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Deep Learning · Generative Models and Autoencoders

Yan Wang, Shijie Zhao, Kexin Zhang, Junlin Li, Li zhang

Although recent research applying text-to-image (T2I) diffusion models to real-world super-resolution (SR) has achieved remarkable progress, the misalignment of their targets leads to a suboptimal trade-off between inference speed and detail fidelity. Specifically, the T2I task requires multiple inference steps to synthesize images matching to prompts and reduces the latent dimension to lower generating difficulty. Contrariwise, SR can restore high-frequency details in fewer inference steps, but it necessitates a more reliable variational auto-encoder (VAE) to preserve input information. However, most diffusion-based SRs are multistep and use 4-channel VAEs, while existing models with 16-channel VAEs are overqualified diffusion transformers, e.g., FLUX (12B). To align the target, we present a one-step diffusion model for generative detail restoration, GenDR, distilled from a tailored diffusion model with a larger latent space. In detail, we train a new SD2.1-VAE16 (0.9B) via representation alignment to expand the latent space without increasing the model size. Regarding step distillation, we propose consistent score identity distillation (CiD) that incorporates SR task-specific loss into score distillation to leverage more SR priors and align the training target. Furthermore, we extend CiD with adversarial learning and representation alignment (CiDA) to enhance perceptual quality and accelerate training. We also polish the pipeline to achieve a more efficient inference. Experimental results demonstrate that GenDR achieves state-of-the-art performance in both quantitative metrics and visual fidelity.

Deep Learning · Generative Models and Autoencoders

Ling Wang, Hao-Xiang Guo, Xinzhou Wang, Fuchun Sun, Kai Sun, Pengkun Liu, Hang Xiao, Zhong Wang, Guangyuan Fu, Eric Li 等

We introduce SceneTransporter, an end-to-end framework for structured 3D scene generation from a single image. While existing methods generate part-level 3D objects, they often fail to organize these parts into distinct instances in open-world scenes. Through a debiased clustering probe, we reveal a critical insight: this failure stems from the lack of structural constraints within the model's internal assignment mechanism. Based on this finding, we reframe the task of structured 3D scene generation as a global correlation assignment problem. To solve this, SceneTransporter formulates and solves an entropic Optimal Transport (OT) objective within the denoising loop of the compositional DiT model. This formulation imposes two powerful structural constraints. First, the resulting transport plan gates cross-attention to enforce an exclusive, one-to-one routing of image patches to part-level 3D latents, preventing entanglement. Second, the competitive nature of the transport encourages the grouping of similar patches, a process that is further regularized by an edge-based cost, to form coherent objects and prevent fragmentation. Extensive experiments show that SceneTransporter outperforms existing methods on open-world scene generation, significantly improving instance-level coherence and geometric fidelity. Code and models will be publicly available at \url{https://2019epwl.github.io/SceneTransporter/}

Deep Learning · Generative Models and Autoencoders

Lingkai Kong, Molei Tao, Yang Liu, Bryan Wang, Jinmiao Fu, Chien-Chih Wang, Huidong Liu

Flow-based Generative Models (FGMs) effectively transform noise into complex data distributions. Incorporating Optimal Transport (OT) to couple noise and data during FGM training has been shown to improve the straightness of flow trajectories, enabling more effective inference. However, existing OT-based methods estimate the OT plan using (mini-)batches of sampled noise and data points, which limits their scalability to large and high-dimensional datasets in FGMs. This paper introduces AlignFlow, a novel approach that leverages Semi-Discrete Optimal Transport (SDOT) to enhance the training of FGMs by establishing an explicit, optimal alignment between noise distribution and data points with guaranteed convergence. SDOT computes a transport map by partitioning the noise space into Laguerre cells, each mapped to a corresponding data point. During FGM training, i.i.d. noise samples are paired with data points via the SDOT map. AlignFlow scales well to large datasets and model architectures with negligible computational overhead. Experimental results show that AlignFlow improves the performance of a wide range of state-of-the-art FGM algorithms and can be integrated as a plug-and-play component. Code is available at: https://github.com/konglk1203/AlignFlow.

