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Deep Learning · Generative Models and Autoencoders

Zhengqi Gao, Kaiwen Zha, Tianyuan Zhang, Zihui Xue, Duane Boning

Guidance techniques are simple yet effective for improving conditional generation in diffusion models. Albeit their empirical success, the practical implementation of guidance diverges significantly from its theoretical motivation. In this paper, we reconcile this discrepancy by replacing the scaled marginal distribution target, which we prove theoretically invalid, with a valid scaled joint distribution objective. Additionally, we show that the established guidance implementations are approximations to the intractable optimal solution under no future foresight constraint. Building on these theoretical insights, we propose rectified gradient guidance (REG), a versatile enhancement designed to boost the performance of existing guidance methods. Experiments on 1D and 2D demonstrate that REG provides a better approximation to the optimal solution than prior guidance techniques, validating the proposed theoretical framework. Extensive experiments on class-conditional ImageNet and text-to-image generation tasks show that incorporating REG consistently improves FID and Inception/CLIP scores across various settings compared to its absence.

Social Aspects · Accountability, Transparency, and Interpretability

Thomas Fel, Ekdeep Singh Lubana, Jacob Prince, Matthew Kowal, Victor Boutin, Isabel Papadimitriou, Binxu Wang, Martin Wattenberg, Demba Ba, Talia Konkle

Sparse Autoencoders (SAEs) have emerged as a powerful framework for machine learning interpretability, enabling the unsupervised decomposition of model representations into a dictionary of abstract, human-interpretable concepts. However, we reveal a fundamental limitation: SAEs exhibit severe instability, as identical models trained on similar datasets can produce sharply different dictionaries, undermining their reliability as an interpretability tool. To address this issue, we draw inspiration from the Archetypal Analysis framework introduced by Cutler & Breiman (1994) and present Archetypal SAEs (A-SAE), wherein dictionary atoms are constrained to the data’s convex hull. This geometric anchoring significantly enhances the stability and plausibility of inferred dictionaries, and their mildly relaxed variants RA-SAEs further match state-of-the-art reconstruction abilities. To rigorously assess dictionary quality learned by SAEs, we introduce two new benchmarks that test (i) plausibility, if dictionaries recover “true” classification directions and (ii) identifiability, if dictionaries disentangle synthetic concept mixtures. Across all evaluations, RA-SAEs consistently yield more structured representations while uncovering novel, semantically meaningful concepts in large-scale vision models.

Deep Learning · Generative Models and Autoencoders

Jeffrey A. Chan-Santiago, praveen tirupattur, Gaurav Kumar Nayak, Gaowen Liu, Mubarak Shah

Dataset distillation has emerged as an effective strategy, significantly reducing training costs and facilitating more efficient model deployment.Recent advances have leveraged generative models to distill datasets by capturing the underlying data distribution. Unfortunately, existing methods require model fine-tuning with distillation losses to encourage diversity and representativeness. However, these methods do not guarantee sample diversity, limiting their performance.We propose a mode-guided diffusion model leveraging a pre-trained diffusion model without the need to fine-tune with distillation losses. Our approach addresses dataset diversity in three stages: Mode Discovery to identify distinct data modes, Mode Guidance to enhance intra-class diversity, and Stop Guidance to mitigate artifacts in synthetic samples that affect performance.We evaluate our approach on ImageNette, ImageIDC, ImageNet-100, and ImageNet-1K, achieving accuracy improvements of 4.4%, 2.9%, 1.6%, and 1.6%, respectively, over state-of-the-art methods. Our method eliminates the need for fine-tuning diffusion models with distillation losses, significantly reducing computational costs.

