Temporal knowledge graph (TKG) reasoning that infers future missing facts is an essential and challenging task. Predicting future events typically relies on closely related historical facts, yielding more accurate results for repetitive or periodic events. However, for future events with sparse historical interactions, the effectiveness of this method, which focuses on leveraging high-frequency historical information, diminishes. Recently, the capabilities of diffusion models in image generation have opened new opportunities for TKG reasoning. Therefore, we propose a graph node diffusion model with dual-domain periodic contrastive learning (DPCL-Diff). Graph node diffusion model (GNDiff) introduces noise into sparsely related events to simulate new events, generating high-quality data that better conforms to the actual distribution. This generative mechanism significantly enhances the model's ability to reason about new events. Additionally, the dual-domain periodic contrastive learning (DPCL) maps periodic and non-periodic event entities to Poincar\'e and Euclidean spaces, leveraging their characteristics to distinguish similar periodic events effectively. Experimental results on four public datasets demonstrate that DPCL-Diff significantly outperforms state-of-the-art TKG models in event prediction, demonstrating our approach's effectiveness. This study also investigates the combined effectiveness of GNDiff and DPCL in TKG tasks.
Rating is a typical user explicit feedback that visually reflects how much a user likes a related item. The (rating) matrix completion is essentially a rating prediction process, which is also a significant problem in recommender systems. Recently, graph neural networks (GNNs) have been widely used in matrix completion, which captures users' preferences over items by formulating a rating matrix as a bipartite graph. However, existing methods are susceptible due to data sparsity and long-tail distribution in real-world scenarios. Moreover, the messaging mechanism of GNNs makes it difficult to capture high-order correlations and constraints between nodes, which are essentially useful in recommendation tasks. To tackle these challenges, we propose a Multi-Channel Hypergraph Contrastive Learning framework for matrix completion, named MHCL. Specifically, MHCL adaptively learns hypergraph structures to capture high-order correlations between nodes and jointly captures local and global collaborative relationships through attention-based cross-view aggregation. Additionally, to consider the magnitude and order information of ratings, we treat different rating subgraphs as different channels, encourage alignment between adjacent ratings, and further achieve the mutual enhancement between different ratings through multi-channel cross-rating contrastive learning. Extensive experiments on five public datasets demonstrate that the proposed method significantly outperforms the current state-of-the-art approaches.
The message-passing mechanism of graph convolutional networks (i.e., GCNs) enables label information to be propagated to a broader range of neighbors, thereby increasing the utilization of labels. However, the label information is not always effectively utilized in the traditional GCN framework. To address this issue, we propose a new two-step framework called ELU-GCN. In the first stage, ELU-GCN conducts graph learning to learn a new graph structure (i.e., ELU-graph), which enables the message passing can effectively utilize label information. In the second stage, we design a new graph contrastive learning on the GCN framework for representation learning by exploring the consistency and mutually exclusive information between the learned ELU graph and the original graph. Moreover, we theoretically demonstrate that the proposed method can ensure the generalization ability of GCNs. Extensive experiments validate the superiority of our method.
Brain networks/graphs derived from resting-state functional MRI (fMRI) help study underlying pathophysiology of neurocognitive disorders by measuring neuronal activities in the brain. Some studies utilize learning-based methods for brain network analysis, but typically suffer from low model generalizability caused by scarce labeled fMRI data. As a notable self-supervised strategy, graph contrastive learning helps leverage auxiliary unlabeled data. But existing methods generally arbitrarily perturb graph nodes/edges to generate augmented graphs, without considering essential topology information of brain networks. To this end, we propose a topology-aware graph augmentation (TGA) framework, comprising a pretext model to train a generalizable encoder on large-scale unlabeled fMRI cohorts and a task-specific model to perform downstream tasks on a small target dataset. In the pretext model, we design two novel topology-aware graph augmentation strategies: (1) hub-preserving node dropping that prioritizes preserving brain hub regions according to node importance, and (2) weight-dependent edge removing that focuses on keeping important functional connectivities based on edge weights. Experiments on 1, 688 fMRI scans suggest that TGA outperforms several state-of-the-art methods.