Social Aspects · Trustworthy Machine Learning

Enoal Gesny, Eva Giboulot, Teddy Furon, Vivien Chappelier

This paper introduces a novel watermarking method for diffusion models. It is based on guiding the diffusion process using the gradient computed from any off-the-shelf watermark decoder. The gradient is guided further using different image augmentations, increasing robustness to attacks against which the decoder was not originally robust, without retraining or fine-tuning. The methodology effectively allows to convert any post-hoc watermarking scheme into a scheme embedding the signal during the diffusion process. We show that this approach is complementary to watermarking techniques modifying the variational autoencoder at the end of the diffusion process. We validate the methods on different diffusion models and detectors. The watermarking guidance does not significantly alter the generated image for a given seed and prompt, preserving both the diversity and quality of generation.

Social Aspects · Accountability, Transparency and Interpretability

Wenjie Sun, Di Wang, Lijie Hu

Polysemy has long been a major challenge in Mechanistic Interpretability (MI), with Sparse Autoencoders (SAEs) emerging as a promising solution. SAEs employ a shared encoder to map inputs to sparse codes, thereby amortizing inference costs across all instances. However, this parameter-sharing paradigm inherently conflicts with the MI community’s emphasis on instance-level optimality, including the consistency and stitchability of monosemantic features. We first reveal the trade-off relationships among various pathological phenomena, including feature absorption, feature splitting, dead latents, and dense latents under global reconstruction-sparsity constraints from the perspective of training dynamics, finding that increased sparsity typically exacerbates multiple pathological phenomena, and attribute this trade-off relationship to amortized inference. By reducing reliance on amortized inference through the introduction of semi-amortized and non-amortized approaches, we observed that various pathological indicators were significantly mitigated, thereby validating our hypothesis. As the first step in this direction, we propose Local Amortized SAE (LocA-SAE), a method that groups polysemantically close latents based on the angular variance. This method is designed to balance the computational cost of per-sample optimization with the limitations of amortized inference. Our work provides insights for understanding SAEs and advocates for a paradigm shift in future research on polysemy disentanglement. The code is available \url{https://github.com/wenjie1835/Local_Amotized_SAEs}.

Deep Learning · Generative Models and Autoencoders

Oswin So, Brian Karrer, Chuchu Fan, Ricky T. Q. Chen, Guan-Horng Liu

Computation methods for solving entropy-regularized reward optimization—a class of problems widely used for fine-tuning generative models—have advanced rapidly. Among those, Adjoint Matching (AM, Domingo-Enrich et al., 2025) has proven highly effective in continuous state spaces with differentiable rewards. Transferring these practical successes to _discrete_ generative modeling, however, remains particularly challenging and largely unexplored, mainly due to the drastic shift in generative model classes to discrete state spaces, which are nowhere differentiable. In this work, we propose Discrete Adjoint Matching (DAM)—a discrete variant of AM for fine-tuning discrete generative models characterized by Continuous-Time Markov Chains, such as diffusion-based large language models. The core of DAM is the introduction of _discrete adjoint_—an estimator of the optimal solution to the original problem but formulated on discrete domains—from which standard matching frameworks can be applied. This is derived via a purely statistical standpoint, in contrast to the control-theoretic viewpoint in AM, thereby opening up new algorithmic opportunities for general adjoint-based estimators. We showcase DAM’s effectiveness on synthetic and mathematical reasoning tasks.

Deep Learning · Generative Models and Autoencoders

Zhengyang Liang, Hao He, Ceyuan Yang, Bo DAI

Diffusion transformers (DiT) have already achieved appealing synthesis and scaling properties in content recreation, \emph{e.g.,} image and video generation. However, scaling laws of DiT are less explored, which usually offer precise predictions regarding optimal model size and data requirements given a specific compute budget. Therefore, experiments across a broad range of compute budgets, from 1e17 to 6e18 FLOPs are conducted to confirm the existence of scaling laws in DiT \emph{for the first time}. Concretely, the loss of pretraining DiT also follows a power-law relationship with the involved compute. Based on the scaling law, we can not only determine the optimal model size and required data but also accurately predict the text-to-image generation loss given a model with 1B parameters and a compute budget of 1.5e21 FLOPs. Additionally, we also demonstrate that the trend of pretraining loss matches the generation performances (e.g., FID), even across various datasets, which complements the mapping from compute to synthesis quality and thus provides a predictable benchmark that assesses model performance and data quality at a reduced cost.

