论文检索

Applications · Genetics, Cell Biology, etc

Mohammad Saleh Refahi, Mahdi Abavisani, Bahrad Sokhansanj, James R Brown, Gail Rosen

Transformers have revolutionized nucleotide sequence analysis, yet capturing long‑range dependencies remains challenging. Recent studies show that autoregressive transformers often exhibit Markovian behavior by relying on fixed-length context windows for next-token prediction. However, standard self-attention mechanisms are computationally inefficient for long sequences due to their quadratic complexity and do not explicitly enforce global transition consistency. We introduce CARMANIA (Context-Aware Regularization with Markovian Integration for Attention-Based Nucleotide Analysis), a self-supervised pretraining framework that augments next-token (NT) prediction with a transition-matrix (TM) loss. The TM loss aligns predicted token transitions with empirically derived n-gram statistics from each input sequence, encouraging the model to capture higher-order dependencies beyond local context. This integration enables CARMANIA to learn organism-specific sequence structures that reflect both evolutionary constraints and functional organization. We evaluate CARMANIA across diverse genomic tasks, including regulatory element prediction, functional gene classification, taxonomic inference, antimicrobial resistance detection, and biosynthetic gene cluster classification. CARMANIA outperforms the previous best long-context model by at least 7\%, matches state-of-the-art on shorter sequences (exceeding prior results on 20/40 tasks while running $\sim$2.5$\times$ faster), and shows particularly strong improvements on enhancer and housekeeping gene classification tasks—including up to a 34\% absolute gain in Matthews correlation coefficient (MCC) for enhancer prediction. The TM loss boosts accuracy in 33 of 40 tasks, especially where local motifs or regulatory patterns drive prediction. This enables more effective modeling of sequence-dependent biological features while maintaining robustness across non-coding and low-signal regions. Code available at https://github.com/EESI/carmania.

Deep Learning · Graph Neural Networks

Haoran Sun, Fei Xiong, Yuanzhe Hu, Liang Wang

Collaborative filtering (CF) methods are now facing the challenge of data sparsity in recommender systems. In order to reduce the effect of data sparsity, researchers proposed contrastive learning methods to extract self-supervised signals from raw data. Contrastive learning methods address this problem by graph augmentation and maximizing the consistency of node representations between different augmented graphs. However, these methods tends to unintentionally distance the target node from its path nodes on the interaction path, thus limiting its effectiveness. In this regard, we propose a solution that uses paths as samples in the contrastive loss function. In order to obtain the path samples, we design a path sampling method. In addition to the contrast of the relationship between the target node and the nodes within the path (intra-path contrast), we also designed a method of contrasting the relationship between the paths (inter-path contrast) to better pull the target node and its path nodes closer to each other. We use Simplifying and Powering Graph Convolution Network (LightGCN) as the basis and combine with a new path-enhanced graph approach proposed for graph augmentation. It effectively improves the performance of recommendation models. Our proposed Path Enhanced Contrastive Loss (PECL) model replaces the common contrastive loss function with our novel loss function, showing significant performance improvement. Experiments on three real-world datasets demonstrate the effectiveness of our model.

Computer Vision · Classification and Understanding

Jiaqi Zhang, Juntuo Wang, Zhixin Sun, John Zou, Randall Balestriero

Large-scale vision foundation models such as DINOv2 boast impressive performances by leveraging massive architectures and training datasets. The expense of large-scale pre-training puts such research out of reach for many, hence limiting scientific advancements. We thus propose a novel pretraining strategy for DINOv2 that simultaneously accelerates convergence–and strengthens robustness to common corruptions as a by-product. Our approach involves a frequency filtering curriculum–low-frequency being seen first–and the Gaussian noise patching augmentation. Applied to a ViT-B/16 backbone trained on ImageNet-1K, while pre-training time is reduced by 1.6×–from 16.64 to 10.32 NVIDIA L40S days–and FLOPs by 2.25×, our method still achieves matching robustness in corruption benchmarks (ImageNet-C) and maintains competitive linear probing performance compared with the DINOv2 baseline. This dual benefit of efficiency and robustness makes large-scale self-supervised foundation modeling more attainable, while opening the door to novel exploration around data curriculum and augmentation as a means to improve self-supervised learning models robustness.

