Transfer learning is a cornerstone of modern machine learning, promising a way to adapt models pretrained on a broad mix of data to new tasks with minimal new data. However, a significant challenge remains in ensuring that transferred features are sufficient to handle unseen datasets, amplified by the difficulty of quantifying whether two tasks are "related". To address these challenges, we evaluate model transfer from a pretraining mixture to each of its component tasks, assessing whether pretrained features can match the performance of task-specific direct training. We identify a fundamental limitation in deep learning models -- an "information saturation bottleneck" -- where networks fail to learn new features once they encode similar competing features during training. When restricted to learning only a subset of key features during pretraining, models will permanently lose critical features for transfer and perform inconsistently on data distributions, even components of the training mixture. Empirical evidence from published studies suggests that this phenomenon is pervasive in deep learning architectures -- factors such as data distribution or ordering affect the features that current representation learning methods can learn over time. This study suggests that relying solely on large-scale networks may not be as effective as focusing on task-specific training, when available. We propose richer feature representations as a potential solution to better generalize across new datasets and, specifically, present existing methods alongside a novel approach, the initial steps towards addressing this challenge.
Unified image understanding and generation has emerged as a promising paradigm in multimodal artificial intelligence. Despite recent progress, the optimal architectural design for such unified models remains an open challenge. In this work, we start by analyzing the modality alignment behaviors of task-specific expert models for understanding and generation, as well as current unified models. Our analysis reveals a crucial observation: understanding tasks benefit from a progressively increasing modality alignment across network depth, which helps build up semantic information for better comprehension; In contrast, generation tasks follow a different trend: modality alignment increases in the early layers but decreases in the deep layers to recover spatial details. These divergent alignment patterns create a fundamental conflict in fully shared Transformer backbones, where a uniform representational flow often leads to performance compromises across two tasks. Motivated by this finding, we introduce UniFork, a novel Y-shaped architecture that shares the shallow layers for cross-task representation learning, while employing task-specific branches in deeper layers to avoid task interference. This design effectively balances shared learning and task specialization. Through extensive ablation experiments, we demonstrate that Unifork consistently outperforms conventional fully shared Transformer architectures, and achieves performance on par with or better than task-specific models.
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.
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.
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.
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.
The local inductive bias of message-passing graph neural networks (GNNs) hampers their ability to exploit key structural information (e.g., connectivity and cycles). Positional encoding (PE) and Persistent Homology (PH) have emerged as two promising approaches to mitigate this issue. PE schemes endow GNNs with location-aware features, while PH methods enhance GNNs with multiresolution topological features. However, a rigorous theoretical characterization of the relative merits and shortcomings of PE and PH has remained elusive. We bridge this gap by establishing that neither paradigm is more expressive than the other, providing novel constructions where one approach fails but the other succeeds. Our insights inform the design of a novel learnable method, PiPE (Persistence-informed Positional Encoding), which is provably more expressive than both PH and PE. PiPE demonstrates strong performance across a variety of tasks (e.g., molecule property prediction, graph classification, and out-of-distribution generalization), thereby advancing the frontiers of graph representation learning. Code is available at https://github.com/Aalto-QuML/PIPE.
Hyperspectral image (HSI) clustering assigns similar pixels to the same class without any annotations, which is an important yet challenging task. For large-scale HSIs, most methods rely on superpixel segmentation and perform superpixel-level clustering based on graph neural networks (GNNs). However, existing GNNs cannot fully exploit the spectral information of the input HSI, and the inaccurate superpixel topological graph may lead to the confusion of different class semantics during information aggregation. To address these challenges, we first propose a structural-spectral graph convolutional operator (SSGCO) tailored for graph-structured HSI superpixels to improve their representation quality through the co-extraction of spatial and spectral features. Second, we propose an evidence-guided adaptive edge learning (EGAEL) module that adaptively predicts and refines edge weights in the superpixel topological graph. We integrate the proposed method into a contrastive learning framework to achieve clustering, where representation learning and clustering are simultaneously conducted. Experiments demonstrate that the proposed method improves clustering accuracy by 2.61%, 6.06%, 4.96% and 3.15% over the best compared methods on four HSI datasets. Our code is available at https://github.com/jhqi/SSGCO-EGAEL.