Despite the promising performance of convolutional neural networks (CNNs) in brain tumor diagnosis from magnetic resonance imaging (MRI), their integration into the clinical workflow has been limited. That is mainly due to the fact that the features contributing to a model's prediction are unclear to radiologists and hence, clinically irrelevant, i.e., lack of explainability. As the invaluable sources of radiologists' knowledge and expertise, radiology reports can be integrated with MRI in a contrastive learning (CL) framework, enabling learning from image-report associations, to improve CNN explainability. In this work, we train a multimodal CL architecture on 3D brain MRI scans and radiology reports to learn informative MRI representations. Furthermore, we integrate tumor location, salient to several brain tumor analysis tasks, into this framework to improve its generalizability. We then apply the learnt image representations to improve explainability and performance of genetic marker classification of pediatric Low-grade Glioma, the most prevalent brain tumor in children, as a downstream task. Our results indicate a Dice score of 31.1% between the model's attention maps and manual tumor segmentation (as an explainability measure) with test classification performance of 87.7%, significantly outperforming the baselines. These enhancements can build trust in our model among radiologists, facilitating its integration into clinical practices for more efficient tumor diagnosis.
Detecting genetic aberrations is crucial in cancer diagnosis, typically through fluorescence in situ hybridization (FISH). However, existing FISH image classification methods face challenges due to signal variability, the need for costly manual annotations and fail to adequately address the intrinsic uncertainty. We introduce a novel approach that leverages synthetic images to eliminate the requirement for manual annotations and utilizes a joint contrastive and classification objective for training to account for inter-class variation effectively. We demonstrate the superior generalization capabilities and uncertainty calibration of our method, which is trained on synthetic data, by testing it on a manually annotated dataset of real-world FISH images. Our model offers superior calibration in terms of classification accuracy and uncertainty quantification with a classification accuracy of 96.7% among the 50% most certain cases. The presented end-to-end method reduces the demands on personnel and time and improves the diagnostic workflow due to its accuracy and adaptability. All code and data is publicly accessible at: https://github.com/SimonBon/FISHing
Federated continual learning (FCL) aims to learn from sequential data stream in the decentralized federated learning setting, while simultaneously mitigating the catastrophic forgetting issue in classical continual learning. Existing FCL methods usually employ typical rehearsal mechanisms, which could result in privacy violations or additional onerous storage and computational burdens. In this work, an efficient and non-IID robust federated continual learning framework, called Federated Prototype-Augmented Prompt Learning (FPPL), is proposed. The FPPL can collaboratively learn lightweight prompts augmented by prototypes without rehearsal. On the client side, a fusion function is employed to fully leverage the knowledge contained in task-specific prompts for alleviating catastrophic forgetting. Additionally, global prototypes aggregated from the server are used to obtain unified representation through contrastive learning, mitigating the impact of non-IID-derived data heterogeneity. On the server side, locally uploaded prototypes are utilized to perform debiasing on the classifier, further alleviating the performance degradation caused by both non-IID and catastrophic forgetting. Empirical evaluations demonstrate the effectiveness of FPPL, achieving notable performance with an efficient design while remaining robust to diverse non-IID degrees. Code is available at: https://github.com/ycheoo/FPPL.
Current volumetric biomedical foundation models struggle to generalize as public 3D datasets are small and do not cover the broad diversity of medical procedures, conditions, anatomical regions, and imaging protocols. We address this by creating a representation learning method that instead anticipates strong domain shifts at training time itself. We first propose a data engine that synthesizes highly variable training samples that enable generalization to new biomedical contexts. To then train a single 3D network for any voxel-level task, we develop a contrastive learning method that pretrains the network to be stable against nuisance imaging variation simulated by the data engine, a key inductive bias for generalization. This network's features can be used as robust representations of input images for downstream tasks and its weights provide a strong, dataset-agnostic initialization for finetuning on new datasets. As a result, we set new standards across both multimodality registration and few-shot segmentation, a first for any 3D biomedical vision model, all without (pre-)training on any existing dataset of real images.