Social Aspects · Fairness, Equity, Justice and Safety

Sungik Choi, Hankook Lee, Moontae Lee

AI-generated image detection has become crucial with the rapid advancement of vision-generative models. Instead of training detectors tailored to specific datasets, we study a training-free approach leveraging self-supervised models without requiring prior data knowledge. These models, pre-trained with augmentations like $\texttt{RandomResizedCrop}$, learn to produce consistent representations across varying resolutions. Motivated by this, we propose $\textbf{WaRPAD},$ a training-free AI-generated image detection algorithm based on self-supervised models. Since neighborhood pixel differences in images are highly sensitive to resizing operations, WaRPAD first defines a base score function that quantifies the sensitivity of image embeddings to perturbations along high-frequency directions extracted via Haar wavelet decomposition. To simulate robustness against cropping augmentation, we rescale each image to a multiple of the model’s input size, divide it into smaller patches, and compute the base score for each patch. The final detection score is then obtained by averaging the scores across all patches. We validate WaRPAD on real datasets of diverse resolutions and domains, and images generated by 23 different generative models. Our method consistently achieves competitive performance and demonstrates strong robustness to test-time corruptions. Furthermore, as invariance to $\texttt{RandomResizedCrop}$ is a common training scheme across self-supervised models, we show that WaRPAD is applicable across self-supervised models.

Social Aspects · Privacy-preserving Statistics and Machine Learning

Xin Yao, Haiyang Zhao, Yimin Chen, Jiawei Guo, Kecheng Huang, Ming Zhao

The Contrastive Language-Image Pretraining (CLIP) model has significantly advanced vision-language modeling by aligning image-text pairs from large-scale web data through self-supervised contrastive learning. Yet, its reliance on uncurated Internet-sourced data exposes it to data poisoning and backdoor risks. While existing studies primarily investigate image-based attacks, the text modality, which is equally central to CLIP's training, remains underexplored. In this work, we introduce ToxicTextCLIP, a framework for generating high-quality adversarial texts that target CLIP during the pre-training phase. The framework addresses two key challenges: semantic misalignment caused by background inconsistency with the target class, and the scarcity of background-consistent texts. To this end, ToxicTextCLIP iteratively applies: 1) a background-aware selector that prioritizes texts with background content aligned to the target class, and 2) a background-driven augmenter that generates semantically coherent and diverse poisoned samples. Extensive experiments on classification and retrieval tasks show that ToxicTextCLIP achieves up to 95.83\% poisoning success and 98.68% backdoor Hit@1, while bypassing RoCLIP, CleanCLIP and SafeCLIP defenses. The source code can be accessed via https://github.com/xinyaocse/ToxicTextCLIP/.

General Machine Learning · Representation Learning

Sara Atito, Josef Kittler, Imran Razzak, Muhammad Awais

Humans understand visual scenes by first capturing a global impression and then refining this understanding into distinct, object-like components. Inspired by this process, we introduce \textbf{C}oncept-\textbf{G}uided \textbf{S}elf-\textbf{S}upervised \textbf{L}earning (CG-SSL), a novel framework that brings structure and interpretability to representation learning through a curriculum of three training phases: (1) global scene encoding, (2) discovery of visual concepts via tokenised cross-attention, and (3) alignment of these concepts across views. Unlike traditional SSL methods, which simply enforce similarity between multiple augmented views of the same image, CG-SSL accounts for the fact that these views may highlight different parts of an object or scene. To address this, our method establishes explicit correspondences between views and aligns the representations of meaningful image regions. At its core, CG-SSL augments standard SSL with a lightweight decoder that learns and refines concept tokens via cross-attention with patch features. The concept tokens are trained using masked concept distillation and a feature-space reconstruction objective. A final alignment stage enforces view consistency by geometrically matching concept regions under heavy augmentation, enabling more compact, robust, and disentangled representations of scene regions. Across multiple backbone sizes, CG-SSL achieves state-of-the-art results on image segmentation benchmarks using $k$-NN and linear probes, substantially outperforming prior methods and approaching, or even surpassing, the performance of leading SSL models trained on over $100\times$ more data. Code and pretrained models will be released.

