Backpropagation (BP) is the cornerstone of deep learning, but its reliance on global gradient synchronization limits scalability and imposes significant memory overhead. We propose Stochastic Variational Propagation (SVP), a scalable alternative that reframes training as hierarchical variational inference. SVP treats layer activations as latent variables and optimizes local Evidence Lower Bounds (ELBOs), enabling independent, local updates while preserving global coherence. However, directly applying KL divergence in layer-wise ELBOs risks inter-layer's representation collapse due to excessive compression. To prevent this, SVP projects activations into low-dimensional spaces via fixed random matrices, ensuring information preservation and representational diversity. Combined with a feature alignment loss for inter-layer consistency, SVP achieves competitive accuracy with BP across diverse architectures (MLPs, CNNs, Transformers) and datasets (MNIST to ImageNet), reduces memory usage by up to 4x, and significantly improves scalability. More broadly, SVP introduces a probabilistic perspective to deep representation learning, opening pathways toward more modular and interpretable neural network design.
Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene regulatory networks (GRN) is essential to understand and predict the effects of genetic perturbations. However, current methods fail to fully leverage gene-related information, and solely rely on simple evaluation metrics to construct coarse-grained GRN. More importantly, they ignore functional differences between biotypes, limiting the ability to capture potential gene interactions. In this work, we leverage pre-trained large language model and DNA sequence model to extract features from gene descriptions and DNA sequence data, respectively, which serve as the initialization for gene representations. Additionally, we introduce gene biotype information for the first time in genetic perturbation, simulating the distinct roles of genes with different biotypes in regulating cellular processes, while capturing implicit gene relationships through graph structure learning (GSL). We propose GRAPE, a heterogeneous graph neural network (HGNN) that leverages gene representations initialized with features from descriptions and sequences, models the distinct roles of genes with different biotypes, and dynamically refines the GRN through GSL. The results on publicly available datasets show that our method achieves state-of-the-art performance.
Tabular data, structured as rows and columns, is among the most prevalent data types in machine learning classification and regression applications. Models for learning from tabular data have continuously evolved, with Deep Neural Networks (DNNs) recently demonstrating promising results through their capability of representation learning. In this survey, we systematically introduce the field of tabular representation learning, covering the background, challenges, and benchmarks, along with the pros and cons of using DNNs. We organize existing methods into three main categories according to their generalization capabilities: specialized, transferable, and general models. Specialized models focus on tasks where training and evaluation occur within the same data distribution. We introduce a hierarchical taxonomy for specialized models based on the key aspects of tabular data -- features, samples, and objectives -- and delve into detailed strategies for obtaining high-quality feature- and sample-level representations. Transferable models are pre-trained on one or more datasets and subsequently fine-tuned on downstream tasks, leveraging knowledge acquired from homogeneous or heterogeneous sources, or even cross-modalities such as vision and language. General models, also known as tabular foundation models, extend this concept further, allowing direct application to downstream tasks without fine-tuning. We group these general models based on the strategies used to adapt across heterogeneous datasets. Additionally, we explore ensemble methods, which integrate the strengths of multiple tabular models. Finally, we discuss representative extensions of tabular learning, including open-environment tabular machine learning, multimodal learning with tabular data, and tabular understanding. More information can be found in the following repository: https://github.com/LAMDA-Tabular/Tabular-Survey.
Masked Image Modeling (MIM) with Vector Quantization (VQ) has achieved great success in both self-supervised pre-training and image generation. However, most existing methods struggle to address the trade-off in shared latent space for generation quality vs. representation learning and efficiency. To push the limits of this paradigm, we propose MergeVQ, which incorporates token merging techniques into VQ-based generative models to bridge the gap between image generation and visual representation learning in a unified architecture. During pre-training, MergeVQ decouples top-k semantics from latent space with the token merge module after self-attention blocks in the encoder for subsequent Look-up Free Quantization (LFQ) and global alignment and recovers their fine-grained details through cross-attention in the decoder for reconstruction. As for the second-stage generation, we introduce MergeAR, which performs KV Cache compression for efficient raster-order prediction. Extensive experiments on ImageNet verify that MergeVQ as an AR generative model achieves competitive performance in both visual representation learning and image generation tasks while maintaining favorable token efficiency and inference speed. The code and model will be available at https://apexgen-x.github.io/MergeVQ.
