We posit that handwriting recognition benefits from complementary cues carried by the rasterized complex glyph and the pen's trajectory, yet most systems exploit only one modality. We introduce an end-to-end network that performs early fusion of offline images and online stroke data within a shared latent space. A patch encoder converts the grayscale crop into fixed-length visual tokens, while a lightweight transformer embeds the $(x, y, \text{pen})$ sequence. Learnable latent queries attend jointly to both token streams, yielding context-enhanced stroke embeddings that are pooled and decoded under a cross-entropy loss objective. Because integration occurs before any high-level classification, temporal cues reinforce each other during representation learning, producing stronger writer independence. Comprehensive experiments on IAMOn-DB and VNOn-DB demonstrate that our approach achieves state-of-the-art accuracy, exceeding previous bests by up to 1\%. Our study also shows adaptation of this pipeline with gesturification on the ISI-Air dataset. Our code can be found here.
Microscopy image analysis is fundamental for different applications, from diagnosis to synthetic engineering and environmental monitoring. Modern acquisition systems have granted the possibility to acquire an escalating amount of images, requiring a consequent development of a large collection of deep learning-based automatic image analysis methods. Although deep neural networks have demonstrated great performance in this field, interpretability, an essential requirement for microscopy image analysis, remains an open challenge. This work proposes a Disentangled Representation Learning (DRL) methodology to enhance model interpretability for microscopy image classification. Exploiting benchmark datasets from three different microscopic image domains (plankton, yeast vacuoles, and human cells), we show how a DRL framework, based on transferring a representation learnt from synthetic data, can provide a good trade-off between accuracy and interpretability in this domain.
Multi-modal learning is a fast growing area in artificial intelligence. It tries to help machines understand complex things by combining information from different sources, like images, text, and audio. By using the strengths of each modality, multi-modal learning allows AI systems to build stronger and richer internal representations. These help machines better interpretation, reasoning, and making decisions in real-life situations. This field includes core techniques such as representation learning (to get shared features from different data types), alignment methods (to match information across modalities), and fusion strategies (to combine them by deep learning models). Although there has been good progress, some major problems still remain. Like dealing with different data formats, missing or incomplete inputs, and defending against adversarial attacks. Researchers now are exploring new methods, such as unsupervised or semi-supervised learning, AutoML tools, to make models more efficient and easier to scale. And also more attention on designing better evaluation metrics or building shared benchmarks, make it easier to compare model performance across tasks and domains. As the field continues to grow, multi-modal learning is expected to improve many areas: computer vision, natural language processing, speech recognition, and healthcare. In the future, it may help to build AI systems that can understand the world in a way more like humans, flexible, context aware, and able to deal with real-world complexity.
Dynamic graphs exhibit complex temporal dynamics due to the interplay between evolving node features and changing network structures. Recently, Graph Neural Controlled Differential Equations (Graph Neural CDEs) successfully adapted Neural CDEs from paths on Euclidean domains to paths on graph domains. Building on this foundation, we introduce Permutation Equivariant Neural Graph CDEs, which project Graph Neural CDEs onto permutation equivariant function spaces. This significantly reduces the model's parameter count without compromising representational power, resulting in more efficient training and improved generalisation. We empirically demonstrate the advantages of our approach through experiments on simulated dynamical systems and real-world tasks, showing improved performance in both interpolation and extrapolation scenarios.
Integrating compositional and symbolic properties into current distributional semantic spaces can enhance the interpretability, controllability, compositionality, and generalisation capabilities of Transformer-based auto-regressive language models (LMs). In this survey, we offer a novel perspective on latent space geometry through the lens of compositional semantics, a direction we refer to as \textit{semantic representation learning}. This direction enables a bridge between symbolic and distributional semantics, helping to mitigate the gap between them. We review and compare three mainstream autoencoder architectures-Variational AutoEncoder (VAE), Vector Quantised VAE (VQVAE), and Sparse AutoEncoder (SAE)-and examine the distinctive latent geometries they induce in relation to semantic structure and interpretability.
Identifiable causal representation learning seeks to uncover the true causal relationships underlying a data generation process. In medical imaging, this presents opportunities to improve the generalisability and robustness of task-specific latent features. This work introduces the concept of grouping observations to learn identifiable representations for disease classification in chest X-rays via an end-to-end framework. Our experiments demonstrate that these causal representations improve generalisability and robustness across multiple classification tasks when grouping is used to enforce invariance w.r.t race, sex, and imaging views.
