We introduce DynaCLR, a self-supervised framework for modeling cell dynamics via contrastive learning of representations of time-lapse datasets. Live cell imaging of cells and organelles is widely used to analyze cellular responses to perturbations. Human annotation of dynamic cell states captured by time-lapse perturbation datasets is laborious and prone to bias. DynaCLR integrates single-cell tracking with time-aware contrastive learning to map images of cells at neighboring time points to neighboring embeddings. Mapping the morphological dynamics of cells to a temporally regularized embedding space makes the annotation, classification, clustering, or interpretation of the cell states more quantitative and efficient. We illustrate the features and applications of DynaCLR with the following experiments: analyzing the kinetics of viral infection in human cells, detecting transient changes in cell morphology due to cell division, and mapping the dynamics of organelles due to viral infection. Models trained with DynaCLR consistently achieve $>95\%$ accuracy for infection state classification, enable the detection of transient cell states and reliably embed unseen experiments. DynaCLR provides a flexible framework for comparative analysis of cell state dynamics due to perturbations, such as infection, gene knockouts, and drugs. We provide PyTorch-based implementations of the model training and inference pipeline (https://github.com/mehta-lab/viscy) and a user interface (https://github.com/czbiohub-sf/napari-iohub) for the visualization and annotation of trajectories of cells in the real space and the embedding space.
Using foundation models enhanced by self-supervised learning (SSL) methods presents an innovative approach to electrocardiogram (ECG) analysis, which is crucial for cardiac health monitoring and diagnosis. This study comprehensively evaluates foundation models for ECGs, leveraging SSL methods, including generative and contrastive learning, on a vast dataset comprising approximately 1.3 million ECG samples. By integrating these methods with consideration of the unique characteristics of ECGs, we developed a Hybrid Learning (HL) for foundation models that improve the precision and reliability of cardiac diagnostics. The HL-based foundation model adeptly captures the intricate details of ECGs, enhancing diagnostic capability. The results underscore the considerable potential of SSL-enhanced foundation models in clinical settings, setting the stage for future research into their scalable applications across a broader range of medical diagnostics. This work sets a new standard in the ECG field, emphasizing the transformative influence of tailored, data-driven model training on the effectiveness and accuracy of medical diagnostics.
Contrastive learning (CL) has emerged as a promising approach for representation learning in time series data by embedding similar pairs closely while distancing dissimilar ones. However, existing CL methods often introduce false negative pairs (FNPs) by neglecting inherent characteristics and then randomly selecting distinct segments as dissimilar pairs, leading to erroneous representation learning, reduced model performance, and overall inefficiency. To address these issues, we systematically define and categorize FNPs in time series into semantic false negative pairs and temporal false negative pairs for the first time: the former arising from overlooking similarities in label categories, which correlates with similarities in non-stationarity and the latter from neglecting temporal proximity. Moreover, we introduce StatioCL, a novel CL framework that captures non-stationarity and temporal dependency to mitigate both FNPs and rectify the inaccuracies in learned representations. By interpreting and differentiating non-stationary states, which reflect the correlation between trends or temporal dynamics with underlying data patterns, StatioCL effectively captures the semantic characteristics and eliminates semantic FNPs. Simultaneously, StatioCL establishes fine-grained similarity levels based on temporal dependencies to capture varying temporal proximity between segments and to mitigate temporal FNPs. Evaluated on real-world benchmark time series classification datasets, StatioCL demonstrates a substantial improvement over state-of-the-art CL methods, achieving a 2.9% increase in Recall and a 19.2% reduction in FNPs. Most importantly, StatioCL also shows enhanced data efficiency and robustness against label scarcity.
Recently, federated multi-view clustering (FedMVC) has emerged to explore cluster structures in multi-view data distributed on multiple clients. Existing approaches often assume that clients are isomorphic and all of them belong to either single-view clients or multi-view clients. Despite their success, these methods also present limitations when dealing with practical FedMVC scenarios involving heterogeneous hybrid views, where a mixture of both single-view and multi-view clients exhibit varying degrees of heterogeneity. In this paper, we propose a novel FedMVC framework, which concurrently addresses two challenges associated with heterogeneous hybrid views, i.e., client gap and view gap. To address the client gap, we design a local-synergistic contrastive learning approach that helps single-view clients and multi-view clients achieve consistency for mitigating heterogeneity among all clients. To address the view gap, we develop a global-specific weighting aggregation method, which encourages global models to learn complementary features from hybrid views. The interplay between local-synergistic contrastive learning and global-specific weighting aggregation mutually enhances the exploration of the data cluster structures distributed on multiple clients. Theoretical analysis and extensive experiments demonstrate that our method can handle the heterogeneous hybrid views in FedMVC and outperforms state-of-the-art methods. The code is available at \url{https://github.com/5Martina5/FMCSC}.