Computer Vision · Image and Video Generation

Shuai Wang, Ziteng Gao, Chenhui Zhu, Weilin Huang, Limin Wang

The current success of diffusion transformers are built on the compressed latent space shaped by the pre-trained variational autoencoder(VAE). However, this two-stage training paradigm inevitably introduces accumulated errors and decoding artifacts. To avoid these problems, researchers return to pixel space modeling but at the cost of complicated cascade pipelines and increased token complexity. Motivated by the simple yet effective diffusion transformer architectures on the latent space, we propose to model pixel space diffusion using a large-patch diffusion transformer and employ neural fields to decode these large patches, leading to a single-stage streamlined end-to-end solution, which we coin as pixel neural field diffusion transformer (**PixNerd**). Thanks to the efficient neural field representation in PixNerd, we achieve **1.93 FID** on ImageNet 256x256 and nearly **8x lower latency** without any complex cascade pipeline or VAE. We also extend our PixNerd framework to text-to-image applications. Our PixNerd-XXL/16 achieves a competitive 0.73 overall score on the GenEval benchmark and 80.9 overall score on the DPG benchmark.

Deep Learning · Generative Models and Autoencoders

Sedjro Salomon Hotegni, Sebastian Peitz

Developing efficient multi-objective optimization methods to compute the Pareto set of optimal compromises between conflicting objectives remains a key challenge, especially for large-scale and expensive problems. To bridge this gap, we introduce SPREAD, a generative framework based on Denoising Diffusion Probabilistic Models (DDPMs). SPREAD first learns a conditional diffusion process over points sampled from the decision space and then, at each reverse diffusion step, refines candidates via a sampling scheme that uses an adaptive multiple gradient descent-inspired update for fast convergence alongside a Gaussian RBF–based repulsion term for diversity. Empirical results on multi-objective optimization benchmarks, including offline and Bayesian surrogate-based settings, show that SPREAD matches or exceeds leading baselines in efficiency, scalability, and Pareto front coverage. Code is available at https://github.com/safe-autonomous-systems/moo-spread .

Deep Learning · Generative Models and Autoencoders

Andrea Fasoli, Monodeep Kar, Chi-Chun Liu, Swagath Venkataramani, Viji Srinivasan, Leland Chang, Naigang Wang

Microscaling data formats leverage per-block tensor quantization to enable aggressive model compression with limited loss in accuracy. Unlocking their potential for efficient training and inference necessitates hardware-friendly implementations that handle matrix multiplications in a native format and adopt efficient error-mitigation strategies. Herein, we reported the emergence of a surprising behavior associated with microscaling quantization, whereas the output of a quantized model degrades as block size is decreased below a given threshold. This behavior clashes with the expectation that a smaller block size should allow for a better representation of the tensor elements. We investigate this phenomenon both experimentally and theoretically, decoupling the sources of quantization error behind it. Experimentally, we analyze the distributions of several Large Language Models and identify the conditions driving the anomalous behavior. Theoretically, we lay down a framework showing remarkable agreement with experimental data from pretrained model distributions and ideal ones. Overall, we show that the anomaly is driven by the interplay between narrow tensor distributions and the limited dynamic range of the quantized scales. Based on these insights, we propose the use of FP8 unsigned E5M3 as a novel hardware-friendly format for the scales in FP4 microscaling data types. We demonstrate that UE5M3 achieves comparable performance to the conventional FP8 unsigned E4M3 scales while obviating the need of global scaling operations on weights and activations.

Deep Learning · Generative Models and Autoencoders

Ishan Jindal, Sai Prashanth Akuthota, Jayant Taneja, SACHIN SHARMA

Large language models achieve strong reasoning performance, but inference strategies such as Self-Consistency (SC) are computationally expensive, as they fully expand all reasoning traces. We introduce PoLR (Path of Least Resistance), the first inference-time method to leverage prefix self-consistency for compute-efficient reasoning. PoLR clusters short prefixes of reasoning traces, identifies the dominant cluster, and expands only a subset of promising paths, preserving the accuracy benefits of SC while substantially reducing token usage and latency. Our theoretical analysis, framed via mutual information and entropy, explains why early reasoning steps encode strong signals predictive of final correctness. Empirically, PoLR consistently matches or exceeds SC across GSM8K, Math500, AIME 2024/2025, and GPQA-Diamond, reducing token usage by up to 60% and wall-clock latency by up to 50%. Moreover, PoLR is fully complementary to adaptive inference methods (e.g., Adaptive Consistency, Early-Stopping SC) and can serve as a drop-in pre-filter, making SC substantially more efficient and scalable without requiring model fine-tuning.

