Language representation learning has emerged as a promising approach for sequential recommendation, thanks to its ability to learn generalizable representations. However, despite its advantages, this approach still struggles with data sparsity and a limited understanding of common-sense user preferences. To address these limitations, we propose $\textbf{JEPA4Rec}$, a framework that combines $\textbf{J}$oint $\textbf{E}$mbedding $\textbf{P}$redictive $\textbf{A}$rchitecture with language modeling of item textual descriptions. JEPA4Rec captures semantically rich and transferable representations, improving recommendation performance and reducing reliance on large-scale pre-training data. Specifically, JEPA4Rec represents items as text sentences by flattening descriptive information such as $\textit{title, category}$, and other attributes. To encode these sentences, we employ a bidirectional Transformer encoder with modified embedding layers tailored for capturing item information in recommendation datasets. We apply masking to text sentences and use them to predict the representations of the unmasked sentences, helping the model learn generalizable item embeddings. To further improve recommendation performance and language understanding, we employ a two-stage training strategy incorporating self-supervised learning losses. Experiments on six real-world datasets demonstrate that JEPA4Rec consistently outperforms state-of-the-art methods, particularly in cross-domain, cross-platform, and low-resource scenarios.
This paper introduces a cutting-edge method for enhancing recommender systems through the integration of generative self-supervised learning (SSL) with a Residual Graph Transformer. Our approach emphasizes the importance of superior data enhancement through the use of pertinent pretext tasks, automated through rationale-aware SSL to distill clear ways of how users and items interact. The Residual Graph Transformer incorporates a topology-aware transformer for global context and employs residual connections to improve graph representation learning. Additionally, an auto-distillation process refines self-supervised signals to uncover consistent collaborative rationales. Experimental evaluations on multiple datasets demonstrate that our approach consistently outperforms baseline methods.
Multimodal protein language models (PLMs) integrate sequence and token-based structural information, serving as a powerful foundation for protein modeling, generation, and design. However, the reliance on tokenizing 3D structures into discrete tokens causes substantial loss of fidelity about fine-grained structural details and correlations. In this paper, we systematically elucidate the design space of multimodal PLMs to overcome their limitations. We identify tokenization loss and inaccurate structure token predictions by the PLMs as major bottlenecks. To address these, our proposed design space covers improved generative modeling, structure-aware architectures and representation learning, and data exploration. Our advancements approach finer-grained supervision, demonstrating that token-based multimodal PLMs can achieve robust structural modeling. The effective design methods dramatically improve the structure generation diversity, and notably, folding abilities of our 650M model by reducing the RMSD from 5.52 to 2.36 on PDB testset, even outperforming 3B baselines and on par with the specialized folding models. Project page and code: https://bytedance.github.io/dplm/dplm-2.1/.
Efficiently acquired and precisely reconstructed imaging are crucial to the success of modern radiation therapy (RT). Computed tomography (CT) and magnetic resonance imaging (MRI) are two common modalities for providing RT treatment planning and delivery guidance/monitoring. In recent decades, artificial intelligence (AI) has emerged as a powerful and widely adopted technique across various fields, valued for its efficiency and convenience enabled by implicit function definition and data-driven feature representation learning. Here, we present a series of AI-driven medical imaging reconstruction frameworks for enhanced radiotherapy, designed to improve CT image reconstruction quality and speed, refine dual-energy CT (DECT) multi-material decomposition (MMD), and significantly accelerate 4D MRI acquisition.
Recent advances in self-supervised deep learning have improved our ability to quantify cellular morphological changes in high-throughput microscopy screens, a process known as morphological profiling. However, most current methods only learn from images, despite many screens being inherently multimodal, as they involve both a chemical or genetic perturbation as well as an image-based readout. We hypothesized that incorporating chemical compound structure during self-supervised pre-training could improve learned representations of images in high-throughput microscopy screens. We introduce a representation learning framework, MICON (Molecular-Image Contrastive Learning), that models chemical compounds as treatments that induce counterfactual transformations of cell phenotypes. MICON significantly outperforms classical hand-crafted features such as CellProfiler and existing deep-learning-based representation learning methods in challenging evaluation settings where models must identify reproducible effects of drugs across independent replicates and data-generating centers. We demonstrate that incorporating chemical compound information into the learning process provides consistent improvements in our evaluation setting and that modeling compounds specifically as treatments in a causal framework outperforms approaches that directly align images and compounds in a single representation space. Our findings point to a new direction for representation learning in morphological profiling, suggesting that methods should explicitly account for the multimodal nature of microscopy screening data.