General Machine Learning · Transfer, Multitask and Meta-learning

guojun lei, Rong Zhang, Tianhang Liu, Hong Li, Zhiyuan Ma, Chi Wang, Weiwei Xu

Recent advancements in video generation models have enabled the creation of diverse and realistic videos, with promising applications in advertising and film production. However, as one of the essential tasks of video generation models, video concept transfer remains significantly challenging. Existing methods generally model video as an entirety, leading to limited flexibility and precision when solely editing specific regions or concepts. To mitigate this dilemma, we propose a novel architecture UniTransfer, which introduces both spatial and diffusion timestep decomposition in a progressive paradigm, achieving precise and controllable video concept transfer. Specifically, in terms of spatial decomposition, we decouple videos into three key components: the foreground subject, the background, and the motion flow. Building upon this decomposed formulation, we further introduce a dual-to-single-stream DiT-based architecture for supporting fine-grained control over different components in the videos. We also introduce a self-supervised pretraining strategy based on random masking to enhance the decomposed representation learning from large-scale unlabeled video data. Inspired by the Chain-of-Thought reasoning paradigm, we further revisit the denoising diffusion process and propose a Chain-of-Prompt (CoP) mechanism to achieve the timestep decomposition. We decompose the denoising process into three stages of different granularity and leverage large language models (LLMs) for stage-specific instructions to guide the generation progressively. We also curate an animal-centric video dataset called OpenAnimal to facilitate the advancement and benchmarking of research in video concept transfer. Extensive experiments demonstrate that our method achieves high-quality and controllable video concept transfer across diverse reference images and scenes, surpassing existing baselines in both visual fidelity and editability.

Deep Learning · Graph Neural Networks

Chendi Qian, Christopher Morris

Linear and quadratic optimization are crucial in numerous real-world applications, ranging from training machine learning models to solving integer linear programs. Recently, learning-to-optimize methods (L2O) for linear (LPs) or quadratic programs (QPs) using message-passing graph neural networks (MPNNs) have gained traction, promising lightweight, data-driven proxies for solving such optimization problems. For example, they replace the costly computation of strong branching scores in branch-and-bound solvers, thereby reducing the need to solve many such optimization problems. However, robust L2O MPNNs remain challenging in data-scarce settings, especially when addressing complex optimization problems such as QPs. This work introduces a principled approach to data augmentation tailored for QPs via MPNNs. Our method leverages theoretically justified data augmentation techniques to generate diverse yet optimality-preserving instances. Furthermore, we integrate these augmentations into a self-supervised contrastive learning framework, thereby pretraining MPNNs for improved performance on L2O tasks. Extensive experiments demonstrate that our approach improves generalization in supervised scenarios and facilitates effective transfer learning to related optimization problems.

Theory · Everything Else

Yu Gui, Cong Ma, Zongming Ma

Multi-modal contrastive learning as a self-supervised representation learning technique has achieved great success in foundation model training, such as CLIP~\citep{radford2021learning}. In this paper, we study the theoretical properties of the learned representations from multi-modal contrastive learning beyond linear representations and specific data distributions. Our analysis reveals that, enabled by temperature optimization, multi-modal contrastive learning not only maximizes mutual information between modalities but also adapts to intrinsic dimensions of data, which can be much lower than user-specified dimensions for representation vectors. Experiments on both synthetic and real-world datasets demonstrate the ability of contrastive learning to learn low-dimensional and informative representations, bridging theoretical insights and practical performance.

