CryoMAE: Few-Shot Cryo-EM Particle Picking with Masked Autoencoders

Cryo-electron microscopy (cryo-EM) emerges as a pivotal technology for determining the architecture of cells, viruses, and protein assemblies at near-atomic resolution. Traditional particle picking, a key step in cryo-EM, struggles with manual effort and automated methods' sensitivity to low signal-to-noise ratio (SNR) and varied particle orientations. Furthermore, existing neural network (NN)-based approaches often require extensive labeled datasets, limiting their practicality. To overcome these obstacles, we introduce cryoMAE, a novel approach based on few-shot learning that harnesses the capabilities of Masked Autoencoders (MAE) to enable efficient selection of single particles in cryo-EM images. Contrary to conventional NN-based techniques, cryoMAE requires only a minimal set of positive particle images for training yet demonstrates high performance in particle detection. Furthermore, the implementation of a self-cross similarity loss ensures distinct features for particle and background regions, thereby enhancing the discrimination capability of cryoMAE. Experiments on large-scale cryo-EM datasets show that cryoMAE outperforms existing state-of-the-art (SOTA) methods, improving 3D reconstruction resolution by up to 22.4%.

Neighbour-level Message Interaction Encoding for Improved Representation Learning on Graphs

Message passing has become the dominant framework in graph representation learning. The essential idea of the message-passing framework is to update node embeddings based on the information aggregated from local neighbours. However, most existing aggregation methods have not encoded neighbour-level message interactions into the aggregated message, resulting in an information lost in embedding generation. And this information lost could be accumulated and become more serious as more layers are added to the graph network model. To address this issue, we propose a neighbour-level message interaction information encoding method for improving graph representation learning. For messages that are aggregated at a node, we explicitly generate an encoding between each message and the rest messages using an encoding function. Then we aggregate these learned encodings and take the sum of the aggregated encoding and the aggregated message to update the embedding for the node. By this way, neighbour-level message interaction information is integrated into the generated node embeddings. The proposed encoding method is a generic method which can be integrated into message-passing graph convolutional networks. Extensive experiments are conducted on six popular benchmark datasets across four highly-demanded tasks. The results show that integrating neighbour-level message interactions achieves improved performance of the base models, advancing the state of the art results for representation learning over graphs.

RandAlign: A Parameter-Free Method for Regularizing Graph Convolutional Networks

Studies continually find that message-passing graph convolutional networks suffer from the over-smoothing issue. Basically, the issue of over-smoothing refers to the phenomenon that the learned embeddings for all nodes can become very similar to one another and therefore are uninformative after repeatedly applying message passing iterations. Intuitively, we can expect the generated embeddings become smooth asymptotically layerwisely, that is each layer of graph convolution generates a smoothed version of embeddings as compared to that generated by the previous layer. Based on this intuition, we propose RandAlign, a stochastic regularization method for graph convolutional networks. The idea of RandAlign is to randomly align the learned embedding for each node with that of the previous layer using randomly interpolation in each graph convolution layer. Through alignment, the smoothness of the generated embeddings is explicitly reduced. To better maintain the benefit yielded by the graph convolution, in the alignment step we introduce to first scale the embedding of the previous layer to the same norm as the generated embedding and then perform random interpolation for aligning the generated embedding. RandAlign is a parameter-free method and can be directly applied without introducing additional trainable weights or hyper-parameters. We experimentally evaluate RandAlign on different graph domain tasks on seven benchmark datasets. The experimental results show that RandAlign is a general method that improves the generalization performance of various graph convolutional network models and also improves the numerical stability of optimization, advancing the state of the art performance for graph representation learning.

Optimal convex $M$-estimation via score matching

In the context of linear regression, we construct a data-driven convex loss function with respect to which empirical risk minimisation yields optimal asymptotic variance in the downstream estimation of the regression coefficients. Our semiparametric approach targets the best decreasing approximation of the derivative of the log-density of the noise distribution. At the population level, this fitting process is a nonparametric extension of score matching, corresponding to a log-concave projection of the noise distribution with respect to the Fisher divergence. The procedure is computationally efficient, and we prove that our procedure attains the minimal asymptotic covariance among all convex $M$-estimators. As an example of a non-log-concave setting, for Cauchy errors, the optimal convex loss function is Huber-like, and our procedure yields an asymptotic efficiency greater than 0.87 relative to the oracle maximum likelihood estimator of the regression coefficients that uses knowledge of this error distribution; in this sense, we obtain robustness without sacrificing much efficiency. Numerical experiments confirm the practical merits of our proposal.