Multivariate time series forecasting requires models to simultaneously capture variable-wise structural dependencies and generalize across diverse tasks. While structural encoders are effective in modeling feature interactions, they lack the capacity to support semantic-level reasoning or task adaptation. Conversely, large language models (LLMs) possess strong generalization capabilities but remain incompatible with raw time series inputs. This gap limits the development of unified, transferable prediction systems. Therefore, we introduce SEED, a structural encoder for embedding-driven decoding, which integrates four stages: a token-aware encoder for patch extraction, a projection module that aligns patches with language model embeddings, a semantic reprogramming mechanism that maps patches to task-aware prototypes, and a frozen language model for prediction. This modular architecture decouples representation learning from inference, enabling efficient alignment between numerical patterns and semantic reasoning. Empirical results demonstrate that the proposed method achieves consistent improvements over strong baselines, and comparative studies on various datasets confirm SEED's role in addressing the structural-semantic modeling gap.
The LifeTime Value (LTV) prediction, which endeavors to forecast the cumulative purchase contribution of a user to a particular item, remains a vital challenge that advertisers are keen to resolve. A precise LTV prediction system enhances the alignment of user interests with meticulously designed advertisements, thereby generating substantial profits for advertisers. Nonetheless, this issue is complicated by the paucity of data typically observed in real-world advertising scenarios. The purchase rate among registered users is often as critically low as 0.1%, resulting in a dataset where the majority of users make only several purchases. Consequently, there is insufficient supervisory signal for effectively training the LTV prediction model. An additional challenge emerges from the interdependencies among tasks with high correlation. It is a common practice to estimate a user's contribution to a game over a specified temporal interval. Varying the lengths of these intervals corresponds to distinct predictive tasks, which are highly correlated. For instance, predictions over a 7-day period are heavily reliant on forecasts made over a 3-day period, where exceptional cases can adversely affect the accuracy of both tasks. In order to comprehensively address the aforementioned challenges, we introduce an innovative framework denoted as Graph-Represented Pareto-Optimal LifeTime Value prediction (GRePO-LTV). Graph representation learning is initially employed to address the issue of data scarcity. Subsequently, Pareto-Optimization is utilized to manage the interdependence of prediction tasks.
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.
Large vision models (LVM) based gait recognition has achieved impressive performance. However, existing LVM-based approaches may overemphasize gait priors while neglecting the intrinsic value of LVM itself, particularly the rich, distinct representations across its multi-layers. To adequately unlock LVM's potential, this work investigates the impact of layer-wise representations on downstream recognition tasks. Our analysis reveals that LVM's intermediate layers offer complementary properties across tasks, integrating them yields an impressive improvement even without rich well-designed gait priors. Building on this insight, we propose a simple and universal baseline for LVM-based gait recognition, termed BiggerGait. Comprehensive evaluations on CCPG, CAISA-B*, SUSTech1K, and CCGR\_MINI validate the superiority of BiggerGait across both within- and cross-domain tasks, establishing it as a simple yet practical baseline for gait representation learning. All the models and code will be publicly available.
Image-based cell profiling aims to create informative representations of cell images. This technique is critical in drug discovery and has greatly advanced with recent improvements in computer vision. Inspired by recent developments in non-contrastive Self-Supervised Learning (SSL), this paper provides an initial exploration into training a generalizable feature extractor for cell images using such methods. However, there are two major challenges: 1) There is a large difference between the distributions of cell images and natural images, causing the view-generation process in existing SSL methods to fail; and 2) Unlike typical scenarios where each representation is based on a single image, cell profiling often involves multiple input images, making it difficult to effectively combine all available information. To overcome these challenges, we propose SSLProfiler, a non-contrastive SSL framework specifically designed for cell profiling. We introduce specialized data augmentation and representation post-processing methods tailored to cell images, which effectively address the issues mentioned above and result in a robust feature extractor. With these improvements, SSLProfiler won the Cell Line Transferability challenge at CVPR 2025.