Deep Learning · Generative Models and Autoencoders

Hila Chefer, Uriel Singer, Amit Zohar, Yuval Kirstain, Adam Polyak, Yaniv Taigman, Lior Wolf, Shelly Sheynin

Despite tremendous recent progress, generative video models still struggle to capture real-world motion, dynamics, and physics. We show that this limitation arises from the conventional pixel reconstruction objective, which biases models toward appearance fidelity at the expense of motion coherence.To address this, we introduce **VideoJAM**, a novel framework that instills an effective motion prior to video generators, by encouraging the model to learn *a joint appearance-motion representation*. VideoJAM is composed of two complementary units. During training, we extend the objective to predict both the generated pixels and their corresponding motion from a single learned representation. During inference, we introduce **Inner-Guidance**, a mechanism that steers the generation toward coherent motion by leveraging the model's own evolving motion prediction as a dynamic guidance signal.Notably, our framework can be applied to any video model with minimal adaptations, requiring no modifications to the training data or scaling of the model.VideoJAM achieves state-of-the-art performance in motion coherence, surpassing highly competitive proprietary models while also enhancing the perceived visual quality of the generations.These findings emphasize that appearance and motion can be complementary and, when effectively integrated, enhance both the visual quality and the coherence of video generation.

General Machine Learning · Representation Learning

Tiansheng Wen, Yifei Wang, Zequn Zeng, Zhong Peng, Yudi Su, Xinyang Liu, Bo Chen, Hongwei Liu, Stefanie Jegelka, Chenyu You

Many large-scale systems rely on high-quality deep representations (embeddings) to facilitate tasks like retrieval, search, and generative modeling. Matryoshka Representation Learning (MRL) recently emerged as a solution for adaptive embedding lengths, but it requires full model retraining and suffers from noticeable performance degradations at short lengths. In this paper, we show that *sparse coding* offers a compelling alternative for achieving adaptive representation with minimal overhead and higher fidelity. We propose **Contrastive Sparse Representation** (**CSR**), a method that specifies pre-trained embeddings into a high-dimensional but *selectively activated* feature space. By leveraging lightweight autoencoding and task-aware contrastive objectives, CSR preserves semantic quality while allowing flexible, cost-effective inference at different sparsity levels. Extensive experiments on image, text, and multimodal benchmarks demonstrate that CSR consistently outperforms MRL in terms of both accuracy and retrieval speed—often by large margins—while also cutting training time to a fraction of that required by MRL. Our results establish sparse coding as a powerful paradigm for adaptive representation learning in real-world applications where efficiency and fidelity are both paramount. Code is available at [this URL.](https://github.com/neilwen987/CSR_Adaptive_Rep)

Deep Learning · Generative Models and Autoencoders

Jaemoo Choi, Jaewoong Choi, Dohyun Kwon

We address the convergence problem in learning the Optimal Transport (OT) map, where the OT Map refers to a map from one distribution to another while minimizing the transport cost. Semi-dual Neural OT, a widely used approach for learning OT Maps with neural networks, often generates spurious solutions that fail to transfer one distribution to another accurately. We identify a sufficient condition under which the max-min solution of Semi-dual Neural OT recovers the true OT Map. Moreover, to address cases when this sufficient condition is not satisfied, we propose a novel method, OTP, which learns both the OT Map and the Optimal Transport Plan, representing the optimal coupling between two distributions. Under sharp assumptions on the distributions, we prove that our model eliminates the spurious solution issue and correctly solves the OT problem. Our experiments show that the OTP model recovers the optimal transport map where existing methods fail and outperforms current OT-based models in image-to-image translation tasks. Notably, the OTP model can learn stochastic transport maps when deterministic OT Maps do not exist, such as one-to-many tasks like colorization.

Deep Learning · Generative Models and Autoencoders

Alessandro Favero, Antonio Sclocchi, Francesco Cagnetta, Pascal Frossard, Matthieu Wyart

Natural data is often organized as a hierarchical composition of features. How many samples do generative models need in order to learn the composition rules, so as to produce a combinatorially large number of novel data? What signal in the data is exploited to learn those rules? We investigate these questions in the context of diffusion models both theoretically and empirically. Theoretically, we consider a simple probabilistic context-free grammar - a tree-like graphical model used to represent the hierarchical and compositional structure of data such as language and images. We demonstrate that diffusion models learn the grammar's composition rules with the sample complexity required for clustering features with statistically similar context, a process similar to the word2vec algorithm. However, this clustering emerges hierarchically: higher-level features associated with longer contexts require more data to be identified. This mechanism leads to a sample complexity that scales polynomially with the said context size. As a result, diffusion models trained on an intermediate dataset size generate data coherent up to a certain scale, but lacking global coherence. We test these predictions across different domains and find remarkable agreement: both generated texts and images achieve progressively larger coherence lengths as the training time or dataset size grows. We discuss connections between the hierarchical clustering mechanism we introduce here and the renormalization group in physics.