The scale diversity of point cloud data presents significant challenges in developing unified representation learning techniques for 3D vision. Currently, there are few unified 3D models, and no existing pre-training method is equally effective for both object- and scene-level point clouds. In this paper, we introduce UniPre3D, the first unified pre-training method that can be seamlessly applied to point clouds of any scale and 3D models of any architecture. Our approach predicts Gaussian primitives as the pre-training task and employs differentiable Gaussian splatting to render images, enabling precise pixel-level supervision and end-to-end optimization. To further regulate the complexity of the pre-training task and direct the model's focus toward geometric structures, we integrate 2D features from pre-trained image models to incorporate well-established texture knowledge. We validate the universal effectiveness of our proposed method through extensive experiments across a variety of object- and scene-level tasks, using diverse point cloud models as backbones. Code is available at https://github.com/wangzy22/UniPre3D.
Faithful evaluation of language model capabilities is crucial for deriving actionable insights that can inform model development. However, rigorous causal evaluations in this domain face significant methodological challenges, including complex confounding effects and prohibitive computational costs associated with extensive retraining. To tackle these challenges, we propose a causal representation learning framework wherein observed benchmark performance is modeled as a linear transformation of a few latent capability factors. Crucially, these latent factors are identified as causally interrelated after appropriately controlling for the base model as a common confounder. Applying this approach to a comprehensive dataset encompassing over 1500 models evaluated across six benchmarks from the Open LLM Leaderboard, we identify a concise three-node linear causal structure that reliably explains the observed performance variations. Further interpretation of this causal structure provides substantial scientific insights beyond simple numerical rankings: specifically, we reveal a clear causal direction starting from general problem-solving capabilities, advancing through instruction-following proficiency, and culminating in mathematical reasoning ability. Our results underscore the essential role of carefully controlling base model variations during evaluation, a step critical to accurately uncovering the underlying causal relationships among latent model capabilities.
Counterfactual image generation presents significant challenges, including preserving identity, maintaining perceptual quality, and ensuring faithfulness to an underlying causal model. While existing auto-encoding frameworks admit semantic latent spaces which can be manipulated for causal control, they struggle with scalability and fidelity. Advancements in diffusion models present opportunities for improving counterfactual image editing, having demonstrated state-of-the-art visual quality, human-aligned perception and representation learning capabilities. Here, we present a suite of diffusion-based causal mechanisms, introducing the notions of spatial, semantic and dynamic abduction. We propose a general framework that integrates semantic representations into diffusion models through the lens of Pearlian causality to edit images via a counterfactual reasoning process. To our knowledge, this is the first work to consider high-level semantic identity preservation for diffusion counterfactuals and to demonstrate how semantic control enables principled trade-offs between faithful causal control and identity preservation.
Self-supervised representation learning for point cloud has demonstrated effectiveness in improving pre-trained model performance across diverse tasks. However, as pre-trained models grow in complexity, fully fine-tuning them for downstream applications demands substantial computational and storage resources. Parameter-efficient fine-tuning (PEFT) methods offer a promising solution to mitigate these resource requirements, yet most current approaches rely on complex adapter and prompt mechanisms that increase tunable parameters. In this paper, we propose PointLoRA, a simple yet effective method that combines low-rank adaptation (LoRA) with multi-scale token selection to efficiently fine-tune point cloud models. Our approach embeds LoRA layers within the most parameter-intensive components of point cloud transformers, reducing the need for tunable parameters while enhancing global feature capture. Additionally, multi-scale token selection extracts critical local information to serve as prompts for downstream fine-tuning, effectively complementing the global context captured by LoRA. The experimental results across various pre-trained models and three challenging public datasets demonstrate that our approach achieves competitive performance with only 3.43% of the trainable parameters, making it highly effective for resource-constrained applications. Source code is available at: https://github.com/songw-zju/PointLoRA.
Extracting meaningful latent representations from high-dimensional sequential data is a crucial challenge in machine learning, with applications spanning natural science and engineering. We introduce InfoDPCCA, a dynamic probabilistic Canonical Correlation Analysis (CCA) framework designed to model two interdependent sequences of observations. InfoDPCCA leverages a novel information-theoretic objective to extract a shared latent representation that captures the mutual structure between the data streams and balances representation compression and predictive sufficiency while also learning separate latent components that encode information specific to each sequence. Unlike prior dynamic CCA models, such as DPCCA, our approach explicitly enforces the shared latent space to encode only the mutual information between the sequences, improving interpretability and robustness. We further introduce a two-step training scheme to bridge the gap between information-theoretic representation learning and generative modeling, along with a residual connection mechanism to enhance training stability. Through experiments on synthetic and medical fMRI data, we demonstrate that InfoDPCCA excels as a tool for representation learning. Code of InfoDPCCA is available at https://github.com/marcusstang/InfoDPCCA.