Deep Learning · Generative Models and Autoencoders

Haoyang Zheng, Xinyang Liu, Xiangrui Kong, Nan Jiang, Zheyuan Hu, Weijian Luo, Wei Deng, Guang Lin

Fast and high-quality language generation is the holy grail that people pursue in the age of AI. In this work, we introduce **Di**screte **Di**ffusion Divergence **Instruct** (**DiDi-Instruct**), a training-based method that initializes from a pre-trained diffusion large language model (dLLM) and distills a few-step student for fast generation. The model distilled with DiDi-Instruct matches or surpasses its dLLM teacher and the GPT-2 baseline while providing up to **64$\times$ acceleration**. The theoretical foundation of DiDi-Instruct is a novel framework based on integral KL-divergence minimization, which leads to a practical training algorithm. We further introduce *grouped reward normalization, intermediate-state matching, and the reward-guided ancestral sampler* to improve *training stability, model coverage, and inference quality*. On the OpenWebText benchmark, DiDi-Instruct achieves perplexity ranging from 62.2 (8 NFEs) to 18.4 (128 NFEs), outperforming prior accelerated dLLMs and the GPT-2 baseline. These gains incur a negligible entropy loss (around $1$%) and reduce additional training wall-clock time by **more than $20\times$** compared to competing dLLM distillation methods. We further validate the robustness and effectiveness of DiDi-Instruct through extensive ablation studies, model scaling, downstream task evaluations, and unconditional protein sequence generation. In conclusion, DiDi-Instruct enables efficient and effective distillation for language generation in the blink of an eye.

General Machine Learning · Representation Learning

Joonhyeong Park, Byoungwoo Park, Chang-Bae Bang, Jungwon Choi, Hyungjin Chung, Byung-Hoon Kim, Juho Lee

Learning robust representations from functional magnetic resonance imaging (fMRI) is fundamentally challenged by the temporal irregularity and noise inherent in data from heterogeneous sources. Existing self-supervised learning (SSL) methods often discard critical temporal information by discretizing or averaging fMRI signals. To address this, we introduce a novel framework that reframes SSL as a Stochastic Optimal Control (SOC) problem. Our approach models brain activity as continuous-time latent dynamics, learning a robust representation of brain dynamics by optimizing a control policy that is agnostic to the temporal irregularity. This SOC framework naturally unifies masked autoencoding (MAE) and joint-embedding prediction (JEPA) to extract compact, control-derived representations. Furthermore, a simulation-free inference strategy ensures computational efficiency and scalability for large-scale fMRI datasets. Our model demonstrates state-of-the-art performance across diverse downstream applications, highlighting the potential of the SOC-based continuous-time representation learning framework.

Deep Learning · Generative Models and Autoencoders

Sonia Cromp, Satya Sai Srinath Namburi GNVV, Catherine Cao, Mohammed Alkhudhayri, Samuel Guo, Nicholas Roberts, Frederic Sala, Sonia Cromp

Large language models (LLMs) have greatly improved the quality of synthetic text data. We aim to extend these advances to tabular data with Tabby, a simple but powerful post-training modification to the standard Transformer language model architecture, enabling its use for tabular dataset synthesis. Tabby represents differences across columns using Gated Mixture-of-Experts, with column-specific sets of parameters. Empirically, Tabby results in data quality near or equal to that of real data. Pairing Tabby with Plain, our novel tabular training technique, we observe up to a $7\%$ improvement in quality (measured by MLE) over previous methods. Additionally, our approach is more flexible than prior strategies and extends beyond tables, to more general structured data. In a structured JSON setting, Tabby outperforms all other methods by $2$-$3$ points and is the only approach with MLE equal to the upper bound of non-synthetic data.