Circuit representation learning has shown promise in advancing Electronic Design Automation (EDA) by capturing structural and functional circuit properties for various tasks. Existing pre-trained solutions rely on graph learning with complex functional supervision, such as truth table simulation. However, they only handle simple and-inverter graphs (AIGs), struggling to fully encode other complex gate functionalities. While large language models (LLMs) excel at functional understanding, they lack the structural awareness for flattened netlists. To advance netlist representation learning, we present NetTAG, a netlist foundation model that fuses gate semantics with graph structure, handling diverse gate types and supporting a variety of functional and physical tasks. Moving beyond existing graph-only methods, NetTAG formulates netlists as text-attributed graphs, with gates annotated by symbolic logic expressions and physical characteristics as text attributes. Its multimodal architecture combines an LLM-based text encoder for gate semantics and a graph transformer for global structure. Pre-trained with gate and graph self-supervised objectives and aligned with RTL and layout stages, NetTAG captures comprehensive circuit intrinsics. Experimental results show that NetTAG consistently outperforms each task-specific method on four largely different functional and physical tasks and surpasses state-of-the-art AIG encoders, demonstrating its versatility.
In autoregressive (AR) image generation, visual tokenizers compress images into compact discrete latent tokens, enabling efficient training of downstream autoregressive models for visual generation via next-token prediction. While scaling visual tokenizers improves image reconstruction quality, it often degrades downstream generation quality -- a challenge not adequately addressed in existing literature. To address this, we introduce GigaTok, the first approach to simultaneously improve image reconstruction, generation, and representation learning when scaling visual tokenizers. We identify the growing complexity of latent space as the key factor behind the reconstruction vs. generation dilemma. To mitigate this, we propose semantic regularization, which aligns tokenizer features with semantically consistent features from a pre-trained visual encoder. This constraint prevents excessive latent space complexity during scaling, yielding consistent improvements in both reconstruction and downstream autoregressive generation. Building on semantic regularization, we explore three key practices for scaling tokenizers:(1) using 1D tokenizers for better scalability, (2) prioritizing decoder scaling when expanding both encoder and decoder, and (3) employing entropy loss to stabilize training for billion-scale tokenizers. By scaling to $\bf{3 \space billion}$ parameters, GigaTok achieves state-of-the-art performance in reconstruction, downstream AR generation, and downstream AR representation quality.
Deep neural networks are often seen as different from other model classes by defying conventional notions of generalization. Popular examples of anomalous generalization behaviour include benign overfitting, double descent, and the success of overparametrization. We argue that these phenomena are not distinct to neural networks, or particularly mysterious. Moreover, this generalization behaviour can be intuitively understood, and rigorously characterized using long-standing generalization frameworks such as PAC-Bayes and countable hypothesis bounds. We present soft inductive biases as a key unifying principle in explaining these phenomena: rather than restricting the hypothesis space to avoid overfitting, embrace a flexible hypothesis space, with a soft preference for simpler solutions that are consistent with the data. This principle can be encoded in many model classes, and thus deep learning is not as mysterious or different from other model classes as it might seem. However, we also highlight how deep learning is relatively distinct in other ways, such as its ability for representation learning, phenomena such as mode connectivity, and its relative universality.
Electronic health record (EHR) foundation models have been an area ripe for exploration with their improved performance in various medical tasks. Despite the rapid advances, there exists a fundamental limitation: Processing unseen medical codes out of the vocabulary. This problem limits the generality of EHR foundation models and the integration of models trained with different vocabularies. To deal with this problem, we propose MedRep for EHR foundation models based on the observational medical outcome partnership (OMOP) common data model (CDM), providing the integrated medical concept representations and the basic data augmentation strategy for patient trajectories. For concept representation learning, we enrich the information of each concept with a minimal definition through large language model (LLM) prompts and enhance the text-based representations through graph ontology of OMOP vocabulary. Trajectory augmentation randomly replaces selected concepts with other similar concepts that have closely related representations to let the model practice with the concepts out-of-vocabulary. Finally, we demonstrate that EHR foundation models trained with MedRep better maintain the prediction performance in external datasets. Our code implementation is publicly available at https://github.com/kicarussays/MedRep.
