For the immanent challenge of insufficiently annotated samples in the medical field, semi-supervised medical image segmentation (SSMIS) offers a promising solution. Despite achieving impressive results in delineating primary target areas, most current methodologies struggle to precisely capture the subtle details of boundaries. This deficiency often leads to significant diagnostic inaccuracies. To tackle this issue, we introduce C3S3, a novel semi-supervised segmentation model that synergistically integrates complementary competition and contrastive selection. This design significantly sharpens boundary delineation and enhances overall precision. Specifically, we develop an Outcome-Driven Contrastive Learning module dedicated to refining boundary localization. Additionally, we incorporate a Dynamic Complementary Competition module that leverages two high-performing sub-networks to generate pseudo-labels, thereby further improving segmentation quality. The proposed C3S3 undergoes rigorous validation on two publicly accessible datasets, encompassing the practices of both MRI and CT scans. The results demonstrate that our method achieves superior performance compared to previous cutting-edge competitors. Especially, on the 95HD and ASD metrics, our approach achieves a notable improvement of at least 6%, highlighting the significant advancements. The code is available at https://github.com/Y-TARL/C3S3.
Link prediction is a classical problem in graph analysis with many practical applications. For directed graphs, recently developed deep learning approaches typically analyze node similarities through contrastive learning and aggregate neighborhood information through graph convolutions. In this work, we propose a novel graph neural network (GNN) framework to fuse feature embedding with community information. We theoretically demonstrate that such hybrid features can improve the performance of directed link prediction. To utilize such features efficiently, we also propose an approach to transform input graphs into directed line graphs so that nodes in the transformed graph can aggregate more information during graph convolutions. Experiments on benchmark datasets show that our approach outperforms the state-of-the-art in most cases when 30%, 40%, 50%, and 60% of the connected links are used as training data, respectively.
Recent developments in neural networks have improved deformable image registration (DIR) by amortizing iterative optimization, enabling fast and accurate DIR results. However, learning-based methods often face challenges with limited training data, large deformations, and tend to underperform compared to iterative approaches when label supervision is unavailable. While iterative methods can achieve higher accuracy in such scenarios, they are considerably slower than learning-based methods. To address these limitations, we propose VoxelOpt, a discrete optimization-based DIR framework that combines the strengths of learning-based and iterative methods to achieve a better balance between registration accuracy and runtime. VoxelOpt uses displacement entropy from local cost volumes to measure displacement signal strength at each voxel, which differs from earlier approaches in three key aspects. First, it introduces voxel-wise adaptive message passing, where voxels with lower entropy receives less influence from their neighbors. Second, it employs a multi-level image pyramid with 27-neighbor cost volumes at each level, avoiding exponential complexity growth. Third, it replaces hand-crafted features or contrastive learning with a pretrained foundational segmentation model for feature extraction. In abdominal CT registration, these changes allow VoxelOpt to outperform leading iterative in both efficiency and accuracy, while matching state-of-the-art learning-based methods trained with label supervision. The source code will be available at https://github.com/tinymilky/VoxelOpt
Expert systems often operate in domains characterized by class-imbalanced tabular data, where detecting rare but critical instances is essential for safety and reliability. While conventional approaches, such as cost-sensitive learning, oversampling, and graph neural networks, provide partial solutions, they suffer from drawbacks like overfitting, label noise, and poor generalization in low-density regions. To address these challenges, we propose QCL-MixNet, a novel Quantum-Informed Contrastive Learning framework augmented with k-nearest neighbor (kNN) guided dynamic mixup for robust classification under imbalance. QCL-MixNet integrates three core innovations: (i) a Quantum Entanglement-inspired layer that models complex feature interactions through sinusoidal transformations and gated attention, (ii) a sample-aware mixup strategy that adaptively interpolates feature representations of semantically similar instances to enhance minority class representation, and (iii) a hybrid loss function that unifies focal reweighting, supervised contrastive learning, triplet margin loss, and variance regularization to improve both intra-class compactness and inter-class separability. Extensive experiments on 18 real-world imbalanced datasets (binary and multi-class) demonstrate that QCL-MixNet consistently outperforms 20 state-of-the-art machine learning, deep learning, and GNN-based baselines in macro-F1 and recall, often by substantial margins. Ablation studies further validate the critical role of each architectural component. Our results establish QCL-MixNet as a new benchmark for tabular imbalance handling in expert systems. Theoretical analyses reinforce its expressiveness, generalization, and optimization robustness.