Uncertainty-Aware Adapter: Adapting Segment Anything Model (SAM) for Ambiguous Medical Image Segmentation

The Segment Anything Model (SAM) gained significant success in natural image segmentation, and many methods have tried to fine-tune it to medical image segmentation. An efficient way to do so is by using Adapters, specialized modules that learn just a few parameters to tailor SAM specifically for medical images. However, unlike natural images, many tissues and lesions in medical images have blurry boundaries and may be ambiguous. Previous efforts to adapt SAM ignore this challenge and can only predict distinct segmentation. It may mislead clinicians or cause misdiagnosis, especially when encountering rare variants or situations with low model confidence. In this work, we propose a novel module called the Uncertainty-aware Adapter, which efficiently fine-tuning SAM for uncertainty-aware medical image segmentation. Utilizing a conditional variational autoencoder, we encoded stochastic samples to effectively represent the inherent uncertainty in medical imaging. We designed a new module on a standard adapter that utilizes a condition-based strategy to interact with samples to help SAM integrate uncertainty. We evaluated our method on two multi-annotated datasets with different modalities: LIDC-IDRI (lung abnormalities segmentation) and REFUGE2 (optic-cup segmentation). The experimental results show that the proposed model outperforms all the previous methods and achieves the new state-of-the-art (SOTA) on both benchmarks. We also demonstrated that our method can generate diverse segmentation hypotheses that are more realistic as well as heterogeneous.

RealNet: A Feature Selection Network with Realistic Synthetic Anomaly for Anomaly Detection

Self-supervised feature reconstruction methods have shown promising advances in industrial image anomaly detection and localization. Despite this progress, these methods still face challenges in synthesizing realistic and diverse anomaly samples, as well as addressing the feature redundancy and pre-training bias of pre-trained feature. In this work, we introduce RealNet, a feature reconstruction network with realistic synthetic anomaly and adaptive feature selection. It is incorporated with three key innovations: First, we propose Strength-controllable Diffusion Anomaly Synthesis (SDAS), a diffusion process-based synthesis strategy capable of generating samples with varying anomaly strengths that mimic the distribution of real anomalous samples. Second, we develop Anomaly-aware Features Selection (AFS), a method for selecting representative and discriminative pre-trained feature subsets to improve anomaly detection performance while controlling computational costs. Third, we introduce Reconstruction Residuals Selection (RRS), a strategy that adaptively selects discriminative residuals for comprehensive identification of anomalous regions across multiple levels of granularity. We assess RealNet on four benchmark datasets, and our results demonstrate significant improvements in both Image AUROC and Pixel AUROC compared to the current state-o-the-art methods. The code, data, and models are available at https://github.com/cnulab/RealNet.

Not just Birds and Cars: Generic, Scalable and Explainable Models for Professional Visual Recognition

Some visual recognition tasks are more challenging then the general ones as they require professional categories of images. The previous efforts, like fine-grained vision classification, primarily introduced models tailored to specific tasks, like identifying bird species or car brands with limited scalability and generalizability. This paper aims to design a scalable and explainable model to solve Professional Visual Recognition tasks from a generic standpoint. We introduce a biologically-inspired structure named Pro-NeXt and reveal that Pro-NeXt exhibits substantial generalizability across diverse professional fields such as fashion, medicine, and art-areas previously considered disparate. Our basic-sized Pro-NeXt-B surpasses all preceding task-specific models across 12 distinct datasets within 5 diverse domains. Furthermore, we find its good scaling property that scaling up Pro-NeXt in depth and width with increasing GFlops can consistently enhances its accuracy. Beyond scalability and adaptability, the intermediate features of Pro-NeXt achieve reliable object detection and segmentation performance without extra training, highlighting its solid explainability. We will release the code to foster further research in this area.