Distribution matching (DM) is a versatile domain-invariant representation learning technique that has been applied to tasks such as fair classification, domain adaptation, and domain translation. Non-parametric DM methods struggle with scalability and adversarial DM approaches suffer from instability and mode collapse. While likelihood-based methods are a promising alternative, they often impose unnecessary biases through fixed priors or require explicit density models (e.g., flows) that can be challenging to train. We address this limitation by introducing a novel approach to training likelihood-based DM using expressive score-based prior distributions. Our key insight is that gradient-based DM training only requires the prior's score function -- not its density -- allowing us to train the prior via denoising score matching. This approach eliminates biases from fixed priors (e.g., in VAEs), enabling more effective use of geometry-preserving regularization, while avoiding the challenge of learning an explicit prior density model (e.g., a flow-based prior). Our method also demonstrates better stability and computational efficiency compared to other diffusion-based priors (e.g., LSGM). Furthermore, experiments demonstrate superior performance across multiple tasks, establishing our score-based method as a stable and effective approach to distribution matching. Source code available at https://github.com/inouye-lab/SAUB.
Self-supervised learning (SSL) has achieved major advances in natural images and video understanding, but challenges remain in domains like echocardiography (heart ultrasound) due to subtle anatomical structures, complex temporal dynamics, and the current lack of domain-specific pre-trained models. Existing SSL approaches such as contrastive, masked modeling, and clustering-based methods struggle with high intersample similarity, sensitivity to low PSNR inputs common in ultrasound, or aggressive augmentations that distort clinically relevant features. We present DISCOVR (Distilled Image Supervision for Cross Modal Video Representation), a self-supervised dual branch framework for cardiac ultrasound video representation learning. DISCOVR combines a clustering-based video encoder that models temporal dynamics with an online image encoder that extracts fine-grained spatial semantics. These branches are connected through a semantic cluster distillation loss that transfers anatomical knowledge from the evolving image encoder to the video encoder, enabling temporally coherent representations enriched with fine-grained semantic understanding. Evaluated on six echocardiography datasets spanning fetal, pediatric, and adult populations, DISCOVR outperforms both specialized video anomaly detection methods and state-of-the-art video-SSL baselines in zero-shot and linear probing setups, and achieves superior segmentation transfer.
The pretraining-and-finetuning paradigm has driven significant advances across domains, such as natural language processing and computer vision, with representative pretraining paradigms such as masked language modeling and next-token prediction. However, in molecular representation learning, the task design remains largely limited to node-level denoising, which is effective at modeling local atomic environments, yet maybe insufficient for capturing the global molecular structure required by graph-level property prediction tasks, such as energy estimation and molecular regression. In this work, we present GeoRecon, a novel graph-level pretraining framework that shifts the focus from individual atoms to the molecule as an integrated whole. GeoRecon introduces a graph-level reconstruction task: during pretraining, the model is trained to generate an informative graph representation capable of accurately guiding reconstruction of the molecular geometry. This encourages the model to learn coherent, global structural features rather than isolated atomic details. Without relying on additional supervision or external data, GeoRecon outperforms node-centric baselines on multiple molecular benchmarks (e.g., QM9, MD17), demonstrating the benefit of incorporating graph-level reconstruction for learning more holistic and geometry-aware molecular embeddings.
Coupling of physics across length and time scales plays an important role in the response of microstructured materials to external loads. In a multi-scale framework, unresolved (subgrid) meso-scale dynamics is upscaled to the homogenized (macro-scale) representation of the heterogeneous material through closure models. Deep learning models trained using meso-scale simulation data are now a popular route to assimilate such closure laws. However, meso-scale simulations are computationally taxing, posing practical challenges in training deep learning-based surrogate models from scratch. In this work, we investigate an alternative meta-learning approach motivated by the idea of tokenization in natural language processing. We show that one can learn a reduced representation of the micro-scale physics to accelerate the meso-scale learning process by tokenizing the meso-scale evolution of the physical fields involved in an archetypal, albeit complex, reactive dynamics problem, \textit{viz.}, shock-induced energy localization in a porous energetic material. A probabilistic latent representation of \textit{micro}-scale dynamics is learned as building blocks for \textit{meso}-scale dynamics. The \textit{meso-}scale latent dynamics model learns the correlation between neighboring building blocks by training over a small dataset of meso-scale simulations. We compare the performance of our model with a physics-aware recurrent convolutional neural network (PARC) trained only on the full meso-scale dataset. We demonstrate that our model can outperform PARC with scarce meso-scale data. The proposed approach accelerates the development of closure models by leveraging inexpensive micro-scale simulations and fast training over a small meso-scale dataset, and can be applied to a range of multi-scale modeling problems.