Deep Learning · Generative Models and Autoencoders

Zeyu Fang, Ming Gu, Sheng Zhou, Jiawei Chen, Qiaoyu Tan, Haishuai Wang, Jiajun Bu

Unsupervised Anomaly Detection (UAD) plays a crucial role in identifying abnormal patterns within data without labeled examples, holding significant practical implications across various domains. Although the individual contributions of representation learning and clustering to anomaly detection are well-established, their interdependencies remain under-explored due to the absence of a unified theoretical framework. Consequently, their collective potential to enhance anomaly detection performance remains largely untapped. To bridge this gap, in this paper, we propose a novel probabilistic mixture model for anomaly detection to establish a theoretical connection among representation learning, clustering, and anomaly detection. By maximizing a novel anomaly-aware data likelihood, representation learning and clustering can effectively reduce the adverse impact of anomalous data and collaboratively benefit anomaly detection. Meanwhile, a theoretically substantiated anomaly score is naturally derived from this framework. Lastly, drawing inspiration from gravitational analysis in physics, we have devised an improved anomaly score that more effectively harnesses the combined power of representation learning and clustering. Extensive experiments, involving 17 baseline methods across 30 diverse datasets, validate the effectiveness and generalization capability of the proposed method, surpassing state-of-the-art methods.

Deep Learning · Generative Models and Autoencoders

Shuangfei Zhai, Ruixiang Zhang, Preetum Nakkiran, David Berthelot, Jiatao Gu, Huangjie Zheng, Tianrong Chen, Miguel Angel Bautista Martin, Navdeep Jaitly, Joshua M Susskind

Normalizing Flows (NFs) are likelihood-based models for continuous inputs. They have demonstrated promising results on both density estimation and generative modeling tasks, but have received relatively little attention in recent years. In this work, we demonstrate that NFs are more powerful than previously believed. We present TarFlow: a simple and scalable architecture that enables highly performant NF models. TarFlow can be thought of as a Transformer-based variant of Masked Autoregressive Flows (MAFs): it consists of a stack of autoregressive Transformer blocks on image patches, alternating the autoregression direction between layers. TarFlow is straightforward to train end-to-end, and capable of directly modeling and generating pixels. We also propose three key techniques to improve sample quality: Gaussian noise augmentation during training, a post training denoising procedure, and an effective guidance method for both class-conditional and unconditional settings. Putting these together, TarFlow sets new state-of-the-art results on likelihood estimation for images, beating the previous best methods by a large margin, and generates samples with quality and diversity comparable to diffusion models, for the first time with a stand-alone NF model. We make our code available at https://github.com/apple/ml-tarflow.

Deep Learning · Generative Models and Autoencoders

Peter Pao-Huang, Mitchell Black, Xiaojie Qiu

Generative modeling of graphs with spatial structure is essential across many applications from computer graphics to spatial genomics. Recent flow-based generative models have achieved impressive results by gradually adding and then learning to remove noise from these graphs. Existing models, however, use graph neural network architectures that are independent of the noise level, limiting their expressiveness. To address this issue, we introduce *Noise-Conditioned Graph Networks* (NCGNs), a class of graph neural networks that dynamically modify their architecture according to the noise level during generation. Our theoretical and empirical analysis reveals that as noise increases, (1) graphs require information from increasingly distant neighbors and (2) graphs can be effectively represented at lower resolutions. Based on these insights, we develop Dynamic Message Passing (DMP), a specific instantiation of NCGNs that adapts both the range and resolution of message passing to the noise level. DMP consistently outperforms noise independent architectures on a variety of domains including $3$D point clouds, spatiotemporal transcriptomics, and images.