Accurate representation to an academic network is of great significance to academic relationship mining like predicting scientific impact. A Latent Factorization of Tensors (LFT) model is one of the most effective models for learning the representation of a target network. However, an academic network is often High-Dimensional and Incomplete (HDI) because the relationships among numerous network entities are impossible to be fully explored, making it difficult for an LFT model to learn accurate representation of the academic network. To address this issue, this paper proposes a Prediction-sampling-based Latent Factorization of Tensors (PLFT) model with two ideas: 1) constructing a cascade LFT architecture to enhance model representation learning ability via learning academic network hierarchical features, and 2) introducing a nonlinear activation-incorporated predicting-sampling strategy to more accurately learn the network representation via generating new academic network data layer by layer. Experimental results from the three real-world academic network datasets show that the PLFT model outperforms existing models when predicting the unexplored relationships among network entities.
Learning node representations is a fundamental problem in graph machine learning. While existing embedding methods effectively preserve local similarity measures, they often fail to capture global functions like graph distances. Inspired by Bourgain's seminal work on Hilbert space embeddings of metric spaces (1985), we study the performance of local distance-preserving node embeddings. Known as landmark-based algorithms, these embeddings approximate pairwise distances by computing shortest paths from a small subset of reference nodes (i.e., landmarks). Our main theoretical contribution shows that random graphs, such as Erd\H{o}s-R\'enyi random graphs, require lower dimensions in landmark-based embeddings compared to worst-case graphs. Empirically, we demonstrate that the GNN-based approximations for the distances to landmarks generalize well to larger networks, offering a scalable alternative for graph representation learning.
This study presents Latent Diffusion Autoencoder (LDAE), a novel encoder-decoder diffusion-based framework for efficient and meaningful unsupervised learning in medical imaging, focusing on Alzheimer disease (AD) using brain MR from the ADNI database as a case study. Unlike conventional diffusion autoencoders operating in image space, LDAE applies the diffusion process in a compressed latent representation, improving computational efficiency and making 3D medical imaging representation learning tractable. To validate the proposed approach, we explore two key hypotheses: (i) LDAE effectively captures meaningful semantic representations on 3D brain MR associated with AD and ageing, and (ii) LDAE achieves high-quality image generation and reconstruction while being computationally efficient. Experimental results support both hypotheses: (i) linear-probe evaluations demonstrate promising diagnostic performance for AD (ROC-AUC: 90%, ACC: 84%) and age prediction (MAE: 4.1 years, RMSE: 5.2 years); (ii) the learned semantic representations enable attribute manipulation, yielding anatomically plausible modifications; (iii) semantic interpolation experiments show strong reconstruction of missing scans, with SSIM of 0.969 (MSE: 0.0019) for a 6-month gap. Even for longer gaps (24 months), the model maintains robust performance (SSIM > 0.93, MSE < 0.004), indicating an ability to capture temporal progression trends; (iv) compared to conventional diffusion autoencoders, LDAE significantly increases inference throughput (20x faster) while also enhancing reconstruction quality. These findings position LDAE as a promising framework for scalable medical imaging applications, with the potential to serve as a foundation model for medical image analysis. Code available at https://github.com/GabrieleLozupone/LDAE
We study $\textit{how}$ rich visual semantic information is represented within various layers and denoising timesteps of different diffusion architectures. We uncover monosemantic interpretable features by leveraging k-sparse autoencoders (k-SAE). We substantiate our mechanistic interpretations via transfer learning using light-weight classifiers on off-the-shelf diffusion models' features. On $4$ datasets, we demonstrate the effectiveness of diffusion features for representation learning. We provide in-depth analysis of how different diffusion architectures, pre-training datasets, and language model conditioning impacts visual representation granularity, inductive biases, and transfer learning capabilities. Our work is a critical step towards deepening interpretability of black-box diffusion models. Code and visualizations available at: https://github.com/revelio-diffusion/revelio
Recommender systems and search engines serve as foundational elements of online platforms, with the former delivering information proactively and the latter enabling users to seek information actively. Unifying both tasks in a shared model is promising since it can enhance user modeling and item understanding. Previous approaches mainly follow a discriminative paradigm, utilizing shared encoders to process input features and task-specific heads to perform each task. However, this paradigm encounters two key challenges: gradient conflict and manual design complexity. From the information theory perspective, these challenges potentially both stem from the same issue -- low mutual information between the input features and task-specific outputs during the optimization process. To tackle these issues, we propose GenSR, a novel generative paradigm for unifying search and recommendation (S&R), which leverages task-specific prompts to partition the model's parameter space into subspaces, thereby enhancing mutual information. To construct effective subspaces for each task, GenSR first prepares informative representations for each subspace and then optimizes both subspaces in one unified model. Specifically, GenSR consists of two main modules: (1) Dual Representation Learning, which independently models collaborative and semantic historical information to derive expressive item representations; and (2) S&R Task Unifying, which utilizes contrastive learning together with instruction tuning to generate task-specific outputs effectively. Extensive experiments on two public datasets show GenSR outperforms state-of-the-art methods across S&R tasks. Our work introduces a new generative paradigm compared with previous discriminative methods and establishes its superiority from the mutual information perspective.