Temporal Betweenness Centrality (TBC) measures how often a node appears on optimal temporal paths, reflecting its importance in temporal networks. However, exact computation is highly expensive, and real-world TBC distributions are extremely imbalanced. The severe imbalance leads learning-based models to overfit to zero-centrality nodes, resulting in inaccurate TBC predictions and failure to identify truly central nodes. Existing graph neural network (GNN) methods either fail to handle such imbalance or ignore temporal dependencies altogether. To address these issues, we propose a scalable and inductive contrastive learning-based GNN (CLGNN) for accurate and efficient TBC prediction. CLGNN builds an instance graph to preserve path validity and temporal order, then encodes structural and temporal features using dual aggregation, i.e., mean and edge-to-node multi-head attention mechanisms, enhanced by temporal path count and time encodings. A stability-based clustering-guided contrastive module (KContrastNet) is introduced to separate high-, median-, and low-centrality nodes in representation space, mitigating class imbalance, while a regression module (ValueNet) estimates TBC values. CLGNN also supports multiple optimal path definitions to accommodate diverse temporal semantics. Extensive experiments demonstrate the effectiveness and efficiency of CLGNN across diverse benchmarks. CLGNN achieves up to a 663.7~$\times$ speedup compared to state-of-the-art exact TBC computation methods. It outperforms leading static GNN baselines with up to 31.4~$\times$ lower MAE and 16.7~$\times$ higher Spearman correlation, and surpasses state-of-the-art temporal GNNs with up to 5.7~$\times$ lower MAE and 3.9~$\times$ higher Spearman correlation.
Predicting individuals' next locations is a core task in human mobility modelling, with wide-ranging implications for urban planning, transportation, public policy and personalised mobility services. Traditional approaches largely depend on location embeddings learned from historical mobility patterns, limiting their ability to encode explicit spatial information, integrate rich urban semantic context, and accommodate previously unseen locations. To address these challenges, we explore the application of CaLLiPer -- a multimodal representation learning framework that fuses spatial coordinates and semantic features of points of interest through contrastive learning -- for location embedding in individual mobility prediction. CaLLiPer's embeddings are spatially explicit, semantically enriched, and inductive by design, enabling robust prediction performance even in scenarios involving emerging locations. Through extensive experiments on four public mobility datasets under both conventional and inductive settings, we demonstrate that CaLLiPer consistently outperforms strong baselines, particularly excelling in inductive scenarios. Our findings highlight the potential of multimodal, inductive location embeddings to advance the capabilities of human mobility prediction systems. We also release the code and data (https://github.com/xlwang233/Into-the-Unknown) to foster reproducibility and future research.
Existing 3D visual grounding methods rely on precise text prompts to locate objects within 3D scenes. Speech, as a natural and intuitive modality, offers a promising alternative. Real-world speech inputs, however, often suffer from transcription errors due to accents, background noise, and varying speech rates, limiting the applicability of existing 3DVG methods. To address these challenges, we propose \textbf{SpeechRefer}, a novel 3DVG framework designed to enhance performance in the presence of noisy and ambiguous speech-to-text transcriptions. SpeechRefer integrates seamlessly with xisting 3DVG models and introduces two key innovations. First, the Speech Complementary Module captures acoustic similarities between phonetically related words and highlights subtle distinctions, generating complementary proposal scores from the speech signal. This reduces dependence on potentially erroneous transcriptions. Second, the Contrastive Complementary Module employs contrastive learning to align erroneous text features with corresponding speech features, ensuring robust performance even when transcription errors dominate. Extensive experiments on the SpeechRefer and peechNr3D datasets demonstrate that SpeechRefer improves the performance of existing 3DVG methods by a large margin, which highlights SpeechRefer's potential to bridge the gap between noisy speech inputs and reliable 3DVG, enabling more intuitive and practical multimodal systems.
High-content screening (HCS) assays based on high-throughput microscopy techniques such as Cell Painting have enabled the interrogation of cells' morphological responses to perturbations at an unprecedented scale. The collection of such data promises to facilitate a better understanding of the relationships between different perturbations and their effects on cellular state. Towards achieving this goal, recent advances in cross-modal contrastive learning could, in theory, be leveraged to learn a unified latent space that aligns perturbations with their corresponding morphological effects. However, the application of such methods to HCS data is not straightforward due to substantial differences in the semantics of Cell Painting images compared to natural images, and the difficulty of representing different classes of perturbations (e.g., small molecule vs CRISPR gene knockout) in a single latent space. In response to these challenges, here we introduce CellCLIP, a cross-modal contrastive learning framework for HCS data. CellCLIP leverages pre-trained image encoders coupled with a novel channel encoding scheme to better capture relationships between different microscopy channels in image embeddings, along with natural language encoders for representing perturbations. Our framework outperforms current open-source models, demonstrating the best performance in both cross-modal retrieval and biologically meaningful downstream tasks while also achieving significant reductions in computation time.
