Cross-Modal Translation and Alignment for Survival Analysis

With the rapid advances in high-throughput sequencing technologies, the focus of survival analysis has shifted from examining clinical indicators to incorporating genomic profiles with pathological images. However, existing methods either directly adopt a straightforward fusion of pathological features and genomic profiles for survival prediction, or take genomic profiles as guidance to integrate the features of pathological images. The former would overlook intrinsic cross-modal correlations. The latter would discard pathological information irrelevant to gene expression. To address these issues, we present a Cross-Modal Translation and Alignment (CMTA) framework to explore the intrinsic cross-modal correlations and transfer potential complementary information. Specifically, we construct two parallel encoder-decoder structures for multi-modal data to integrate intra-modal information and generate cross-modal representation. Taking the generated cross-modal representation to enhance and recalibrate intra-modal representation can significantly improve its discrimination for comprehensive survival analysis. To explore the intrinsic crossmodal correlations, we further design a cross-modal attention module as the information bridge between different modalities to perform cross-modal interactions and transfer complementary information. Our extensive experiments on five public TCGA datasets demonstrate that our proposed framework outperforms the state-of-the-art methods.

Enabling Quartile-based Estimated-Mean Gradient Aggregation As Baseline for Federated Image Classifications

Federated Learning (FL) has revolutionized how we train deep neural networks by enabling decentralized collaboration while safeguarding sensitive data and improving model performance. However, FL faces two crucial challenges: the diverse nature of data held by individual clients and the vulnerability of the FL system to security breaches. This paper introduces an innovative solution named Estimated Mean Aggregation (EMA) that not only addresses these challenges but also provides a fundamental reference point as a $\mathsf{baseline}$ for advanced aggregation techniques in FL systems. EMA's significance lies in its dual role: enhancing model security by effectively handling malicious outliers through trimmed means and uncovering data heterogeneity to ensure that trained models are adaptable across various client datasets. Through a wealth of experiments, EMA consistently demonstrates high accuracy and area under the curve (AUC) compared to alternative methods, establishing itself as a robust baseline for evaluating the effectiveness and security of FL aggregation methods. EMA's contributions thus offer a crucial step forward in advancing the efficiency, security, and versatility of decentralized deep learning in the context of FL.

Soft Merging: A Flexible and Robust Soft Model Merging Approach for Enhanced Neural Network Performance

Stochastic Gradient Descent (SGD), a widely used optimization algorithm in deep learning, is often limited to converging to local optima due to the non-convex nature of the problem. Leveraging these local optima to improve model performance remains a challenging task. Given the inherent complexity of neural networks, the simple arithmetic averaging of the obtained local optima models in undesirable results. This paper proposes a {\em soft merging} method that facilitates rapid merging of multiple models, simplifies the merging of specific parts of neural networks, and enhances robustness against malicious models with extreme values. This is achieved by learning gate parameters through a surrogate of the $l_0$ norm using hard concrete distribution without modifying the model weights of the given local optima models. This merging process not only enhances the model performance by converging to a better local optimum, but also minimizes computational costs, offering an efficient and explicit learning process integrated with stochastic gradient descent. Thorough experiments underscore the effectiveness and superior performance of the merged neural networks.

Multi-view Self-supervised Disentanglement for General Image Denoising

With its significant performance improvements, the deep learning paradigm has become a standard tool for modern image denoisers. While promising performance has been shown on seen noise distributions, existing approaches often suffer from generalisation to unseen noise types or general and real noise. It is understandable as the model is designed to learn paired mapping (e.g. from a noisy image to its clean version). In this paper, we instead propose to learn to disentangle the noisy image, under the intuitive assumption that different corrupted versions of the same clean image share a common latent space. A self-supervised learning framework is proposed to achieve the goal, without looking at the latent clean image. By taking two different corrupted versions of the same image as input, the proposed Multi-view Self-supervised Disentanglement (MeD) approach learns to disentangle the latent clean features from the corruptions and recover the clean image consequently. Extensive experimental analysis on both synthetic and real noise shows the superiority of the proposed method over prior self-supervised approaches, especially on unseen novel noise types. On real noise, the proposed method even outperforms its supervised counterparts by over 3 dB.

Progressive Feature Adjustment for Semi-supervised Learning from Pretrained Models

As an effective way to alleviate the burden of data annotation, semi-supervised learning (SSL) provides an attractive solution due to its ability to leverage both labeled and unlabeled data to build a predictive model. While significant progress has been made recently, SSL algorithms are often evaluated and developed under the assumption that the network is randomly initialized. This is in sharp contrast to most vision recognition systems that are built from fine-tuning a pretrained network for better performance. While the marriage of SSL and a pretrained model seems to be straightforward, recent literature suggests that naively applying state-of-the-art SSL with a pretrained model fails to unleash the full potential of training data. In this paper, we postulate the underlying reason is that the pretrained feature representation could bring a bias inherited from the source data, and the bias tends to be magnified through the self-training process in a typical SSL algorithm. To overcome this issue, we propose to use pseudo-labels from the unlabelled data to update the feature extractor that is less sensitive to incorrect labels and only allow the classifier to be trained from the labeled data. More specifically, we progressively adjust the feature extractor to ensure its induced feature distribution maintains a good class separability even under strong input perturbation. Through extensive experimental studies, we show that the proposed approach achieves superior performance over existing solutions.