Applications · Neuroscience, Cognitive Science

Vinam Arora, Divyansha Lachi, Ian Knight, Mehdi Azabou, Blake Richards, Cole Hurwitz, Joshua H Siegle, Eva L Dyer

Identifying the functional identity of individual neurons is essential for interpreting circuit dynamics, yet it remains a major challenge in large-scale _in vivo_ recordings where anatomical and molecular labels are often unavailable. Here we introduce NuCLR, a self-supervised framework that learns context-aware representations of neuron identity by modeling each neuron's role within the broader population. NuCLR employs a spatio-temporal transformer that captures both within-neuron dynamics and across-neuron interactions. It is trained with a sample-wise contrastive objective that encourages temporally-stable and discriminative embeddings. Across multiple open-access datasets, NuCLR outperforms prior methods in both cell type and brain region classification. Critically, it exhibits strong zero-shot generalization to entirely new populations, without any retraining or access to stimulus labels. Furthermore, we demonstrate that our framework scales effectively with data size. Overall, our results demonstrate that modeling population context is crucial for understanding neuron identity and that rich signal for cell-typing and neuron localization is present in neural activity alone. Code available at: https://github.com/nerdslab/nuclr.

Applications · Robotics

Jingyi Tian, Le Wang, Sanping Zhou, Sen Wang, lijiayi, Gang Hua

Learning generalizable robotic manipulation policies remains a key challenge due to the scarcity of diverse real-world training data. While recent approaches have attempted to mitigate this through self-supervised representation learning, most either rely on 2D vision pretraining paradigms such as masked image modeling, which primarily focus on static semantics or scene geometry, or utilize large-scale video prediction models that emphasize 2D dynamics, thus failing to jointly learn the geometry, semantics, and dynamics required for effective manipulation. In this paper, we present DynaRend, a representation learning framework that learns 3D-aware and dynamics-informed triplane features via masked reconstruction and future prediction using differentiable volumetric rendering. By pretraining on multi-view RGB-D video data, DynaRend jointly captures spatial geometry, future dynamics, and task semantics in a unified triplane representation. The learned representations can be effectively transferred to downstream robotic manipulation tasks via action value map prediction. We evaluate DynaRend on two challenging benchmarks, RLBench and Colosseum, as well as in real-world robotic experiments, demonstrating substantial improvements in policy success rate, generalization to environmental perturbations, and real-world applicability across diverse manipulation tasks.

Computer Vision · Vision Models & Multimodal

Haiming Zhang, Yiyao Zhu, Wending Zhou, Xu Yan, Yingjie CAI, Bingbing Liu, Shuguang Cui, Zhen Li

Sparse Perception Models (SPMs) adopt a query-driven paradigm that forgoes explicit dense BEV or volumetric construction, enabling highly efficient computation and accelerated inference. In this paper, we introduce SQS, a novel query-based splatting pre-training specifically designed to advance SPMs in autonomous driving. SQS introduces a plug-in module that predicts 3D Gaussian representations from sparse queries during pre-training, leveraging self-supervised splatting to learn fine-grained contextual features through the reconstruction of multi-view images and depth maps. During fine-tuning, the pre-trained Gaussian queries are seamlessly integrated into downstream networks via query interaction mechanisms that explicitly connect pre-trained queries with task-specific queries, effectively accommodating the diverse requirements of occupancy prediction and 3D object detection. Extensive experiments on autonomous driving benchmarks demonstrate that SQS delivers considerable performance gains across multiple query-based 3D perception tasks, notably in occupancy prediction and 3D object detection, outperforming prior state-of-the-art pre-training approaches by a significant margin (i.e., +1.3 mIoU on occupancy prediction and +1.0 NDS on 3D detection).

General Machine Learning · Representation Learning

Jesimon Barreto, Carlos Caetano, Andre Araujo, William Schwartz

Foundation models have advanced computer vision by enabling strong performance across diverse tasks through large-scale pretraining and supervised fine-tuning. However, they may underperform in domains with distribution shifts and scarce labels, where supervised fine-tuning may be infeasible. While continued self-supervised learning for model adaptation is common for generative language models, this strategy has not proven effective for vision-centric encoder models. To address this challenge, we introduce a novel formulation of self-supervised fine-tuning for vision foundation models, where the model is adapted to a new domain without requiring annotations, leveraging only short multi-view object-centric videos. Our method is referred to as VESSA: **V**ideo-based obj**E**ct-centric **S**elf-**S**upervised **A**daptation for visual foundation models. VESSA's training technique is based on a self-distillation paradigm, where it is critical to carefully tune prediction heads and deploy parameter-efficient adaptation techniques – otherwise, the model may quickly forget its pretrained knowledge and reach a degraded state. VESSA benefits significantly from multi-view object observations sourced from different frames in an object-centric video, efficiently learning robustness to varied capture conditions, without the need of annotations. Through comprehensive experiments with 3 vision foundation models on 2 datasets, VESSA demonstrates consistent improvements in downstream classification tasks, compared to the base models and previous adaptation methods. Code is publicly available at https://github.com/jesimonbarreto/VESSA.