Cells in multicellular organisms coordinate to form functional and structural niches. With spatial transcriptomics enabling gene expression profiling in spatial contexts, it has been revealed that spatial niches serve as cohesive and recurrent units in physiological and pathological processes. These observations suggest universal tissue organization principles encoded by conserved niche patterns, and call for a query-based niche analytical paradigm beyond current computational tools. In this work, we defined the Niche Query Task, which is to identify similar niches across ST samples given a niche of interest (NOI). We further developed QueST, a specialized method for solving this task. QueST models each niche as a subgraph, uses contrastive learning to learn discriminative niche embeddings, and incorporates adversarial training to mitigate batch effects. In simulations and benchmark datasets, QueST outperformed existing methods repurposed for niche querying, accurately capturing niche structures in heterogeneous environments and demonstrating strong generalizability across diverse sequencing platforms. Applied to tertiary lymphoid structures in renal and lung cancers, QueST revealed functionally distinct niches associated with patient prognosis and uncovered conserved and divergent spatial architectures across cancer types. These results demonstrate that QueST enables systematic, quantitative profiling of spatial niches across samples, providing a powerful tool to dissect spatial tissue architecture in health and disease.
Image style transfer has attracted widespread attention in the past few years. Despite its remarkable results, it requires additional style images available as references, making it less flexible and inconvenient. Using text is the most natural way to describe the style. More importantly, text can describe implicit abstract styles, like styles of specific artists or art movements. In this paper, we propose a Contrastive Learning for Artistic Style Transfer (CLAST) that leverages advanced image-text encoders to control arbitrary style transfer. We introduce a supervised contrastive training strategy to effectively extract style descriptions from the image-text model (i.e., CLIP), which aligns stylization with the text description. To this end, we also propose a novel and efficient adaLN based state space models that explore style-content fusion. Finally, we achieve a text-driven image style transfer. Extensive experiments demonstrate that our approach outperforms the state-of-the-art methods in artistic style transfer. More importantly, it does not require online fine-tuning and can render a 512x512 image in 0.03s.
Person re-identification(ReID), as a crucial technology in the field of security, plays a vital role in safety inspections, personnel counting, and more. Most current ReID approaches primarily extract features from images, which are easily affected by objective conditions such as clothing changes and occlusions. In addition to cameras, we leverage widely available routers as sensing devices by capturing gait information from pedestrians through the Channel State Information (CSI) in WiFi signals and contribute a multimodal dataset. We employ a two-stream network to separately process video understanding and signal analysis tasks, and conduct multi-modal fusion and contrastive learning on pedestrian video and WiFi data. Extensive experiments in real-world scenarios demonstrate that our method effectively uncovers the correlations between heterogeneous data, bridges the gap between visual and signal modalities, significantly expands the sensing range, and improves ReID accuracy across multiple sensors.
Echocardiography is the most widely used cardiac imaging modality, capturing ultrasound video data to assess cardiac structure and function. Artificial intelligence (AI) in echocardiography has the potential to streamline manual tasks and improve reproducibility and precision. However, most echocardiography AI models are single-view, single-task systems that do not synthesize complementary information from multiple views captured during a full exam, and thus lead to limited performance and scope of applications. To address this problem, we introduce EchoPrime, a multi-view, view-informed, video-based vision-language foundation model trained on over 12 million video-report pairs. EchoPrime uses contrastive learning to train a unified embedding model for all standard views in a comprehensive echocardiogram study with representation of both rare and common diseases and diagnoses. EchoPrime then utilizes view-classification and a view-informed anatomic attention model to weight video-specific interpretations that accurately maps the relationship between echocardiographic views and anatomical structures. With retrieval-augmented interpretation, EchoPrime integrates information from all echocardiogram videos in a comprehensive study and performs holistic comprehensive clinical echocardiography interpretation. In datasets from two independent healthcare systems, EchoPrime achieves state-of-the art performance on 23 diverse benchmarks of cardiac form and function, surpassing the performance of both task-specific approaches and prior foundation models. Following rigorous clinical evaluation, EchoPrime can assist physicians in the automated preliminary assessment of comprehensive echocardiography.