Applications · Computer Vision

Wenhao Wang, Yifan Sun, Zongxin Yang, Zhentao Tan, Zhengdong Hu, Yi Yang

Text-guided image-to-image diffusion models excel in translating images based on textual prompts, allowing for precise and creative visual modifications. However, such a powerful technique can be misused for *spreading misinformation*, *infringing on copyrights*, and *evading content tracing*. This motivates us to introduce the task of origin **ID**entification for text-guided **I**mage-to-image **D**iffusion models (**ID$\mathbf{^2}$**), aiming to retrieve the original image of a given translated query. A straightforward solution to ID$^2$ involves training a specialized deep embedding model to extract and compare features from both query and reference images. However, due to *visual discrepancy* across generations produced by different diffusion models, this similarity-based approach fails when training on images from one model and testing on those from another, limiting its effectiveness in real-world applications. To solve this challenge of the proposed ID$^2$ task, we contribute the first dataset and a theoretically guaranteed method, both emphasizing generalizability. The curated dataset, **OriPID**, contains abundant **Ori**gins and guided **P**rompts, which can be used to train and test potential **ID**entification models across various diffusion models. In the method section, we first prove the *existence* of a linear transformation that minimizes the distance between the pre-trained Variational Autoencoder embeddings of generated samples and their origins. Subsequently, it is demonstrated that such a simple linear transformation can be *generalized* across different diffusion models. Experimental results show that the proposed method achieves satisfying generalization performance, significantly surpassing similarity-based methods (+31.6% mAP), even those with generalization designs. The project is available at https://id2icml.github.io.

Applications · Social Sciences

Rajiv Movva, Kenny Peng, Nikhil Garg, Jon Kleinberg, Emma Pierson

We describe HypotheSAEs, a general method to hypothesize interpretable relationships between text data (e.g., headlines) and a target variable (e.g., clicks). HypotheSAEs has three steps: (1) train a sparse autoencoder on text embeddings to produce interpretable features describing the data distribution, (2) select features that predict the target variable, and (3) generate a natural language interpretation of each feature (e.g., *mentions being surprised or shocked*) using an LLM. Each interpretation serves as a hypothesis about what predicts the target variable. Compared to baselines, our method better identifies reference hypotheses on synthetic datasets (at least +0.06 in F1) and produces more predictive hypotheses on real datasets (~twice as many significant findings), despite requiring 1-2 orders of magnitude less compute than recent LLM-based methods. HypotheSAEs also produces novel discoveries on two well-studied tasks: explaining partisan differences in Congressional speeches and identifying drivers of engagement with online headlines.

Deep Learning · Other Representation Learning

Vladimir Zaigrajew, Hubert Baniecki, Przemysław Biecek

Sparse autoencoders (SAEs) are useful for detecting and steering interpretable features in neural networks, with particular potential for understanding complex multimodal representations. Given their ability to uncover interpretable features, SAEs are particularly valuable for analyzing vision-language models (e.g., CLIP and SigLIP), which are fundamental building blocks in modern large-scale systems yet remain challenging to interpret and control. However, current SAE methods are limited by optimizing both reconstruction quality and sparsity simultaneously, as they rely on either activation suppression or rigid sparsity constraints. To this end, we introduce Matryoshka SAE (MSAE), a new architecture that learns hierarchical representations at multiple granularities simultaneously, enabling a direct optimization of both metrics without compromise. MSAE establishes a state-of-the-art Pareto frontier between reconstruction quality and sparsity for CLIP, achieving 0.99 cosine similarity and less than 0.1 fraction of variance unexplained while maintaining 80\% sparsity. Finally, we demonstrate the utility of MSAE as a tool for interpreting and controlling CLIP by extracting over 120 semantic concepts from its representation to perform concept-based similarity search and bias analysis in downstream tasks like CelebA. We make the codebase available at https://github.com/WolodjaZ/MSAE.