Temporal interaction graphs (TIGs), defined by sequences of timestamped interaction events, have become ubiquitous in real-world applications due to their capability to model complex dynamic system behaviors. As a result, temporal interaction graph representation learning (TIGRL) has garnered significant attention in recent years. TIGRL aims to embed nodes in TIGs into low-dimensional representations that effectively preserve both structural and temporal information, thereby enhancing the performance of downstream tasks such as classification, prediction, and clustering within constantly evolving data environments. In this paper, we begin by introducing the foundational concepts of TIGs and emphasize the critical role of temporal dependencies. We then propose a comprehensive taxonomy of state-of-the-art TIGRL methods, systematically categorizing them based on the types of information utilized during the learning process to address the unique challenges inherent to TIGs. To facilitate further research and practical applications, we curate the source of datasets and benchmarks, providing valuable resources for empirical investigations. Finally, we examine key open challenges and explore promising research directions in TIGRL, laying the groundwork for future advancements that have the potential to shape the evolution of this field.
Heterogeneous graph neural networks (HeteGNNs) have demonstrated strong abilities to learn node representations by effectively extracting complex structural and semantic information in heterogeneous graphs. Most of the prevailing HeteGNNs follow the neighborhood aggregation paradigm, leveraging meta-path based message passing to learn latent node representations. However, due to the pairwise nature of meta-paths, these models fail to capture high-order relations among nodes, resulting in suboptimal performance. Additionally, the challenge of ``over-squashing'', where long-range message passing in HeteGNNs leads to severe information distortion, further limits the efficacy of these models. To address these limitations, this paper proposes MGA-HHN, a Multi-Granular Attention based Heterogeneous Hypergraph Neural Network for heterogeneous graph representation learning. MGA-HHN introduces two key innovations: (1) a novel approach for constructing meta-path based heterogeneous hypergraphs that explicitly models higher-order semantic information in heterogeneous graphs through multiple views, and (2) a multi-granular attention mechanism that operates at both the node and hyperedge levels. This mechanism enables the model to capture fine-grained interactions among nodes sharing the same semantic context within a hyperedge type, while preserving the diversity of semantics across different hyperedge types. As such, MGA-HHN effectively mitigates long-range message distortion and generates more expressive node representations. Extensive experiments on real-world benchmark datasets demonstrate that MGA-HHN outperforms state-of-the-art models, showcasing its effectiveness in node classification, node clustering and visualization tasks.
Estimating treatment effects from observational data is challenging due to two main reasons: (a) hidden confounding, and (b) covariate mismatch (control and treatment groups not having identical distributions). Long lines of works exist that address only either of these issues. To address the former, conventional techniques that require detailed knowledge in the form of causal graphs have been proposed. For the latter, covariate matching and importance weighting methods have been used. Recently, there has been progress in combining testable independencies with partial side information for tackling hidden confounding. A common framework to address both hidden confounding and selection bias is missing. We propose neural architectures that aim to learn a representation of pre-treatment covariates that is a valid adjustment and also satisfies covariate matching constraints. We combine two different neural architectures: one based on gradient matching across domains created by subsampling a suitable anchor variable that assumes causal side information, followed by the other, a covariate matching transformation. We prove that approximately invariant representations yield approximate valid adjustment sets which would enable an interval around the true causal effect. In contrast to usual sensitivity analysis, where an unknown nuisance parameter is varied, we have a testable approximation yielding a bound on the effect estimate. We also outperform various baselines with respect to ATE and PEHE errors on causal benchmarks that include IHDP, Jobs, Cattaneo, and an image-based Crowd Management dataset.
The Contrastive Language-Image Pre-training (CLIP) framework has become a widely used approach for multimodal representation learning, particularly in image-text retrieval and clustering. However, its efficacy is constrained by three key limitations: (1) text token truncation, (2) isolated image-text encoding, and (3) deficient compositionality due to bag-of-words behavior. While recent Multimodal Large Language Models (MLLMs) have demonstrated significant advances in generalized vision-language understanding, their potential for learning transferable multimodal representations remains underexplored.In this work, we present UniME (Universal Multimodal Embedding), a novel two-stage framework that leverages MLLMs to learn discriminative representations for diverse downstream tasks. In the first stage, we perform textual discriminative knowledge distillation from a powerful LLM-based teacher model to enhance the embedding capability of the MLLM\'s language component. In the second stage, we introduce hard negative enhanced instruction tuning to further advance discriminative representation learning. Specifically, we initially mitigate false negative contamination and then sample multiple hard negatives per instance within each batch, forcing the model to focus on challenging samples. This approach not only improves discriminative power but also enhances instruction-following ability in downstream tasks. We conduct extensive experiments on the MMEB benchmark and multiple retrieval tasks, including short and long caption retrieval and compositional retrieval. Results demonstrate that UniME achieves consistent performance improvement across all tasks, exhibiting superior discriminative and compositional capabilities.