The conventional targeted adversarial attacks add a small perturbation to an image to make neural network models estimate the image as a predefined target class, even if it is not the correct target class. Recently, for visual-language models (VLMs), the focus of targeted adversarial attacks is to generate a perturbation that makes VLMs answer intended target text outputs. For example, they aim to make a small perturbation on an image to make VLMs' answers change from "there is an apple" to "there is a baseball." However, answering just intended text outputs is insufficient for tricky questions like "if there is a baseball, tell me what is below it." This is because the target of the adversarial attacks does not consider the overall integrity of the original image, thereby leading to a lack of visual reasoning. In this work, we focus on generating targeted adversarial examples with visual reasoning against VLMs. To this end, we propose 1) a novel adversarial attack procedure -- namely, Replace-then-Perturb and 2) a contrastive learning-based adversarial loss -- namely, Contrastive-Adv. In Replace-then-Perturb, we first leverage a text-guided segmentation model to find the target object in the image. Then, we get rid of the target object and inpaint the empty space with the desired prompt. By doing this, we can generate a target image corresponding to the desired prompt, while maintaining the overall integrity of the original image. Furthermore, in Contrastive-Adv, we design a novel loss function to obtain better adversarial examples. Our extensive benchmark results demonstrate that Replace-then-Perturb and Contrastive-Adv outperform the baseline adversarial attack algorithms. We note that the source code to reproduce the results will be available.
Temporal Heterogeneous Networks play a crucial role in capturing the dynamics and heterogeneity inherent in various real-world complex systems, rendering them a noteworthy research avenue for link prediction. However, existing methods fail to capture the fine-grained differential distribution patterns and temporal dynamic characteristics, which we refer to as spatial heterogeneity and temporal heterogeneity. To overcome such limitations, we propose a novel \textbf{C}ontrastive Learning-based \textbf{L}ink \textbf{P}rediction model, \textbf{CLP}, which employs a multi-view hierarchical self-supervised architecture to encode spatial and temporal heterogeneity. Specifically, aiming at spatial heterogeneity, we develop a spatial feature modeling layer to capture the fine-grained topological distribution patterns from node- and edge-level representations, respectively. Furthermore, aiming at temporal heterogeneity, we devise a temporal information modeling layer to perceive the evolutionary dependencies of dynamic graph topologies from time-level representations. Finally, we encode the spatial and temporal distribution heterogeneity from a contrastive learning perspective, enabling a comprehensive self-supervised hierarchical relation modeling for the link prediction task. Extensive experiments conducted on four real-world dynamic heterogeneous network datasets verify that our \mymodel consistently outperforms the state-of-the-art models, demonstrating an average improvement of 10.10\%, 13.44\% in terms of AUC and AP, respectively.
In real-world applications, the success of completing a task is often determined by multiple key steps which are distant in time steps and have to be achieved in a fixed time order. For example, the key steps listed on the cooking recipe should be achieved one-by-one in the right time order. These key steps can be regarded as subgoals of the task and their time orderings are described as temporal ordering constraints. However, in many real-world problems, subgoals or key states are often hidden in the state space and their temporal ordering constraints are also unknown, which make it challenging for previous RL algorithms to solve this kind of tasks. In order to address this issue, in this work we propose a novel RL algorithm for {\bf l}earning hidden {\bf s}ubgoals under {\bf t}emporal {\bf o}rdering {\bf c}onstraints (LSTOC). We propose a new contrastive learning objective which can effectively learn hidden subgoals (key states) and their temporal orderings at the same time, based on first-occupancy representation and temporal geometric sampling. In addition, we propose a sample-efficient learning strategy to discover subgoals one-by-one following their temporal order constraints by building a subgoal tree to represent discovered subgoals and their temporal ordering relationships. Specifically, this tree can be used to improve the sample efficiency of trajectory collection, fasten the task solving and generalize to unseen tasks. The LSTOC framework is evaluated on several environments with image-based observations, showing its significant improvement over baseline methods.
A crucial question in active patient care is determining if a treatment is having the desired effect, especially when changes are subtle over short periods. We propose using inter-patient data to train models that can learn to detect these fine-grained changes within a single patient. Specifically, can a model trained on multi-patient scans predict subtle changes in an individual patient's scans? Recent years have seen increasing use of deep learning (DL) in predicting diseases using biomedical imaging, such as predicting COVID-19 severity using lung ultrasound (LUS) data. While extensive literature exists on successful applications of DL systems when well-annotated large-scale datasets are available, it is quite difficult to collect a large corpus of personalized datasets for an individual. In this work, we investigate the ability of recent computer vision models to learn fine-grained differences while being trained on data showing larger differences. We evaluate on an in-house LUS dataset and a public ADNI brain MRI dataset. We find that models pre-trained on clips from multiple patients can better predict fine-grained differences in scans from a single patient by employing contrastive learning.