General Machine Learning · Transfer, Multitask and Meta-learning

Jaekyun Park, Hye Won Chung

In the era of large-scale foundation models, fully fine-tuning pretrained networks for each downstream task is often prohibitively resource-intensive. Prompt tuning offers a lightweight alternative by introducing tunable prompts while keeping the backbone frozen. However, existing visual prompt tuning methods often fail to specialize the prompts or enrich the representation space--especially when applied to self-supervised backbones. We show that these limitations become especially pronounced in challenging tasks and data-scarce settings, where effective adaptation is most critical. In this work, we introduce VIPAMIN, a visual prompt initialization strategy that enhances adaptation of self-supervised models by (1) aligning prompts with semantically informative regions in the embedding space, and (2) injecting novel representational directions beyond the pretrained subspace. Despite its simplicity--requiring only a single forward pass and lightweight operations--VIPAMIN consistently improves performance across diverse tasks and dataset sizes, setting a new state of the art in visual prompt tuning.

General Machine Learning · Representation Learning

Achleshwar Luthra, Tianbao Yang, Tomer Galanti

Despite its empirical success, the theoretical foundations of self-supervised contrastive learning (CL) are not yet fully established. In this work, we address this gap by showing that standard CL objectives implicitly approximate a supervised variant we call the negatives-only supervised contrastive loss (NSCL), which excludes same-class contrasts. We prove that the gap between the CL and NSCL losses vanishes as the number of semantic classes increases, under a bound that is both label-agnostic and architecture-independent. We characterize the geometric structure of the global minimizers of the NSCL loss: the learned representations exhibit augmentation collapse, within-class collapse, and class centers that form a simplex equiangular tight frame. We further introduce a new bound on the few-shot error of linear-probing. This bound depends on two measures of feature variability—within-class dispersion and variation along the line between class centers. We show that directional variation dominates the bound and that the within-class dispersion's effect diminishes as the number of labeled samples increases. These properties enable CL and NSCL-trained representations to support accurate few-shot label recovery using simple linear probes. Finally, we empirically validate our theoretical findings: the gap between CL and NSCL losses decays at a rate of $\mathcal{O}(\frac{1}{\#\text{classes}})$; the two losses are highly correlated; minimizing the CL loss implicitly brings the NSCL loss close to the value achieved by direct minimization; and the proposed few-shot error bound provides a tight estimate of probing performance in practice.

General Machine Learning · Representation Learning

Naghmeh Ghanooni, Waleed Mustafa, Dennis Wagner, Sophie Fellenz, Anthony Lin, Marius Kloft

Neural networks generally prefer simple and easy-to-learn features. When these features are spuriously correlated with the labels, the network's performance can suffer, particularly for underrepresented classes or concepts. Self-supervised representation learning methods, such as contrastive learning, are especially prone to this issue, often resulting in worse performance on downstream tasks. We identify a key spectral signature of this failure: early reliance on dominant singular modes of the learned feature matrix. To mitigate this, we propose a novel framework that promotes a uniform eigenspectrum of the feature covariance matrix, encouraging diverse and semantically rich representations. Our method operates in a fully self-supervised setting, without relying on ground-truth labels or any additional information. Empirical results on SimCLR and SimSiam demonstrate consistent gains in robustness and transfer performance, suggesting broad applicability across self-supervised learning paradigms. Code: https://github.com/NaghmehGh/SpuriousCorrelation_SSRL