Masked video modeling, such as VideoMAE, is an effective paradigm for video self-supervised learning (SSL). However, they are primarily based on reconstructing pixel-level details on natural videos which have substantial temporal redundancy, limiting their capability for semantic representation and sufficient encoding of motion dynamics. To address these issues, this paper introduces a novel SSL approach for video representation learning, dubbed as SMILE, by infusing both spatial and motion semantics. In SMILE, we leverage image-language pretrained models, such as CLIP, to guide the learning process with their high-level spatial semantics. We enhance the representation of motion by introducing synthetic motion patterns in the training data, allowing the model to capture more complex and dynamic content. Furthermore, using SMILE, we establish a new self-supervised video learning paradigm capable of learning strong video representations without requiring any natural video data. We have carried out extensive experiments on 7 datasets with various downstream scenarios. SMILE surpasses current state-of-the-art SSL methods, showcasing its effectiveness in learning more discriminative and generalizable video representations. Code is available: https://github.com/fmthoker/SMILE
Modeling the joint distribution of data samples and their properties allows to construct a single model for both data generation and property prediction, with synergistic benefits reaching beyond purely generative or predictive models. However, training joint models presents daunting architectural and optimization challenges. Here, we propose Hyformer, a transformer-based joint model that successfully blends the generative and predictive functionalities, using an alternating attention mechanism and a joint pre-training scheme. We show that Hyformer is simultaneously optimized for molecule generation and property prediction, while exhibiting synergistic benefits in conditional sampling, out-of-distribution property prediction and representation learning. Finally, we demonstrate the benefits of joint learning in a drug design use case of discovering novel antimicrobial~peptides.
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards understanding the genetic information of (novel) organisms, as well as learning shared patterns across evolutionarily diverse species. The current state of the art are graphical models usually trained per organism and requiring manually curated datasets. However, these models lack the flexibility to incorporate deep learning representation learning techniques that have in recent years been transformative in the analysis of pro tein sequences, and which could potentially help gene finders exploit the growing number of the sequenced genomes to expand performance across multiple organisms. Here, we propose a novel approach, combining learned embeddings of raw genetic sequences with exact decoding using a latent conditional random field. We show that the model achieves performance matching the current state of the art, while increasing training robustness, and removing the need for manually fitted length distributions. As language models for DNA improve, this paves the way for more performant cross-organism gene-finders.
Discovering molecules with desirable molecular properties, including ADMET profiles, is of great importance in drug discovery. Existing approaches typically employ deep learning models, such as Graph Neural Networks (GNNs) and Transformers, to predict these molecular properties by learning from diverse chemical information. However, these models often fail to efficiently capture and utilize the hierarchical nature of molecular structures, and often lack mechanisms for effective interaction among multi-level features. To address these limitations, we propose a Hierarchical Interaction Message Passing Mechanism, which serves as the foundation of our novel model, the Hierarchical Interaction Message Net (HimNet). Our method enables interaction-aware representation learning across atomic, motif, and molecular levels via hierarchical attention-guided message passing. This design allows HimNet to effectively balance global and local information, ensuring rich and task-relevant feature extraction for downstream property prediction tasks, such as Blood-Brain Barrier Permeability (BBBP). We systematically evaluate HimNet on eleven datasets, including eight widely-used MoleculeNet benchmarks and three challenging, high-value datasets for metabolic stability, malaria activity, and liver microsomal clearance, covering a broad range of pharmacologically relevant properties. Extensive experiments demonstrate that HimNet achieves the best or near-best performance in most molecular property prediction tasks. Furthermore, our method exhibits promising hierarchical interpretability, aligning well with chemical intuition on representative molecules. We believe that HimNet offers an accurate and efficient solution for molecular activity and ADMET property prediction, contributing to advanced decision-making in the early stages of drug discovery.