A Privacy-Preserving Framework with Multi-Modal Data for Cross-Domain Recommendation

Cross-domain recommendation (CDR) aims to enhance recommendation accuracy in a target domain with sparse data by leveraging rich information in a source domain, thereby addressing the data-sparsity problem. Some existing CDR methods highlight the advantages of extracting domain-common and domain-specific features to learn comprehensive user and item representations. However, these methods can't effectively disentangle these components as they often rely on simple user-item historical interaction information (such as ratings, clicks, and browsing), neglecting the rich multi-modal features. Additionally, they don't protect user-sensitive data from potential leakage during knowledge transfer between domains. To address these challenges, we propose a Privacy-Preserving Framework with Multi-Modal Data for Cross-Domain Recommendation, called P2M2-CDR. Specifically, we first design a multi-modal disentangled encoder that utilizes multi-modal information to disentangle more informative domain-common and domain-specific embeddings. Furthermore, we introduce a privacy-preserving decoder to mitigate user privacy leakage during knowledge transfer. Local differential privacy (LDP) is utilized to obfuscate the disentangled embeddings before inter-domain exchange, thereby enhancing privacy protection. To ensure both consistency and differentiation among these obfuscated disentangled embeddings, we incorporate contrastive learning-based domain-inter and domain-intra losses. Extensive Experiments conducted on four real-world datasets demonstrate that P2M2-CDR outperforms other state-of-the-art single-domain and cross-domain baselines.

Causal Disentanglement for Regulating Social Influence Bias in Social Recommendation

Social recommendation systems face the problem of social influence bias, which can lead to an overemphasis on recommending items that friends have interacted with. Addressing this problem is crucial, and existing methods often rely on techniques such as weight adjustment or leveraging unbiased data to eliminate this bias. However, we argue that not all biases are detrimental, i.e., some items recommended by friends may align with the user's interests. Blindly eliminating such biases could undermine these positive effects, potentially diminishing recommendation accuracy. In this paper, we propose a Causal Disentanglement-based framework for Regulating Social influence Bias in social recommendation, named CDRSB, to improve recommendation performance. From the perspective of causal inference, we find that the user social network could be regarded as a confounder between the user and item embeddings (treatment) and ratings (outcome). Due to the presence of this social network confounder, two paths exist from user and item embeddings to ratings: a non-causal social influence path and a causal interest path. Building upon this insight, we propose a disentangled encoder that focuses on disentangling user and item embeddings into interest and social influence embeddings. Mutual information-based objectives are designed to enhance the distinctiveness of these disentangled embeddings, eliminating redundant information. Additionally, a regulatory decoder that employs a weight calculation module to dynamically learn the weights of social influence embeddings for effectively regulating social influence bias has been designed. Experimental results on four large-scale real-world datasets Ciao, Epinions, Dianping, and Douban book demonstrate the effectiveness of CDRSB compared to state-of-the-art baselines.

Enhancing Weakly Supervised 3D Medical Image Segmentation through Probabilistic-aware Learning

3D medical image segmentation is a challenging task with crucial implications for disease diagnosis and treatment planning. Recent advances in deep learning have significantly enhanced fully supervised medical image segmentation. However, this approach heavily relies on labor-intensive and time-consuming fully annotated ground-truth labels, particularly for 3D volumes. To overcome this limitation, we propose a novel probabilistic-aware weakly supervised learning pipeline, specifically designed for 3D medical imaging. Our pipeline integrates three innovative components: a probability-based pseudo-label generation technique for synthesizing dense segmentation masks from sparse annotations, a Probabilistic Multi-head Self-Attention network for robust feature extraction within our Probabilistic Transformer Network, and a Probability-informed Segmentation Loss Function to enhance training with annotation confidence. Demonstrating significant advances, our approach not only rivals the performance of fully supervised methods but also surpasses existing weakly supervised methods in CT and MRI datasets, achieving up to 18.1% improvement in Dice scores for certain organs. The code is available at https://github.com/runminjiang/PW4MedSeg.