Yuxuan Yang, Dalin Zhang, Yuxuan Liang, Hua Lu, Gang Chen, Huan Li

Time Series Forecasting (TSF) is a crucial task in various domains, yet existing TSF models rely heavily on high-quality data and insufficiently exploit all available data. This paper explores a novel self-supervised approach to re-label time series datasets by inherently constructing candidate datasets. During the optimization of a simple reconstruction network, intermediates are used as pseudo labels in a self-supervised paradigm, improving generalization for any predictor. We introduce the Self-Correction with Adaptive Mask (SCAM), which discards overfitted components and selectively replaces them with pseudo labels generated from reconstructions. Additionally, we incorporate Spectral Norm Regularization (SNR) to further suppress overfitting from a loss landscape perspective. Our experiments on eleven real-world datasets demonstrate that SCAM consistently improves the performance of various backbone models. This work offers a new perspective on constructing datasets and enhancing the generalization of TSF models through self-supervised learning. The code is available at https://github.com/SuDIS-ZJU/SCAM.

General Machine Learning · Representation Learning

Julie Mordacq, David Loiseaux, Vicky Kalogeiton, Steve OUDOT

Self-supervised learning (SSL) has emerged as a powerful paradigm for learning representations without labeled data, often by enforcing invariance to input transformations such as rotations or blurring. Recent studies have highlighted two pivotal properties for effective representations: (i) avoiding dimensional collapse-where the learned features occupy only a low-dimensional subspace, and (ii) enhancing uniformity of the induced distribution. In this work, we introduce T-REGS, a simple regularization framework for SSL based on the length of the Minimum Spanning Tree (MST) over the learned representation. We provide theoretical analysis demonstrating that T-REGS simultaneously mitigates dimensional collapse and promotes distribution uniformity on arbitrary compact Riemannian manifolds. Several experiments on synthetic data and on classical SSL benchmarks validate the effectiveness of our approach at enhancing representation quality.

Reinforcement Learning · Deep RL

Long Ma, Fangwei Zhong, Yizhou Wang

Modern causal language models, followed by rapid developments in discrete diffusion models, can now produce a wide variety of interesting and useful content. However, these families of models are predominantly trained to output tokens with a fixed (left-to-right) or random order, which may deviate from the logical order in which tokens are generated originally. In this paper, we observe that current causal and diffusion models encounter difficulties in problems that require adaptive token generation orders to solve tractably, which we characterize with the $\mathcal{V}$-information framework. Motivated by this, we propose Reinforced Context Order Recovery (ReCOR), a reinforcement-learning-based framework to extract adaptive, data-dependent token generation orders from text data without annotations. Self-supervised by token prediction statistics, ReCOR estimates the hardness of predicting every unfilled token and adaptively selects the next token during both training and inference. Experiments on challenging reasoning and planning datasets demonstrate the superior performance of ReCOR compared with baselines, sometimes outperforming oracle models supervised with the ground-truth order.

Run Luo, Renke Shan, Longze Chen, Ziqiang Liu, Lu Wang, Min Yang, Xiaobo Xia

Large vision-language models (LVLMs) have emerged as foundational tools for real-world AI applications. Despite their remarkable capabilities, current LVLMs process entire images at the token level, leading to significant inefficiencies compared to human cognition, which selectively focuses on high-level vision concepts. This token-level redundancy becomes increasingly problematic for high-resolution images and long video sequences, resulting in large computational costs and limited scalability in practical applications. To address this limitation, we introduce the concept of a vision concept model, a novel paradigm that enables LVLMs to dynamically extract the most relevant vision concepts from complex inputs, based on task-specific instructions. To optimize this vision concept modeling process, we propose VCM, a self-supervised framework that leverages vision-language correlations across diverse instances. VCM is designed to learn meaningful vision concepts without the need for expensive concept-level annotations. At its core, it employs a forward-backward optimization algorithm that supports LVLMs to adjust concept granularity and spatial alignment dynamically. Experiments demonstrate that VCM remarkably reduces computational costs (e.g., achieving up to 85\% fewer FLOPs for LLaVA-1.5-7B), while maintaining strong performance across a series of vision-language tasks. The codebase is available at https://github.com/RainBowLuoCS/VCM.