Traditional instrumental variable (IV) estimators face a fundamental constraint: they can only accommodate as many endogenous treatment variables as available instruments. This limitation becomes particularly challenging in settings where the treatment is presented in a high-dimensional and unstructured manner (e.g. descriptions of patient treatment pathways in a hospital). In such settings, researchers typically resort to applying unsupervised dimension reduction techniques to learn a low-dimensional treatment representation prior to implementing IV regression analysis. We show that such methods can suffer from substantial omitted variable bias due to implicit regularization in the representation learning step. We propose a novel approach to construct treatment representations by explicitly incorporating instrumental variables during the representation learning process. Our approach provides a framework for handling high-dimensional endogenous variables with limited instruments. We demonstrate both theoretically and empirically that fitting IV models on these instrument-informed representations ensures identification of directions that optimize outcome prediction. Our experiments show that our proposed methodology improves upon the conventional two-stage approaches that perform dimension reduction without incorporating instrument information.
Proteins are fundamental to biology, executing diverse functions through complex physicochemical interactions, and they hold transformative potential across medicine, materials science, and environmental applications. Protein Language Models (pLMs) aim to unlock insights from the vast space of unlabeled protein sequences by learning rich, semantic representations from primary sequences via masked language modeling. However, these models typically exhibit limited generative capacity. In this work, we introduce the Diffusion Sequence Model (DSM), a novel pLM trained with masked diffusion to enable both high-quality representation learning and generative protein design. DSM builds upon the ESM2 architecture by incorporating a masked forward diffusion process inspired by the LLaDA framework. After training, DSM is capable of generating diverse, biomimetic sequences that align with expected amino acid compositions, secondary structures, and predicted functions, even with 90\% token corruption. Furthermore, DSM's learned representations match or exceed those of similarly sized pLMs on downstream tasks. We also introduce DSM(ppi), a variant fine-tuned to generate protein binders by attending to target sequences. We demonstrate DSM(ppi)'s effectiveness on the challenging Bench-tested Binder Benchmark (BenchBB), where both DSM and DSM(ppi) produce candidates with superior predicted binding affinity compared to known binders. Our results establish masked diffusion as a powerful paradigm for unifying protein representation and generation in a single framework.
Deciphering protein function remains a fundamental challenge in protein representation learning. The task presents significant difficulties for protein language models (PLMs) due to the sheer volume of functional annotation categories and the highly imbalanced distribution of annotated instances across biological ontologies. Inspired by the remarkable success of reinforcement learning from human feedback (RLHF) in large language model (LLM) alignment, we propose AnnoDPO, a novel multi-modal framework for protein function prediction that leverages Direct Preference Optimization (DPO) to enhance annotation learning. Our methodology addresses the dual challenges of annotation scarcity and category imbalance through preference-aligned training objectives, establishing a new paradigm for biological knowledge integration in protein representation learning.
Proteins are central to biological systems, participating as building blocks across all forms of life. Despite advancements in understanding protein functions through protein sequence analysis, there remains potential for further exploration in integrating protein structural information. We argue that the structural information of proteins is not only limited to their 3D information but also encompasses information from amino acid molecules (local information) to protein-protein structure similarity (global information). To address this, we propose \textbf{GLProtein}, the first framework in protein pre-training that incorporates both global structural similarity and local amino acid details to enhance prediction accuracy and functional insights. GLProtein innovatively combines protein-masked modelling with triplet structure similarity scoring, protein 3D distance encoding and substructure-based amino acid molecule encoding. Experimental results demonstrate that GLProtein outperforms previous methods in several bioinformatics tasks, including predicting protein-protein interaction, contact prediction, and so on.
Distributed fiber-optic acoustic sensing (DAS) has emerged as a transformative approach for distributed vibration measurement with high spatial resolution and long measurement range while maintaining cost-efficiency. However, the two-dimensional spatial-temporal DAS signals present analytical challenges. The abstract signal morphology lacking intuitive physical correspondence complicates human interpretation, and its unique spatial-temporal coupling renders conventional image processing methods suboptimal. This study investigates spatial-temporal characteristics and proposes a self-supervised pre-training framework that learns signals' representations through a mask-reconstruction task. This framework is named the DAS Masked AutoEncoder (DAS-MAE). The DAS-MAE learns high-level representations (e.g., event class) without using labels. It achieves up to 1% error and 64.5% relative improvement (RI) over the semi-supervised baseline in few-shot classification tasks. In a practical external damage prevention application, DAS-MAE attains a 5.0% recognition error, marking a 75.7% RI over supervised training from scratch. These results demonstrate the high-performance and universal representations learned by the DAS-MAE framework, highlighting its potential as a foundation model for analyzing massive unlabeled DAS signals.