Automatic sample identification (ASID), the detection and identification of portions of audio recordings that have been reused in new musical works, is an essential but challenging task in the field of audio query-based retrieval. While a related task, audio fingerprinting, has made significant progress in accurately retrieving musical content under "real world" (noisy, reverberant) conditions, ASID systems struggle to identify samples that have undergone musical modifications. Thus, a system robust to common music production transformations such as time-stretching, pitch-shifting, effects processing, and underlying or overlaying music is an important open challenge. In this work, we propose a lightweight and scalable encoding architecture employing a Graph Neural Network within a contrastive learning framework. Our model uses only 9% of the trainable parameters compared to the current state-of-the-art system while achieving comparable performance, reaching a mean average precision (mAP) of 44.2%. To enhance retrieval quality, we introduce a two-stage approach consisting of an initial coarse similarity search for candidate selection, followed by a cross-attention classifier that rejects irrelevant matches and refines the ranking of retrieved candidates - an essential capability absent in prior models. In addition, because queries in real-world applications are often short in duration, we benchmark our system for short queries using new fine-grained annotations for the Sample100 dataset, which we publish as part of this work.
3D visual grounding (3DVG) is a critical task in scene understanding that aims to identify objects in 3D scenes based on text descriptions. However, existing methods rely on separately pre-trained vision and text encoders, resulting in a significant gap between the two modalities in terms of spatial geometry and semantic categories. This discrepancy often causes errors in object positioning and classification. The paper proposes UniSpace-3D, which innovatively introduces a unified representation space for 3DVG, effectively bridging the gap between visual and textual features. Specifically, UniSpace-3D incorporates three innovative designs: i) a unified representation encoder that leverages the pre-trained CLIP model to map visual and textual features into a unified representation space, effectively bridging the gap between the two modalities; ii) a multi-modal contrastive learning module that further reduces the modality gap; iii) a language-guided query selection module that utilizes the positional and semantic information to identify object candidate points aligned with textual descriptions. Extensive experiments demonstrate that UniSpace-3D outperforms baseline models by at least 2.24% on the ScanRefer and Nr3D/Sr3D datasets. The code will be made available upon acceptance of the paper.
Phishing attacks remain one of the most prevalent and persistent cybersecurity threat with attackers continuously evolving and intensifying tactics to evade the general detection system. Despite significant advances in artificial intelligence and machine learning, faithfully reproducing the interpretable reasoning with classification and explainability that underpin phishing judgments remains challenging. Due to recent advancement in Natural Language Processing, Large Language Models (LLMs) show a promising direction and potential for improving domain specific phishing classification tasks. However, enhancing the reliability and robustness of classification models requires not only accurate predictions from LLMs but also consistent and trustworthy explanations aligning with those predictions. Therefore, a key question remains: can LLMs not only classify phishing emails accurately but also generate explanations that are reliably aligned with their predictions and internally self-consistent? To answer these questions, we have fine-tuned transformer based models, including BERT, Llama models, and Wizard, to improve domain relevance and make them more tailored to phishing specific distinctions, using Binary Sequence Classification, Contrastive Learning (CL) and Direct Preference Optimization (DPO). To that end, we examined their performance in phishing classification and explainability by applying the ConsistenCy measure based on SHAPley values (CC SHAP), which measures prediction explanation token alignment to test the model's internal faithfulness and consistency and uncover the rationale behind its predictions and reasoning. Overall, our findings show that Llama models exhibit stronger prediction explanation token alignment with higher CC SHAP scores despite lacking reliable decision making accuracy, whereas Wizard achieves better prediction accuracy but lower CC SHAP scores.
Multimodal contrastive learning models like CLIP have demonstrated remarkable vision-language alignment capabilities, yet their vulnerability to backdoor attacks poses critical security risks. Attackers can implant latent triggers that persist through downstream tasks, enabling malicious control of model behavior upon trigger presentation. Despite great success in recent defense mechanisms, they remain impractical due to strong assumptions about attacker knowledge or excessive clean data requirements. In this paper, we introduce InverTune, the first backdoor defense framework for multimodal models under minimal attacker assumptions, requiring neither prior knowledge of attack targets nor access to the poisoned dataset. Unlike existing defense methods that rely on the same dataset used in the poisoning stage, InverTune effectively identifies and removes backdoor artifacts through three key components, achieving robust protection against backdoor attacks. Specifically, InverTune first exposes attack signatures through adversarial simulation, probabilistically identifying the target label by analyzing model response patterns. Building on this, we develop a gradient inversion technique to reconstruct latent triggers through activation pattern analysis. Finally, a clustering-guided fine-tuning strategy is employed to erase the backdoor function with only a small amount of arbitrary clean data, while preserving the original model capabilities. Experimental results show that InverTune reduces the average attack success rate (ASR) by 97.87% against the state-of-the-art (SOTA) attacks while limiting clean accuracy (CA) degradation to just 3.07%. This work establishes a new paradigm for securing multimodal systems, advancing security in foundation model deployment without compromising performance.