Exploring Domain-Specific Enhancements for a Neural Foley Synthesizer

Foley sound synthesis refers to the creation of authentic, diegetic sound effects for media, such as film or radio. In this study, we construct a neural Foley synthesizer capable of generating mono-audio clips across seven predefined categories. Our approach introduces multiple enhancements to existing models in the text-to-audio domain, with the goal of enriching the diversity and acoustic characteristics of the generated foleys. Notably, we utilize a pre-trained encoder that retains acoustical and musical attributes in intermediate embeddings, implement class-conditioning to enhance differentiability among foley classes in their intermediate representations, and devise an innovative transformer-based architecture for optimizing self-attention computations on very large inputs without compromising valuable information. Subsequent to implementation, we present intermediate outcomes that surpass the baseline, discuss practical challenges encountered in achieving optimal results, and outline potential pathways for further research.

Code Representation Pre-training with Complements from Program Executions

Large language models (LLMs) for natural language processing have been grafted onto programming language modeling for advancing code intelligence. Although it can be represented in the text format, code is syntactically more rigorous in order to be properly compiled or interpreted to perform a desired set of behaviors given any inputs. In this case, existing works benefit from syntactic representations to learn from code less ambiguously in the forms of abstract syntax tree, control-flow graph, etc. However, programs with the same purpose can be implemented in various ways showing different syntactic representations while the ones with similar implementations can have distinct behaviors. Though trivially demonstrated during executions, such semantics about functionality are challenging to be learned directly from code, especially in an unsupervised manner. Hence, in this paper, we propose FuzzPretrain to explore the dynamic information of programs revealed by their test cases and embed it into the feature representations of code as complements. The test cases are obtained with the assistance of a customized fuzzer and are only required during pre-training. FuzzPretrain yielded more than 6%/9% mAP improvements on code search over its counterparts trained with only source code or AST, respectively. Our extensive experimental results show the benefits of learning discriminative code representations with program executions.

DARC: Distribution-Aware Re-Coloring Model for Generalizable Nucleus Segmentation

Nucleus segmentation is usually the first step in pathological image analysis tasks. Generalizable nucleus segmentation refers to the problem of training a segmentation model that is robust to domain gaps between the source and target domains. The domain gaps are usually believed to be caused by the varied image acquisition conditions, e.g., different scanners, tissues, or staining protocols. In this paper, we argue that domain gaps can also be caused by different foreground (nucleus)-background ratios, as this ratio significantly affects feature statistics that are critical to normalization layers. We propose a Distribution-Aware Re-Coloring (DARC) model that handles the above challenges from two perspectives. First, we introduce a re-coloring method that relieves dramatic image color variations between different domains. Second, we propose a new instance normalization method that is robust to the variation in foreground-background ratios. We evaluate the proposed methods on two H$\&$E stained image datasets, named CoNSeP and CPM17, and two IHC stained image datasets, called DeepLIIF and BC-DeepLIIF. Extensive experimental results justify the effectiveness of our proposed DARC model. Codes are available at \url{https://github.com/csccsccsccsc/DARC

Using Large Language Models to Automate Category and Trend Analysis of Scientific Articles: An Application in Ophthalmology

Purpose: In this paper, we present an automated method for article classification, leveraging the power of Large Language Models (LLM). The primary focus is on the field of ophthalmology, but the model is extendable to other fields. Methods: We have developed a model based on Natural Language Processing (NLP) techniques, including advanced LLMs, to process and analyze the textual content of scientific papers. Specifically, we have employed zero-shot learning (ZSL) LLM models and compared against Bidirectional and Auto-Regressive Transformers (BART) and its variants, and Bidirectional Encoder Representations from Transformers (BERT), and its variant such as distilBERT, SciBERT, PubmedBERT, BioBERT. Results: The classification results demonstrate the effectiveness of LLMs in categorizing large number of ophthalmology papers without human intervention. Results: To evalute the LLMs, we compiled a dataset (RenD) of 1000 ocular disease-related articles, which were expertly annotated by a panel of six specialists into 15 distinct categories. The model achieved mean accuracy of 0.86 and mean F1 of 0.85 based on the RenD dataset. Conclusion: The proposed framework achieves notable improvements in both accuracy and efficiency. Its application in the domain of ophthalmology showcases its potential for knowledge organization and retrieval in other domains too. We performed trend analysis that enables the researchers and clinicians to easily categorize and retrieve relevant papers, saving time and effort in literature review and information gathering as well as identification of emerging scientific trends within different disciplines. Moreover, the extendibility of the model to other scientific fields broadens its impact in facilitating research and trend analysis across diverse disciplines.

Unsupervised Domain Adaptation for Anatomical Landmark Detection

Recently, anatomical landmark detection has achieved great progresses on single-domain data, which usually assumes training and test sets are from the same domain. However, such an assumption is not always true in practice, which can cause significant performance drop due to domain shift. To tackle this problem, we propose a novel framework for anatomical landmark detection under the setting of unsupervised domain adaptation (UDA), which aims to transfer the knowledge from labeled source domain to unlabeled target domain. The framework leverages self-training and domain adversarial learning to address the domain gap during adaptation. Specifically, a self-training strategy is proposed to select reliable landmark-level pseudo-labels of target domain data with dynamic thresholds, which makes the adaptation more effective. Furthermore, a domain adversarial learning module is designed to handle the unaligned data distributions of two domains by learning domain-invariant features via adversarial training. Our experiments on cephalometric and lung landmark detection show the effectiveness of the method, which reduces the domain gap by a large margin and outperforms other UDA methods consistently. The code is available at https://github.com/jhb86253817/UDA_Med_Landmark.