One-shot medical image segmentation (MIS) is crucial for medical analysis due to the burden of medical experts on manual annotation. The recent emergence of the segment anything model (SAM) has demonstrated remarkable adaptation in MIS but cannot be directly applied to one-shot medical image segmentation (MIS) due to its reliance on labor-intensive user interactions and the high computational cost. To cope with these limitations, we propose a novel SAM-guided robust representation learning framework, named RRL-MedSAM, to adapt SAM to one-shot 3D MIS, which exploits the strong generalization capabilities of the SAM encoder to learn better feature representation. We devise a dual-stage knowledge distillation (DSKD) strategy to distill general knowledge between natural and medical images from the foundation model to train a lightweight encoder, and then adopt a mutual exponential moving average (mutual-EMA) to update the weights of the general lightweight encoder and medical-specific encoder. Specifically, pseudo labels from the registration network are used to perform mutual supervision for such two encoders. Moreover, we introduce an auto-prompting (AP) segmentation decoder which adopts the mask generated from the general lightweight model as a prompt to assist the medical-specific model in boosting the final segmentation performance. Extensive experiments conducted on three public datasets, i.e., OASIS, CT-lung demonstrate that the proposed RRL-MedSAM outperforms state-of-the-art one-shot MIS methods for both segmentation and registration tasks. Especially, our lightweight encoder uses only 3\% of the parameters compared to the encoder of SAM-Base.
Decomposing a deep neural network's learned representations into interpretable features could greatly enhance its safety and reliability. To better understand features, we adopt a geometric perspective, viewing them as a learned coordinate system for mapping an embedded data distribution. We motivate a model of a generic data distribution as a random lattice and analyze its properties using percolation theory. Learned features are categorized into context, component, and surface features. The model is qualitatively consistent with recent findings in mechanistic interpretability and suggests directions for future research.
Accurate prediction of material properties facilitates the discovery of novel materials with tailored functionalities. Deep learning models have recently shown superior accuracy and flexibility in capturing structure-property relationships. However, these models often rely on supervised learning, which requires large, well-annotated datasets an expensive and time-consuming process. Self-supervised learning (SSL) offers a promising alternative by pretraining on large, unlabeled datasets to develop foundation models that can be fine-tuned for material property prediction. In this work, we propose supervised pretraining, where available class information serves as surrogate labels to guide learning, even when downstream tasks involve unrelated material properties. We evaluate this strategy on two state-of-the-art SSL models and introduce a novel framework for supervised pretraining. To further enhance representation learning, we propose a graph-based augmentation technique that injects noise to improve robustness without structurally deforming material graphs. The resulting foundation models are fine-tuned for six challenging material property predictions, achieving significant performance gains over baselines, ranging from 2% to 6.67% improvement in mean absolute error (MAE) and establishing a new benchmark in material property prediction. This study represents the first exploration of supervised pertaining with surrogate labels in material property prediction, advancing methodology and application in the field.
Recommender systems (RS) have become essential in filtering information and personalizing content for users. RS techniques have traditionally relied on modeling interactions between users and items as well as the features of content using models specific to each task. The emergence of foundation models (FMs), large scale models trained on vast amounts of data such as GPT, LLaMA and CLIP, is reshaping the recommendation paradigm. This survey provides a comprehensive overview of the Foundation Models for Recommender Systems (FM4RecSys), covering their integration in three paradigms: (1) Feature-Based augmentation of representations, (2) Generative recommendation approaches, and (3) Agentic interactive systems. We first review the data foundations of RS, from traditional explicit or implicit feedback to multimodal content sources. We then introduce FMs and their capabilities for representation learning, natural language understanding, and multi-modal reasoning in RS contexts. The core of the survey discusses how FMs enhance RS under different paradigms. Afterward, we examine FM applications in various recommendation tasks. Through an analysis of recent research, we highlight key opportunities that have been realized as well as challenges encountered. Finally, we outline open research directions and technical challenges for next-generation FM4RecSys. This survey not only reviews the state-of-the-art methods but also provides a critical analysis of the trade-offs among the feature-based, the generative, and the agentic paradigms, outlining key open issues and future research directions.