Self-supervised pre-training has achieved remarkable success in NLP and 2D vision. However, these advances have yet to translate to 3D data. Techniques like masked reconstruction face inherent challenges on unstructured point clouds, while many contrastive learning tasks lack in complexity and informative value. In this paper, we present Pic@Point, an effective contrastive learning method based on structural 2D-3D correspondences. We leverage image cues rich in semantic and contextual knowledge to provide a guiding signal for point cloud representations at various abstraction levels. Our lightweight approach outperforms state-of-the-art pre-training methods on several 3D benchmarks.
Long-term Video Question Answering (VideoQA) is a challenging vision-and-language bridging task focusing on semantic understanding of untrimmed long-term videos and diverse free-form questions, simultaneously emphasizing comprehensive cross-modal reasoning to yield precise answers. The canonical approaches often rely on off-the-shelf feature extractors to detour the expensive computation overhead, but often result in domain-independent modality-unrelated representations. Furthermore, the inherent gradient blocking between unimodal comprehension and cross-modal interaction hinders reliable answer generation. In contrast, recent emerging successful video-language pre-training models enable cost-effective end-to-end modeling but fall short in domain-specific ratiocination and exhibit disparities in task formulation. Toward this end, we present an entirely end-to-end solution for long-term VideoQA: Multi-granularity Contrastive cross-modal collaborative Generation (MCG) model. To derive discriminative representations possessing high visual concepts, we introduce Joint Unimodal Modeling (JUM) on a clip-bone architecture and leverage Multi-granularity Contrastive Learning (MCL) to harness the intrinsically or explicitly exhibited semantic correspondences. To alleviate the task formulation discrepancy problem, we propose a Cross-modal Collaborative Generation (CCG) module to reformulate VideoQA as a generative task instead of the conventional classification scheme, empowering the model with the capability for cross-modal high-semantic fusion and generation so as to rationalize and answer. Extensive experiments conducted on six publicly available VideoQA datasets underscore the superiority of our proposed method.
On social media sharing platforms, some posts are inherently destined for popularity. Therefore, understanding the reasons behind this phenomenon and predicting popularity before post publication holds significant practical value. The previous work predominantly focuses on enhancing post content extraction for better prediction results. However, certain factors introduced by social platforms also impact post popularity, which has not been extensively studied. For instance, users are more likely to engage with posts from individuals they follow, potentially influencing the popularity of these posts. We term these factors, unrelated to the explicit attractiveness of content, as implicit social factors. Through the analysis of users' post browsing behavior (also validated in public datasets), we propose three implicit social factors related to popularity, including content relevance, user influence similarity, and user identity. To model the proposed social factors, we introduce three supervised contrastive learning tasks. For different task objectives and data types, we assign them to different encoders and control their gradient flows to achieve joint optimization. We also design corresponding sampling and augmentation algorithms to improve the effectiveness of contrastive learning. Extensive experiments on the Social Media Popularity Dataset validate the superiority of our proposed method and also confirm the important role of implicit social factors in popularity prediction. We open source the code at https://github.com/Daisy-zzz/PPCL.git.
Despite the remarkable advancements in Visual Question Answering (VQA), the challenge of mitigating the language bias introduced by textual information remains unresolved. Previous approaches capture language bias from a coarse-grained perspective. However, the finer-grained information within a sentence, such as context and keywords, can result in different biases. Due to the ignorance of fine-grained information, most existing methods fail to sufficiently capture language bias. In this paper, we propose a novel causal intervention training scheme named CIBi to eliminate language bias from a finer-grained perspective. Specifically, we divide the language bias into context bias and keyword bias. We employ causal intervention and contrastive learning to eliminate context bias and improve the multi-modal representation. Additionally, we design a new question-only branch based on counterfactual generation to distill and eliminate keyword bias. Experimental results illustrate that CIBi is applicable to various VQA models, yielding competitive performance.
We introduce GENomic Encoding REpresentation with Language Model (GENEREL), a framework designed to bridge genetic and biomedical knowledge bases. What sets GENEREL apart is its ability to fine-tune language models to infuse biological knowledge behind clinical concepts such as diseases and medications. This fine-tuning enables the model to capture complex biomedical relationships more effectively, enriching the understanding of how genomic data connects to clinical outcomes. By constructing a unified embedding space for biomedical concepts and a wide range of common SNPs from sources such as patient-level data, biomedical knowledge graphs, and GWAS summaries, GENEREL aligns the embeddings of SNPs and clinical concepts through multi-task contrastive learning. This allows the model to adapt to diverse natural language representations of biomedical concepts while bypassing the limitations of traditional code mapping systems across different data sources. Our experiments demonstrate GENEREL's ability to effectively capture the nuanced relationships between SNPs and clinical concepts. GENEREL also emerges to discern the degree of relatedness, potentially allowing for a more refined identification of concepts. This pioneering approach in constructing a unified embedding system for both SNPs and biomedical concepts enhances the potential for data integration and discovery in biomedical research.