Accurate prediction of molecular metabolic stability (MS) is critical for drug research and development but remains challenging due to the complex interplay of molecular interactions. Despite recent advances in graph neural networks (GNNs) for MS prediction, current approaches face two critical limitations: (1) incomplete molecular modeling due to atom-centric message-passing mechanisms that disregard bond-level topological features, and (2) prediction frameworks that lack reliable uncertainty quantification. To address these challenges, we propose TrustworthyMS, a novel contrastive learning framework designed for uncertainty-aware metabolic stability prediction. First, a molecular graph topology remapping mechanism synchronizes atom-bond interactions through edge-induced feature propagation, capturing both localized electronic effects and global conformational constraints. Second, contrastive topology-bond alignment enforces consistency between molecular topology views and bond patterns via feature alignment, enhancing representation robustness. Third, uncertainty modeling through Beta-Binomial uncertainty quantification enables simultaneous prediction and confidence calibration under epistemic uncertainty. Through extensive experiments, our results demonstrate that TrustworthyMS outperforms current state-of-the-art methods in terms of predictive performance.
Virtual screening (VS) is a critical component of modern drug discovery, yet most existing methods--whether physics-based or deep learning-based--are developed around holo protein structures with known ligand-bound pockets. Consequently, their performance degrades significantly on apo or predicted structures such as those from AlphaFold2, which are more representative of real-world early-stage drug discovery, where pocket information is often missing. In this paper, we introduce an alignment-and-aggregation framework to enable accurate virtual screening under structural uncertainty. Our method comprises two core components: (1) a tri-modal contrastive learning module that aligns representations of the ligand, the holo pocket, and cavities detected from structures, thereby enhancing robustness to pocket localization error; and (2) a cross-attention based adapter for dynamically aggregating candidate binding sites, enabling the model to learn from activity data even without precise pocket annotations. We evaluated our method on a newly curated benchmark of apo structures, where it significantly outperforms state-of-the-art methods in blind apo setting, improving the early enrichment factor (EF1%) from 11.75 to 37.19. Notably, it also maintains strong performance on holo structures. These results demonstrate the promise of our approach in advancing first-in-class drug discovery, particularly in scenarios lacking experimentally resolved protein-ligand complexes.
Modern neural recording techniques such as two-photon imaging allow to acquire vast time-series datasets with responses of hundreds or thousands of neurons. Contrastive learning is a powerful self-supervised framework for learning representations of complex datasets. Existing applications for neural time series rely on generic data augmentations and do not exploit the multi-trial data structure inherent in many neural datasets. Here we present TRACE, a new contrastive learning framework that averages across different subsets of trials to generate positive pairs. TRACE allows to directly learn a two-dimensional embedding, combining ideas from contrastive learning and neighbor embeddings. We show that TRACE outperforms other methods, resolving fine response differences in simulated data. Further, using in vivo recordings, we show that the representations learned by TRACE capture both biologically relevant continuous variation, cell-type-related cluster structure, and can assist data quality control.