With the rapid advancement of Multimodal Large Language Models (MLLMs), an increasing number of researchers are exploring their application in recommendation systems. However, the high latency associated with large models presents a significant challenge for such use cases. The EReL@MIR workshop provided a valuable opportunity to experiment with various approaches aimed at improving the efficiency of multimodal representation learning for information retrieval tasks. As part of the competition's requirements, participants were mandated to submit a technical report detailing their methodologies and findings. Our team was honored to receive the award for Task 2 - Winner (Multimodal CTR Prediction). In this technical report, we present our methods and key findings. Additionally, we propose several directions for future work, particularly focusing on how to effectively integrate recommendation signals into multimodal representations. The codebase for our implementation is publicly available at: https://github.com/Lattice-zjj/MMCTR_Code, and the trained model weights can be accessed at: https://huggingface.co/FireFlyCourageous/MMCTR_DIN_MicroLens_1M_x1.
Multimodal click-through rate (CTR) prediction is a key technique in industrial recommender systems. It leverages heterogeneous modalities such as text, images, and behavioral logs to capture high-order feature interactions between users and items, thereby enhancing the system's understanding of user interests and its ability to predict click behavior. The primary challenge in this field lies in effectively utilizing the rich semantic information from multiple modalities while satisfying the low-latency requirements of online inference in real-world applications. To foster progress in this area, the Multimodal CTR Prediction Challenge Track of the WWW 2025 EReL@MIR Workshop formulates the problem into two tasks: (1) Task 1 of Multimodal Item Embedding: this task aims to explore multimodal information extraction and item representation learning methods that enhance recommendation tasks; and (2) Task 2 of Multimodal CTR Prediction: this task aims to explore what multimodal recommendation model can effectively leverage multimodal embedding features and achieve better performance. In this paper, we propose a novel model for Task 2, named Quadratic Interest Network (QIN) for Multimodal CTR Prediction. Specifically, QIN employs adaptive sparse target attention to extract multimodal user behavior features, and leverages Quadratic Neural Networks to capture high-order feature interactions. As a result, QIN achieved an AUC of 0.9798 on the leaderboard and ranked second in the competition. The model code, training logs, hyperparameter configurations, and checkpoints are available at https://github.com/salmon1802/QIN.
Personalized image generation has emerged as a promising direction in multimodal content creation. It aims to synthesize images tailored to individual style preferences (e.g., color schemes, character appearances, layout) and semantic intentions (e.g., emotion, action, scene contexts) by leveraging user-interacted history images and multimodal instructions. Despite notable progress, existing methods -- whether based on diffusion models, large language models, or Large Multimodal Models (LMMs) -- struggle to accurately capture and fuse user style preferences and semantic intentions. In particular, the state-of-the-art LMM-based method suffers from the entanglement of visual features, leading to Guidance Collapse, where the generated images fail to preserve user-preferred styles or reflect the specified semantics. To address these limitations, we introduce DRC, a novel personalized image generation framework that enhances LMMs through Disentangled Representation Composition. DRC explicitly extracts user style preferences and semantic intentions from history images and the reference image, respectively, to form user-specific latent instructions that guide image generation within LMMs. Specifically, it involves two critical learning stages: 1) Disentanglement learning, which employs a dual-tower disentangler to explicitly separate style and semantic features, optimized via a reconstruction-driven paradigm with difficulty-aware importance sampling; and 2) Personalized modeling, which applies semantic-preserving augmentations to effectively adapt the disentangled representations for robust personalized generation. Extensive experiments on two benchmarks demonstrate that DRC shows competitive performance while effectively mitigating the guidance collapse issue, underscoring the importance of disentangled representation learning for controllable and effective personalized image generation.
User sequence modeling is crucial for modern large-scale recommendation systems, as it enables the extraction of informative representations of users and items from their historical interactions. These user representations are widely used for a variety of downstream tasks to enhance users' online experience. A key challenge for learning these representations is the lack of labeled training data. While self-supervised learning (SSL) methods have emerged as a promising solution for learning representations from unlabeled data, many existing approaches rely on extensive negative sampling, which can be computationally expensive and may not always be feasible in real-world scenario. In this work, we propose an adaptation of Barlow Twins, a state-of-the-art SSL methods, to user sequence modeling by incorporating suitable augmentation methods. Our approach aims to mitigate the need for large negative sample batches, enabling effective representation learning with smaller batch sizes and limited labeled data. We evaluate our method on the MovieLens-1M, MovieLens-20M, and Yelp datasets, demonstrating that our method consistently outperforms the widely-used dual encoder model across three downstream tasks, achieving an 8%-20% improvement in accuracy. Our findings underscore the effectiveness of our approach in extracting valuable sequence-level information for user modeling, particularly in scenarios where labeled data is scarce and negative examples are limited.