Deep Learning · Generative Models and Autoencoders

Wenhao SUN, Rong-Cheng Tu, Jingyi Liao, Zhao Jin, Dacheng Tao

Diffusion Transformers (DiTs) have proven effective in generating high-quality videos but are hindered by high computational costs. Existing video diffusion sampling acceleration methods often rely on costly fine-tuning or exhibit limited generalization capabilities. We propose Asymmetric Reduction and Restoration (**AsymRnR**), **a training-free and model-agnostic method to accelerate video DiTs**. It builds on the observation that redundancies of feature tokens in DiTs vary significantly across different model blocks, denoising steps, and feature types. Our AsymRnR asymmetrically reduces redundant tokens in the attention operation, achieving acceleration with negligible degradation in output quality and, in some cases, even improving it. We also tailored a reduction schedule to distribute the reduction across components adaptively. To further accelerate this process, we introduce a matching cache for more efficient reduction. Backed by theoretical foundations and extensive experimental validation, AsymRnR integrates into state-of-the-art video DiTs and offers substantial speedup.

Social Aspects · Accountability, Transparency, and Interpretability

Xingyi Yang, Constantin Venhoff, Ashkan Khakzar, Christian Schroeder de Witt, Puneet Dokania, Adel Bibi, Phil Torr

Neurons in large language models often exhibit \emph{polysemanticity}, simultaneously encoding multiple unrelated concepts and obscuring interpretability. Instead of relying on post-hoc methods, we present \textbf{MoE-X}, a mixture-of-experts (MoE) language model designed to be \emph{intrinsically} interpretable. Our approach is motivated by the observation that, in language models, wider networks with sparse activations are more likely to capture interpretable factors. however, directly training such large sparse networks is computationally prohibitive. MoE architectures offer a scalable alternative by activating only a subset of experts for any given input, inherently aligning with interpretability objectives. In MoE-X, we establish this connection by rewriting the MoE layer as an equivalent sparse, large MLP. This approach enables efficient scaling of the hidden size while maintaining sparsity. To further enhance interpretability, we enforce sparse activation within each expert and redesign the routing mechanism to prioritize experts with the highest activation sparsity. These designs ensure that only the most salient features are routed and processed by the experts. We evaluate MoE-X on chess and natural language tasks, showing that it achieves performance comparable to dense models while significantly improving interpretability. MoE-X achieves a perplexity better than GPT-2, with interpretability surpassing even sparse autoencoder (SAE)-based approaches.

Deep Learning · Sequential Models, Time series

Xingjian Wu, Xiangfei Qiu, Hongfan Gao, Jilin Hu, Bin Yang, Chenjuan Guo

Probabilistic Time Series Forecasting (PTSF) plays a crucial role in decision-making across various fields, including economics, energy, and transportation. Most existing methods excell at short-term forecasting, while overlooking the hurdles of Long-term Probabilistic Time Series Forecasting (LPTSF). As the forecast horizon extends, the inherent nonlinear dynamics have a significant adverse effect on prediction accuracy, and make generative models inefficient by increasing the cost of each iteration. To overcome these limitations, we introduce $K^2$VAE, an efficient VAE-based generative model that leverages a KoopmanNet to transform nonlinear time series into a linear dynamical system, and devises a KalmanNet to refine predictions and model uncertainty in such linear system, which reduces error accumulation in long-term forecasting. Extensive experiments demonstrate that $K^2$VAE outperforms state-of-the-art methods in both short- and long-term PTSF, providing a more efficient and accurate solution.