Contrastive learning for single object centric images has achieved remarkable progress on unsupervised representation, but suffering inferior performance on the widespread images with multiple objects. In this paper, we propose a simple but effective method, Multiple Object Stitching (MOS), to refine the unsupervised representation for multi-object images. Specifically, we construct the multi-object images by stitching the single object centric ones, where the objects in the synthesized multi-object images are predetermined. Hence, compared to the existing contrastive methods, our method provides additional object correspondences between multi-object images without human annotations. In this manner, our method pays more attention to the representations of each object in multi-object image, thus providing more detailed representations for complicated downstream tasks, such as object detection and semantic segmentation. Experimental results on ImageNet, CIFAR and COCO datasets demonstrate that our proposed method achieves the leading unsupervised representation performance on both single object centric images and multi-object ones. The source code is available at https://github.com/visresearch/MultipleObjectStitching.
What are the essential components of world models? How far do we get with world models that are not employing RNNs, transformers, discrete representations, and image reconstructions? This paper introduces SGF, a Simple, Good, and Fast world model that uses self-supervised representation learning, captures short-time dependencies through frame and action stacking, and enhances robustness against model errors through data augmentation. We extensively discuss SGF's connections to established world models, evaluate the building blocks in ablation studies, and demonstrate good performance through quantitative comparisons on the Atari 100k benchmark.
We present TextAtari, a benchmark for evaluating language agents on very long-horizon decision-making tasks spanning up to 100,000 steps. By translating the visual state representations of classic Atari games into rich textual descriptions, TextAtari creates a challenging test bed that bridges sequential decision-making with natural language processing. The benchmark includes nearly 100 distinct tasks with varying complexity, action spaces, and planning horizons, all rendered as text through an unsupervised representation learning framework (AtariARI). We evaluate three open-source large language models (Qwen2.5-7B, Gemma-7B, and Llama3.1-8B) across three agent frameworks (zero-shot, few-shot chain-of-thought, and reflection reasoning) to assess how different forms of prior knowledge affect performance on these long-horizon challenges. Four scenarios-Basic, Obscured, Manual Augmentation, and Reference-based-investigate the impact of semantic understanding, instruction comprehension, and expert demonstrations on agent decision-making. Our results reveal significant performance gaps between language agents and human players in extensive planning tasks, highlighting challenges in sequential reasoning, state tracking, and strategic planning across tens of thousands of steps. TextAtari provides standardized evaluation protocols, baseline implementations, and a framework for advancing research at the intersection of language models and planning.
With over 1,000,000 images from more than 10,000 exposures using state-of-the-art high-contrast imagers (e.g., Gemini Planet Imager, VLT/SPHERE) in the search for exoplanets, can artificial intelligence (AI) serve as a transformative tool in imaging Earth-like exoplanets in the coming decade? In this paper, we introduce a benchmark and explore this question from a polarimetric image representation learning perspective. Despite extensive investments over the past decade, only a few new exoplanets have been directly imaged. Existing imaging approaches rely heavily on labor-intensive labeling of reference stars, which serve as background to extract circumstellar objects (disks or exoplanets) around target stars. With our POLARIS (POlarized Light dAta for total intensity Representation learning of direct Imaging of exoplanetary Systems) dataset, we classify reference star and circumstellar disk images using the full public SPHERE/IRDIS polarized-light archive since 2014, requiring less than 10 percent manual labeling. We evaluate a range of models including statistical, generative, and large vision-language models and provide baseline performance. We also propose an unsupervised generative representation learning framework that integrates these models, achieving superior performance and enhanced representational power. To our knowledge, this is the first uniformly reduced, high-quality exoplanet imaging dataset, rare in astrophysics and machine learning. By releasing this dataset and baselines, we aim to equip astrophysicists with new tools and engage data scientists in advancing direct exoplanet imaging, catalyzing major interdisciplinary breakthroughs.
A limitation of modern document retrieval embedding methods is that they typically encode passages (chunks) from the same documents independently, often overlooking crucial contextual information from the rest of the document that could greatly improve individual chunk representations. In this work, we introduce ConTEB (Context-aware Text Embedding Benchmark), a benchmark designed to evaluate retrieval models on their ability to leverage document-wide context. Our results show that state-of-the-art embedding models struggle in retrieval scenarios where context is required. To address this limitation, we propose InSeNT (In-sequence Negative Training), a novel contrastive post-training approach which combined with late chunking pooling enhances contextual representation learning while preserving computational efficiency. Our method significantly improves retrieval quality on ConTEB without sacrificing base model performance. We further find chunks embedded with our method are more robust to suboptimal chunking strategies and larger retrieval corpus sizes. We open-source all artifacts at https://github.com/illuin-tech/contextual-embeddings.