The scarcity of annotations poses a significant challenge in medical image analysis. Large-scale pre-training has emerged as a promising label-efficient solution, owing to the utilization of large-scale data, large models, and advanced pre-training techniques. However, its development in medical images remains underexplored. The primary challenge lies in harnessing large-scale unlabeled data and learning high-level semantics without annotations. We observe that 3D medical images exhibit consistent geometric context, i.e., consistent geometric relations between different organs, which leads to a promising way for learning consistent representations. Motivated by this, we introduce a simple-yet-effective Volume Contrast (VoCo) framework to leverage geometric context priors for self-supervision. Given an input volume, we extract base crops from different regions to construct positive and negative pairs for contrastive learning. Then we predict the contextual position of a random crop by contrasting its similarity to the base crops. In this way, VoCo encodes the inherent geometric context into model representations, facilitating high-level semantic learning without annotations. Specifically, we (1) introduce the largest medical pre-training dataset PreCT-160K; (2) investigate scaling laws and propose guidelines for tailoring different model sizes to various medical tasks; (3) build a benchmark encompassing 48 medical tasks. Extensive experiments highlight the superiority of VoCo. Codes at https://github.com/Luffy03/Large-Scale-Medical.
Given the wide adoption of multimodal sensors (e.g., camera, lidar, radar) by autonomous vehicles (AVs), deep analytics to fuse their outputs for a robust perception become imperative. However, existing fusion methods often make two assumptions rarely holding in practice: i) similar data distributions for all inputs and ii) constant availability for all sensors. Because, for example, lidars have various resolutions and failures of radars may occur, such variability often results in significant performance degradation in fusion. To this end, we present tREADi, an adaptive inference system that accommodates the variability of multimodal sensory data and thus enables robust and efficient perception. t-READi identifies variation-sensitive yet structure-specific model parameters; it then adapts only these parameters while keeping the rest intact. t-READi also leverages a cross-modality contrastive learning method to compensate for the loss from missing modalities. Both functions are implemented to maintain compatibility with existing multimodal deep fusion methods. The extensive experiments evidently demonstrate that compared with the status quo approaches, t-READi not only improves the average inference accuracy by more than 6% but also reduces the inference latency by almost 15x with the cost of only 5% extra memory overhead in the worst case under realistic data and modal variations.
Accurate diagnosis of brain abnormalities is greatly enhanced by the inclusion of complementary multi-parametric MRI imaging data. There is significant potential to develop a universal pre-training model that can be quickly adapted for image modalities and various clinical scenarios. However, current models often rely on uni-modal image data, neglecting the cross-modal correlations among different image modalities or struggling to scale up pre-training in the presence of missing modality data. In this paper, we propose BrainMVP, a multi-modal vision pre-training framework for brain image analysis using multi-parametric MRI scans. First, we collect 16,022 brain MRI scans (over 2.4 million images), encompassing eight MRI modalities sourced from a diverse range of centers and devices. Then, a novel pre-training paradigm is proposed for the multi-modal MRI data, addressing the issue of missing modalities and achieving multi-modal information fusion. Cross-modal reconstruction is explored to learn distinctive brain image embeddings and efficient modality fusion capabilities. A modality-wise data distillation module is proposed to extract the essence representation of each MR image modality for both the pre-training and downstream application purposes. Furthermore, we introduce a modality-aware contrastive learning module to enhance the cross-modality association within a study. Extensive experiments on downstream tasks demonstrate superior performance compared to state-of-the-art pre-training methods in the medical domain, with Dice Score improvement of 0.28%-14.47% across six segmentation benchmarks and a consistent accuracy improvement of 0.65%-18.07% in four individual classification tasks.
The combination of semi-supervised learning (SemiSL) and contrastive learning (CL) has been successful in medical image segmentation with limited annotations. However, these works often rely on pretext tasks that lack the specificity required for pixel-level segmentation, and still face overfitting issues due to insufficient supervision signals resulting from too few annotations. Therefore, this paper proposes an affinity-graph-guided semi-supervised contrastive learning framework (Semi-AGCL) by establishing additional affinity-graph-based supervision signals between the student and teacher network, to achieve medical image segmentation with minimal annotations without pretext. The framework first designs an average-patch-entropy-driven inter-patch sampling method, which can provide a robust initial feature space without relying on pretext tasks. Furthermore, the framework designs an affinity-graph-guided loss function, which can improve the quality of the learned representation and the model generalization ability by exploiting the inherent structure of the data, thus mitigating overfitting. Our experiments indicate that with merely 10% of the complete annotation set, our model approaches the accuracy of the fully annotated baseline, manifesting a marginal deviation of only 2.52%. Under the stringent conditions where only 5% of the annotations are employed, our model exhibits a significant enhancement in performance surpassing the second best baseline by 23.09% on the dice metric and achieving an improvement of 26.57% on the notably arduous CRAG and ACDC datasets.
