowledge into the model, including the regulatory relations among genes or proteins (e.g., gene regulatory networks (GRN), protein-protein interaction networks (PPI)) and the hierarchical relations among genes, proteins and pathways (e.g., several genes/proteins are contained in a pathway). Moreover, BFReg-NN also has the ability to provide new biologically meaningful insights because of its white-box characteristics. Experimental results on different gene expression-based tasks verify the superiority of BFReg-NN compared with baselines. Our case studies also show that the key insights found by BFReg-NN are consistent with the biological literature.

Minghui Chen, Ruinan Jin, Wenlong Deng et al.

Recent studies highlight the promise of LLM-based prompt optimization, especially with TextGrad, which automates differentiation'' via texts and backpropagates textual feedback. This approach facilitates training in various real-world applications that do not support numerical gradient propagation or loss calculation. In this paper, we systematically explore the potential and challenges of incorporating textual gradient into Federated Learning (FL). Our contributions are fourfold. Firstly, we introduce a novel FL paradigm, Federated Textual Gradient (FedTextGrad), that allows clients to upload locally optimized prompts derived from textual gradients, while the server aggregates the received prompts. Unlike traditional FL frameworks, which are designed for numerical aggregation, FedTextGrad is specifically tailored for handling textual data, expanding the applicability of FL to a broader range of problems that lack well-defined numerical loss functions. Secondly, building on this design, we conduct extensive experiments to explore the feasibility of FedTextGrad. Our findings highlight the importance of properly tuning key factors (e.g., local steps) in FL training. Thirdly, we highlight a major challenge in FedTextGrad aggregation: retaining essential information from distributed prompt updates. Last but not least, in response to this issue, we improve the vanilla variant of FedTextGrad by providing actionable guidance to the LLM when summarizing client prompts by leveraging the Uniform Information Density principle. Through this principled study, we enable the adoption of textual gradients in FL for optimizing LLMs, identify important issues, and pinpoint future directions, thereby opening up a new research area that warrants further investigation.

José Ignacio Orlando, Huazhu Fu, João Barbossa Breda et al.

Glaucoma is one of the leading causes of irreversible but preventable blindness in working age populations. Color fundus photography (CFP) is the most cost-effective imaging modality to screen for retinal disorders. However, its application to glaucoma has been limited to the computation of a few related biomarkers such as the vertical cup-to-disc ratio. Deep learning approaches, although widely applied for medical image analysis, have not been extensively used for glaucoma assessment due to the limited size of the available data sets. Furthermore, the lack of a standardize benchmark strategy makes difficult to compare existing methods in a uniform way. In order to overcome these issues we set up the Retinal Fundus Glaucoma Challenge, REFUGE (\url{https://refuge.grand-challenge.org}), held in conjunction with MICCAI 2018. The challenge consisted of two primary tasks, namely optic disc/cup segmentation and glaucoma classification. As part of REFUGE, we have publicly released a data set of 1200 fundus images with ground truth segmentations and clinical glaucoma labels, currently the largest existing one. We have also built an evaluation framework to ease and ensure fairness in the comparison of different models, encouraging the development of novel techniques in the field. 12 teams qualified and participated in the online challenge. This paper summarizes their methods and analyzes their corresponding results. In particular, we observed that two of the top-ranked teams outperformed two human experts in the glaucoma classification task. Furthermore, the segmentation results were in general consistent with the ground truth annotations, with complementary outcomes that can be further exploited by ensembling the results.

Xiaoxiao Li, Vivek Singh, Yifan Wu et al.

Tracking organ motion is important in image-guided interventions, but motion annotations are not always easily available. Thus, we propose Repetitive Motion Estimation Network (RMEN) to recover cardiac and respiratory signals. It learns the spatio-temporal repetition patterns, embedding high dimensional motion manifolds to 1D vectors with partial motion phase boundary annotations. Compared with the best alternative models, our proposed RMEN significantly decreased the QRS peaks detection offsets by 59.3%. Results showed that RMEN could handle the irregular cardiac and respiratory motion cases. Repetitive motion patterns learned by RMEN were visualized and indicated in the feature maps.