As large language models (LLMs) continue to revolutionize AI research, there is a growing interest in building large-scale brain foundation models to advance neuroscience. While most existing brain foundation models are pre-trained on time-series signals or region-of-interest (ROI) features, we propose a novel graph-based pre-training paradigm for constructing a brain graph foundation model. In this paper, we introduce the Brain Graph Foundation Model, termed BrainGFM, a unified framework that leverages graph contrastive learning and graph masked autoencoders for large-scale fMRI-based pre-training. BrainGFM is pre-trained on a diverse mixture of brain atlases with varying parcellations, significantly expanding the pre-training corpus and enhancing the model's ability to generalize across heterogeneous fMRI-derived brain representations. To support efficient and versatile downstream transfer, we integrate both graph prompts and language prompts into the model design, enabling BrainGFM to flexibly adapt to a wide range of atlases, neurological and psychiatric disorders, and task settings. Furthermore, we employ meta-learning to optimize the graph prompts, facilitating strong generalization to previously unseen disorders under both few-shot and zero-shot learning conditions via language-guided prompting. BrainGFM is pre-trained on 27 neuroimaging datasets spanning 25 common neurological and psychiatric disorders, encompassing 2 types of brain atlases (functional and anatomical) across 8 widely-used parcellations, and covering over 25,000 subjects, 60,000 fMRI scans, and a total of 400,000 graph samples aggregated across all atlases and parcellations. The code is available at: https://github.com/weixinxu666/BrainGFM
Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular processes by enabling gene expression analysis at the individual cell level. Clustering allows for the identification of cell types and the further discovery of intrinsic patterns in single-cell data. However, the high dimensionality and sparsity of scRNA-seq data continue to challenge existing clustering models. In this paper, we introduce JojoSCL, a novel self-supervised contrastive learning framework for scRNA-seq clustering. By incorporating a shrinkage estimator based on hierarchical Bayesian estimation, which adjusts gene expression estimates towards more reliable cluster centroids to reduce intra-cluster dispersion, and optimized using Stein's Unbiased Risk Estimate (SURE), JojoSCL refines both instance-level and cluster-level contrastive learning. Experiments on ten scRNA-seq datasets substantiate that JojoSCL consistently outperforms prevalent clustering methods, with further validation of its practicality through robustness analysis and ablation studies. JojoSCL's code is available at: https://github.com/ziwenwang28/JojoSCL.
Large-scale ASR models have achieved remarkable gains in accuracy and robustness. However, fairness issues remain largely unaddressed despite their critical importance in real-world applications. In this work, we introduce FairASR, a system that mitigates demographic bias by learning representations that are uninformative about group membership, enabling fair generalization across demographic groups. Leveraging a multi-demographic dataset, our approach employs a gradient reversal layer to suppress demographic-discriminative features while maintaining the ability to capture generalizable speech patterns through an unsupervised contrastive loss. Experimental results show that FairASR delivers competitive overall ASR performance while significantly reducing performance disparities across different demographic groups.
Accurately estimating high-resolution carbon emissions is crucial for effective emission governance and mitigation planning. While conventional methods for precise carbon accounting are hindered by substantial data collection efforts, the rise of open data and advanced learning techniques offers a promising solution. Once an open data-based prediction model is developed and trained, it can easily infer emissions for new areas based on available open data. To address this, we incorporate two modalities of open data, satellite images and point-of-interest (POI) data, to predict high-resolution urban carbon emissions, with satellite images providing macroscopic and static and POI data offering fine-grained and relatively dynamic functionality information. However, estimating high-resolution carbon emissions presents two significant challenges: the intertwined and implicit effects of various functionalities on carbon emissions, and the complex spatial contiguity correlations that give rise to the agglomeration effect. Our model, OpenCarbon, features two major designs that target the challenges: a cross-modality information extraction and fusion module to extract complementary functionality information from two modules and model their interactions, and a neighborhood-informed aggregation module to capture the spatial contiguity correlations. Extensive experiments demonstrate our model's superiority, with a significant performance gain of 26.6\% on R2. Further generalizability tests and case studies also show OpenCarbon's capacity to capture the intrinsic relation between urban functionalities and carbon emissions, validating its potential to empower efficient carbon governance and targeted carbon mitigation planning. Codes and data are available: https://github.com/JinweiZzz/OpenCarbon.
With the rapid advancement of deep learning technology, pre-trained encoder models have demonstrated exceptional feature extraction capabilities, playing a pivotal role in the research and application of deep learning. However, their widespread use has raised significant concerns about the risk of training data privacy leakage. This paper systematically investigates the privacy threats posed by membership inference attacks (MIAs) targeting encoder models, focusing on contrastive learning frameworks. Through experimental analysis, we reveal the significant impact of model architecture complexity on membership privacy leakage: As more advanced encoder frameworks improve feature-extraction performance, they simultaneously exacerbate privacy-leakage risks. Furthermore, this paper proposes a novel membership inference attack method based on the p-norm of feature vectors, termed the Embedding Lp-Norm Likelihood Attack (LpLA). This method infers membership status, by leveraging the statistical distribution characteristics of the p-norm of feature vectors. Experimental results across multiple datasets and model architectures demonstrate that LpLA outperforms existing methods in attack performance and robustness, particularly under limited attack knowledge and query volumes. This study not only uncovers the potential risks of privacy leakage in contrastive learning frameworks, but also provides a practical basis for privacy protection research in encoder models. We hope that this work will draw greater attention to the privacy risks associated with self-supervised learning models and shed light on the importance of a balance between model utility and training data privacy. Our code is publicly available at: https://github.com/SeroneySun/LpLA_code.