Deep Learning · Generative Models and Autoencoders

Zian Li, Cai Zhou, Xiyuan Wang, Xingang Peng, Muhan Zhang

Recent advances in molecular generative models have demonstrated great promise for accelerating scientific discovery, particularly in drug design. However, these models often struggle to generate high-quality molecules, especially in conditional scenarios where specific molecular properties must be satisfied. In this work, we introduce GeoRCG, a general framework to improve molecular generative models by integrating geometric representation conditions with provable theoretical guarantees. We decompose the generation process into two stages: first, generating an informative geometric representation; second, generating a molecule conditioned on the representation. Compared with single-stage generation, the easy-to-generate representation in the first stage guides the second stage generation toward a high-quality molecule in a goal-oriented way. Leveraging EDM and SemlaFlow as base generators, we observe significant quality improvements in unconditional molecule generation on the widely used QM9 and GEOM-DRUG datasets. More notably, in the challenging conditional molecular generation task, our framework achieves an average 50\% performance improvement over state-of-the-art approaches, highlighting the superiority of conditioning on semantically rich geometric representations. Furthermore, with such representation guidance, the number of diffusion steps can be reduced to as small as 100 while largely preserving the generation quality achieved with 1,000 steps, thereby significantly reducing the generation iterations needed.

Deep Learning · Generative Models and Autoencoders

François Cornet, Federico Bergamin, Arghya Bhowmik, Juan Garcia-Lastra, Jes Frellsen, Mikkel Schmidt

Generative modeling of crystalline materials using diffusion models presents a series of challenges: the data distribution is characterized by inherent symmetries and involves multiple modalities, with some defined on specific manifolds. Notably, the treatment of fractional coordinates representing atomic positions in the unit cell requires careful consideration, as they lie on a hypertorus. In this work, we introduce Kinetic Langevin Diffusion for Materials (KLDM), a novel diffusion model for crystalline materials generation, where the key innovation resides in the modeling of the coordinates. Instead of resorting to Riemannian diffusion on the hypertorus directly, we generalize Trivialized Diffusion Model (TDM) to account for the symmetries inherent to crystals. By coupling coordinates with auxiliary Euclidean variables representing velocities, the diffusion process is now offset to a flat space. This allows us to effectively perform diffusion on the hypertorus while providing a training objective that accounts for the periodic translation symmetry of the true data distribution. We evaluate KLDM on both Crystal Structure Prediction (CSP) and De-novo Generation (DNG) tasks, demonstrating its competitive performance with current state-of-the-art models.

Deep Learning · Graph Neural Networks

Zhiqiang Wang, Xiaoyi Wang, Jianqing Liang

Graph Neural Ordinary Differential Equations (GODE) integrate the Variational Autoencoder (VAE) framework with differential equations, effectively modeling latent space uncertainty and continuous dynamics, excelling in graph data evolution and incompleteness. However, existing GODE face challenges in capturing time-varying relationships and nonlinear node state evolution, which limits their ability to model complex dynamic graphs. To address these issues, we propose the ControlSynth Graph ODE (CSG-ODE). In the VAE encoding phase, CSG-ODE introduces an information transmission-based inter-node importance weighting mechanism, integrating it with latent correlations to guide adaptive graph convolutional recurrent networks for temporal node embedding. During decoding, CSG-ODE employs ODE to model node dynamics, capturing nonlinear evolution through sub-networks with nonlinear activations. For scenarios or prediction tasks that require stability, we extend CSG-ODE to stable CSG-ODE (SCSG-ODE) by constraining weight matrices to learnable anti-symmetric forms, theoretically ensuring enhanced stability. Experiments on traffic, motion capture, and simulated physical systems datasets demonstrate that CSG-ODE outperforms state-of-the-art GODE, while SCSG-ODE achieves both superior performance and optimal stability.

Deep Learning · Generative Models and Autoencoders

Charles O'Neill, Alim Gumran, David Klindt

A recent line of work has shown promise in using sparse autoencoders (SAEs) to uncover interpretable features in neural network representations. However, the simple linear-nonlinear encoding mechanism in SAEs limits their ability to perform accurate sparse inference. Using compressed sensing theory, we prove that an SAE encoder is inherently insufficient for accurate sparse inference, even in solvable cases. We then decouple encoding and decoding processes to empirically explore conditions where more sophisticated sparse inference methods outperform traditional SAE encoders. Our results reveal substantial performance gains with minimal compute increases in correct inference of sparse codes. We demonstrate this generalises to SAEs applied to large language models, where more expressive encoders achieve greater interpretability. This work opens new avenues for understanding neural network representations and analysing large language model activations.