Contrastive learning methods, such as CLIP, leverage naturally paired data-for example, images and their corresponding text captions-to learn general representations that transfer efficiently to downstream tasks. While such approaches are generally applied to two modalities, domains such as robotics, healthcare, and video need to support many types of data at once. We show that the pairwise application of CLIP fails to capture joint information between modalities, thereby limiting the quality of the learned representations. To address this issue, we present Symile, a simple contrastive learning approach that captures higher-order information between any number of modalities. Symile provides a flexible, architecture-agnostic objective for learning modality-specific representations. To develop Symile's objective, we derive a lower bound on total correlation, and show that Symile representations for any set of modalities form a sufficient statistic for predicting the remaining modalities. Symile outperforms pairwise CLIP, even with modalities missing in the data, on cross-modal classification and retrieval across several experiments including on an original multilingual dataset of 33M image, text and audio samples and a clinical dataset of chest X-rays, electrocardiograms, and laboratory measurements. All datasets and code used in this work are publicly available at https://github.com/rajesh-lab/symile.
Point cloud registration, a fundamental task in 3D vision, has achieved remarkable success with learning-based methods in outdoor environments. Unsupervised outdoor point cloud registration methods have recently emerged to circumvent the need for costly pose annotations. However, they fail to establish reliable optimization objectives for unsupervised training, either relying on overly strong geometric assumptions, or suffering from poor-quality pseudo-labels due to inadequate integration of low-level geometric and high-level contextual information. We have observed that in the feature space, latent new inlier correspondences tend to cluster around respective positive anchors that summarize features of existing inliers. Motivated by this observation, we propose a novel unsupervised registration method termed INTEGER to incorporate high-level contextual information for reliable pseudo-label mining. Specifically, we propose the Feature-Geometry Coherence Mining module to dynamically adapt the teacher for each mini-batch of data during training and discover reliable pseudo-labels by considering both high-level feature representations and low-level geometric cues. Furthermore, we propose Anchor-Based Contrastive Learning to facilitate contrastive learning with anchors for a robust feature space. Lastly, we introduce a Mixed-Density Student to learn density-invariant features, addressing challenges related to density variation and low overlap in the outdoor scenario. Extensive experiments on KITTI and nuScenes datasets demonstrate that our INTEGER achieves competitive performance in terms of accuracy and generalizability.
Current mainstream SAR image object detection methods still lack robustness when dealing with unknown objects in open environments. Open-set detection aims to enable detectors trained on a closed set to detect all known objects and identify unknown objects in open-set environments. The key challenges are how to improve the generalization to potential unknown objects and reduce the empirical classification risk of known categories under strong supervision. To address these challenges, a novel open-set aircraft detector for SAR images is proposed, named Open-Set Aircraft Detection (OSAD), which is equipped with three dedicated components: global context modeling (GCM), location quality-driven pseudo labeling generation (LPG), and prototype contrastive learning (PCL). GCM effectively enhances the network's representation of objects by attention maps which is formed through the capture of long sequential positional relationships. LPG leverages clues about object positions and shapes to optimize localization quality, avoiding overfitting to known category information and enhancing generalization to potential unknown objects. PCL employs prototype-based contrastive encoding loss to promote instance-level intra-class compactness and inter-class variance, aiming to minimize the overlap between known and unknown distributions and reduce the empirical classification risk of known categories. Extensive experiments have demonstrated that the proposed method can effectively detect unknown objects and exhibit competitive performance without compromising closed-set performance. The highest absolute gain which ranges from 0 to 18.36% can be achieved on the average precision of unknown objects.
Cross-modal text-molecule retrieval model aims to learn a shared feature space of the text and molecule modalities for accurate similarity calculation, which facilitates the rapid screening of molecules with specific properties and activities in drug design. However, previous works have two main defects. First, they are inadequate in capturing modality-shared features considering the significant gap between text sequences and molecule graphs. Second, they mainly rely on contrastive learning and adversarial training for cross-modality alignment, both of which mainly focus on the first-order similarity, ignoring the second-order similarity that can capture more structural information in the embedding space. To address these issues, we propose a novel cross-modal text-molecule retrieval model with two-fold improvements. Specifically, on the top of two modality-specific encoders, we stack a memory bank based feature projector that contain learnable memory vectors to extract modality-shared features better. More importantly, during the model training, we calculate four kinds of similarity distributions (text-to-text, text-to-molecule, molecule-to-molecule, and molecule-to-text similarity distributions) for each instance, and then minimize the distance between these similarity distributions (namely second-order similarity losses) to enhance cross-modal alignment. Experimental results and analysis strongly demonstrate the effectiveness of our model. Particularly, our model achieves SOTA performance, outperforming the previously-reported best result by 6.4%.