Graph Contrastive Learning (GCL) excels at managing noise and fluctuations in input data, making it popular in various fields (e.g., social networks, and knowledge graphs). Our study finds that the difference in high-frequency information between augmented graphs is greater than that in low-frequency information. However, most existing GCL methods focus mainly on the time domain (low-frequency information) for node feature representations and cannot make good use of high-frequency information to speed up model convergence. Furthermore, existing GCL paradigms optimize graph embedding representations by pulling the distance between positive sample pairs closer and pushing the distance between positive and negative sample pairs farther away, but our theoretical analysis shows that graph contrastive learning benefits from pushing negative pairs farther away rather than pulling positive pairs closer. To solve the above-mentioned problems, we propose a novel spectral GCL framework without positive samples, named SpeGCL. Specifically, to solve the problem that existing GCL methods cannot utilize high-frequency information, SpeGCL uses a Fourier transform to extract high-frequency and low-frequency information of node features, and constructs a contrastive learning mechanism in a Fourier space to obtain better node feature representation. Furthermore, SpeGCL relies entirely on negative samples to refine the graph embedding. We also provide a theoretical justification for the efficacy of using only negative samples in SpeGCL. Extensive experiments on un-supervised learning, transfer learning, and semi-supervised learning have validated the superiority of our SpeGCL framework over the state-of-the-art GCL methods.
Graph autoencoders (GAEs) are self-supervised learning models that can learn meaningful representations of graph-structured data by reconstructing the input graph from a low-dimensional latent space. Over the past few years, GAEs have gained significant attention in academia and industry. In particular, the recent advent of GAEs with masked autoencoding schemes marks a significant advancement in graph self-supervised learning research. While numerous GAEs have been proposed, the underlying mechanisms of GAEs are not well understood, and a comprehensive benchmark for GAEs is still lacking. In this work, we bridge the gap between GAEs and contrastive learning by establishing conceptual and methodological connections. We revisit the GAEs studied in previous works and demonstrate how contrastive learning principles can be applied to GAEs. Motivated by these insights, we introduce lrGAE (left-right GAE), a general and powerful GAE framework that leverages contrastive learning principles to learn meaningful representations. Our proposed lrGAE not only facilitates a deeper understanding of GAEs but also sets a new benchmark for GAEs across diverse graph-based learning tasks. The source code for lrGAE, including the baselines and all the code for reproducing the results, is publicly available at https://github.com/EdisonLeeeee/lrGAE.
Few-shot graph anomaly detection (GAD) has recently garnered increasing attention, which aims to discern anomalous patterns among abundant unlabeled test nodes under the guidance of a limited number of labeled training nodes. Existing few-shot GAD approaches typically adopt meta-training methods trained on richly labeled auxiliary networks to facilitate rapid adaptation to target networks that possess sparse labels. However, these proposed methods often assume that the auxiliary and target networks exist in the same data distributions-an assumption rarely holds in practical settings. This paper explores a more prevalent and complex scenario of cross-domain few-shot GAD, where the goal is to identify anomalies within sparsely labeled target graphs using auxiliary graphs from a related, yet distinct domain. The challenge here is nontrivial owing to inherent data distribution discrepancies between the source and target domains, compounded by the uncertainties of sparse labeling in the target domain. In this paper, we propose a simple and effective framework, termed CDFS-GAD, specifically designed to tackle the aforementioned challenges. CDFS-GAD first introduces a domain-adaptive graph contrastive learning module, which is aimed at enhancing cross-domain feature alignment. Then, a prompt tuning module is further designed to extract domain-specific features tailored to each domain. Moreover, a domain-adaptive hypersphere classification loss is proposed to enhance the discrimination between normal and anomalous instances under minimal supervision, utilizing domain-sensitive norms. Lastly, a self-training strategy is introduced to further refine the predicted scores, enhancing its reliability in few-shot settings. Extensive experiments on twelve real-world cross-domain data pairs demonstrate the effectiveness of the proposed CDFS-GAD framework in comparison to various existing GAD methods.