Contrastive Learning (CL) has recently emerged as a powerful technique in recommendation systems, particularly for its capability to harness self-supervised signals from perturbed views to mitigate the persistent challenge of data sparsity. The process of constructing perturbed views of the user-item bipartite graph and performing contrastive learning between perturbed views in a graph convolutional network (GCN) is called graph contrastive learning (GCL), which aims to enhance the robustness of representation learning. Although existing GCL-based models are effective, the weight assignment method for perturbed views has not been fully explored. A critical problem in existing GCL-based models is the irrational allocation of feature attention. This problem limits the model's ability to effectively leverage crucial features, resulting in suboptimal performance. To address this, we propose a Weighted Graph Contrastive Learning framework (WeightedGCL). Specifically, WeightedGCL applies a robust perturbation strategy, which perturbs only the view of the final GCN layer. In addition, WeightedGCL incorporates a squeeze and excitation network (SENet) to dynamically weight the features of the perturbed views. Our WeightedGCL strengthens the model's focus on crucial features and reduces the impact of less relevant information. Extensive experiments on widely used datasets demonstrate that our WeightedGCL achieves significant accuracy improvements compared to competitive baselines.
Fine-grained text-to-image retrieval aims to retrieve a fine-grained target image with a given text query. Existing methods typically assume that each training image is accurately depicted by its textual descriptions. However, textual descriptions can be ambiguous and fail to depict discriminative visual details in images, leading to inaccurate representation learning. To alleviate the effects of text ambiguity, we propose a Multi-Modal Reference learning framework to learn robust representations. We first propose a multi-modal reference construction module to aggregate all visual and textual details of the same object into a comprehensive multi-modal reference. The multi-modal reference hence facilitates the subsequent representation learning and retrieval similarity computation. Specifically, a reference-guided representation learning module is proposed to use multi-modal references to learn more accurate visual and textual representations. Additionally, we introduce a reference-based refinement method that employs the object references to compute a reference-based similarity that refines the initial retrieval results. Extensive experiments are conducted on five fine-grained text-to-image retrieval datasets for different text-to-image retrieval tasks. The proposed method has achieved superior performance over state-of-the-art methods. For instance, on the text-to-person image retrieval dataset RSTPReid, our method achieves the Rank1 accuracy of 56.2\%, surpassing the recent CFine by 5.6\%.
Protein representation learning is critical for numerous biological tasks. Recently, large transformer-based protein language models (pLMs) pretrained on large scale protein sequences have demonstrated significant success in sequence-based tasks. However, pLMs lack structural information. Conversely, graph neural networks (GNNs) designed to leverage 3D structural information have shown promising generalization in protein-related prediction tasks, but their effectiveness is often constrained by the scarcity of labeled structural data. Recognizing that sequence and structural representations are complementary perspectives of the same protein entity, we propose a multimodal bidirectional hierarchical fusion framework to effectively merge these modalities. Our framework employs attention and gating mechanisms to enable effective interaction between pLMs-generated sequential representations and GNN-extracted structural features, improving information exchange and enhancement across layers of the neural network. Based on the framework, we further introduce local Bi-Hierarchical Fusion with gating and global Bi-Hierarchical Fusion with multihead self-attention approaches. Through extensive experiments on a diverse set of protein-related tasks, our method demonstrates consistent improvements over strong baselines and existing fusion techniques in a variety of protein representation learning benchmarks, including react (enzyme/EC classification), model quality assessment (MQA), protein-ligand binding affinity prediction (LBA), protein-protein binding site prediction (PPBS), and B cell epitopes prediction (BCEs). Our method establishes a new state-of-the-art for multimodal protein representation learning, emphasizing the efficacy of BIHIERARCHICAL FUSION in bridging sequence and structural modalities.