Material discovery is a critical research area with profound implications for various industries. In this work, we introduce MatExpert, a novel framework that leverages Large Language Models (LLMs) and contrastive learning to accelerate the discovery and design of new solid-state materials. Inspired by the workflow of human materials design experts, our approach integrates three key stages: retrieval, transition, and generation. First, in the retrieval stage, MatExpert identifies an existing material that closely matches the desired criteria. Second, in the transition stage, MatExpert outlines the necessary modifications to transform this material formulation to meet specific requirements outlined by the initial user query. Third, in the generation state, MatExpert performs detailed computations and structural generation to create new materials based on the provided information. Our experimental results demonstrate that MatExpert outperforms state-of-the-art methods in material generation tasks, achieving superior performance across various metrics including validity, distribution, and stability. As such, MatExpert represents a meaningful advancement in computational material discovery using langauge-based generative models.
State-of-the-art models for relation extraction (RE) in the biomedical domain consider finetuning BioBERT using classification, but they may suffer from the anisotropy problem. Contrastive learning methods can reduce this anisotropy phenomena, and also help to avoid class collapse in any classification problem. In the present paper, a new training method called biological non-contrastive relation extraction (BioNCERE) is introduced for relation extraction without using any named entity labels for training to reduce annotation costs. BioNCERE uses transfer learning and non-contrastive learning to avoid full or dimensional collapse as well as bypass overfitting. It resolves RE in three stages by leveraging transfer learning two times. By freezing the weights learned in previous stages in the proposed pipeline and by leveraging non-contrastive learning in the second stage, the model predicts relations without any knowledge of named entities. Experiments have been done on SemMedDB that are almost similar to State-of-the-art performance on RE without using the information of named entities.
This work introduces JEMA (Joint Embedding with Multimodal Alignment), a novel co-learning framework tailored for laser metal deposition (LMD), a pivotal process in metal additive manufacturing. As Industry 5.0 gains traction in industrial applications, efficient process monitoring becomes increasingly crucial. However, limited data and the opaque nature of AI present challenges for its application in an industrial setting. JEMA addresses this challenges by leveraging multimodal data, including multi-view images and metadata such as process parameters, to learn transferable semantic representations. By applying a supervised contrastive loss function, JEMA enables robust learning and subsequent process monitoring using only the primary modality, simplifying hardware requirements and computational overhead. We investigate the effectiveness of JEMA in LMD process monitoring, focusing specifically on its generalization to downstream tasks such as melt pool geometry prediction, achieved without extensive fine-tuning. Our empirical evaluation demonstrates the high scalability and performance of JEMA, particularly when combined with Vision Transformer models. We report an 8% increase in performance in multimodal settings and a 1% improvement in unimodal settings compared to supervised contrastive learning. Additionally, the learned embedding representation enables the prediction of metadata, enhancing interpretability and making possible the assessment of the added metadata's contributions. Our framework lays the foundation for integrating multisensor data with metadata, enabling diverse downstream tasks within the LMD domain and beyond.
Foundation models have recently gained significant attention because of their generalizability and adaptability across multiple tasks and data distributions. Although medical foundation models have emerged, solutions for cardiac imaging, especially echocardiography videos, are still unexplored. In this paper, we introduce EchoFM, a foundation model specifically designed to represent and analyze echocardiography videos. In EchoFM, we propose a self-supervised learning framework that captures both spatial and temporal variability patterns through a spatio-temporal consistent masking strategy and periodic-driven contrastive learning. This framework can effectively capture the spatio-temporal dynamics of echocardiography and learn the representative video features without any labels. We pre-train our model on an extensive dataset comprising over 290,000 echocardiography videos covering 26 scan views across different imaging modes, with up to 20 million frames of images. The pre-trained EchoFM can then be easily adapted and fine-tuned for a variety of downstream tasks, serving as a robust backbone model. Our evaluation was systemically designed for four downstream tasks after the echocardiography examination routine. Experiment results show that EchoFM surpasses state-of-the-art methods, including specialized echocardiography methods, self-supervised pre-training models, and general-purposed pre-trained foundation models, across all downstream tasks.