Fleets of robo-taxis offering on-demand transportation services, commonly known as Autonomous Mobility-on-Demand (AMoD) systems, hold significant promise for societal benefits, such as reducing pollution, energy consumption, and urban congestion. However, orchestrating these systems at scale remains a critical challenge, with existing coordination algorithms often failing to exploit the systems' full potential. This work introduces a novel decision-making framework that unites mathematical modeling with data-driven techniques. In particular, we present the AMoD coordination problem through the lens of reinforcement learning and propose a graph network-based framework that exploits the main strengths of graph representation learning, reinforcement learning, and classical operations research tools. Extensive evaluations across diverse simulation fidelities and scenarios demonstrate the flexibility of our approach, achieving superior system performance, computational efficiency, and generalizability compared to prior methods. Finally, motivated by the need to democratize research efforts in this area, we release publicly available benchmarks, datasets, and simulators for network-level coordination alongside an open-source codebase designed to provide accessible simulation platforms and establish a standardized validation process for comparing methodologies. Code available at: https://github.com/StanfordASL/RL4AMOD
Speech-preserving facial expression manipulation (SPFEM) aims to modify a talking head to display a specific reference emotion while preserving the mouth animation of source spoken contents. Thus, emotion and content information existing in reference and source inputs can provide direct and accurate supervision signals for SPFEM models. However, the intrinsic intertwining of these elements during the talking process poses challenges to their effectiveness as supervisory signals. In this work, we propose to learn content and emotion priors as guidance augmented with contrastive learning to learn decoupled content and emotion representation via an innovative Contrastive Decoupled Representation Learning (CDRL) algorithm. Specifically, a Contrastive Content Representation Learning (CCRL) module is designed to learn audio feature, which primarily contains content information, as content priors to guide learning content representation from the source input. Meanwhile, a Contrastive Emotion Representation Learning (CERL) module is proposed to make use of a pre-trained visual-language model to learn emotion prior, which is then used to guide learning emotion representation from the reference input. We further introduce emotion-aware and emotion-augmented contrastive learning to train CCRL and CERL modules, respectively, ensuring learning emotion-independent content representation and content-independent emotion representation. During SPFEM model training, the decoupled content and emotion representations are used to supervise the generation process, ensuring more accurate emotion manipulation together with audio-lip synchronization. Extensive experiments and evaluations on various benchmarks show the effectiveness of the proposed algorithm.
Knowledge-based Vision Question Answering (KB-VQA) systems address complex visual-grounded questions requiring external knowledge, such as web-sourced encyclopedia articles. Existing methods often use sequential and separate frameworks for the retriever and the generator with limited parametric knowledge sharing. However, since both retrieval and generation tasks require accurate understanding of contextual and external information, such separation can potentially lead to suboptimal system performance. Another key challenge is the integration of multimodal information. General-purpose multimodal pre-trained models, while adept at multimodal representation learning, struggle with fine-grained retrieval required for knowledge-intensive visual questions. Recent specialized pre-trained models mitigate the issue, but are computationally expensive. To bridge the gap, we propose a Unified Retrieval-Augmented VQA framework (UniRVQA). UniRVQA adapts general multimodal pre-trained models for fine-grained knowledge-intensive tasks within a unified framework, enabling cross-task parametric knowledge sharing and the extension of existing multimodal representation learning capability. We further introduce a reflective-answering mechanism that allows the model to explicitly evaluate and refine its knowledge boundary. Additionally, we integrate late interaction into the retrieval-augmented generation joint training process to enhance fine-grained understanding of queries and documents. Our approach achieves competitive performance against state-of-the-art models, delivering a significant 4.7% improvement in answering accuracy, and brings an average 7.5% boost in base MLLMs' VQA performance.