Deep Learning · Generative Models and Autoencoders

Taishi Nakamura, Satoki Ishikawa, Masaki Kawamura, Okamoto, Daisuke Nohara, Jun Suzuki, Rio Yokota

Empirical scaling laws have driven the evolution of large language models (LLMs), yet their coefficients shift whenever the model architecture or data pipeline changes. Mixture‑of‑Experts (MoE) models, now standard in state‑of‑the‑art systems, introduce a new sparsity dimension that current dense‑model frontiers overlook. We investigate how MoE sparsity influences two distinct capability regimes: memorization skills and reasoning skills. By training MoE families that vary total parameters, active parameters, and top-$k$ routing under fixed compute budgets, we disentangle pre-training loss from downstream accuracy. Our results reveal two principles. First, Active FLOPs: models with identical training loss but greater active compute achieve higher reasoning accuracy. Second, Total tokens per parameter (TPP): memorization tasks improve with more parameters, while reasoning tasks benefit from optimal TPP, indicating that reasoning is data-hungry. Neither reinforcement learning post-training (GRPO) nor increased test-time compute alters these trends. We therefore argue that optimal MoE sparsity must be determined jointly by active FLOPs and TPP, revising the classical picture of compute-optimal scaling. All code, data sources, and logs are released to facilitate reproducibility and future work.

Applications · Genetics, Cell Biology, Health, etc

Hiren Madhu, João Felipe Rocha, Tinglin Huang, Siddharth Viswanath, Smita Krishnaswamy, Rex Ying

Single-cell transcriptomics and proteomics have become a great source for data-driven insights into biology, enabling the use of advanced deep learning methods to understand cellular heterogeneity and gene expression at the single-cell level. With the advent of spatial-omics data, we have the promise of characterizing cells within their tissue context as it provides both spatial coordinates and intra-cellular transcriptional or protein counts. Beyond transcriptomics, proteomics offers a complementary view by directly measuring proteins, which are the primary effectors of cellular function and key therapeutic targets. However, existing models either ignore the spatial information or the complex genetic and proteomic programs within cells. Thus they cannot infer how cell internal regulation adapts to microenvironmental cues. Furthermore, these models often utilize fixed gene vocabularies, hindering their generalizability to datasets with different genes than pretraining. In this paper, we introduce HEIST, a hierarchical graph transformer foundation model for spatial transcriptomics and proteomics. HEIST models tissues as hierarchical graphs. The higher level graph is a spatial cell graph, and each cell in turn, is represented by its lower level gene co-expression network graph. Rather than using a fixed gene vocabulary, HEIST computes gene embeddings from its co-expression network and cellular context. HEIST achieves this by performing both intra-level and cross-level message passing to utilize the hierarchy in its embeddings and can thus generalize to novel datatypes including spatial proteomics without retraining. HEIST is pretrained on 22.3M cells from 124 tissues across 15 organs using spatially-aware contrastive and masked autoencoding objectives. Unsupervised analysis of HEIST embeddings reveals spatially informed subpopulations missed by prior models. Downstream evaluations demonstrate generalizability to proteomics data and state-of-the-art performance in clinical outcome prediction, cell type annotation, and gene imputation across multiple technologies.

Deep Learning · Generative Models and Autoencoders

Oskar Kviman, Kirill Tamogashev, Nicola Branchini, Víctor Elvira, Jens Lagergren, Nikolay Malkin

Learning the dynamics of a process given sampled observations at several time points is an important but difficult task in many scientific applications. When no ground-truth trajectories are available, but one has only snapshots of data taken at discrete time steps, the problem of modelling the dynamics, and thus inferring the underlying trajectories, can be solved by multi-marginal generalisations of flow matching algorithms. This paper introduces a novel flow matching method that overcomes the limitations of existing multi-marginal trajectory inference algorithms. Our proposed method, ALI-CFM, uses a GAN-inspired adversarial loss to fit neurally parameterised interpolant curves between source and target points such that the marginal distributions at intermediate time points are close to the observed distributions. The resulting interpolants are smooth trajectories that, as we show, are unique under mild assumptions. These interpolants are subsequently marginalised by a flow matching algorithm, yielding a trained vector field for the underlying dynamics. ALI-CFM outperforms existing baselines on spatial transcriptomics and cell tracking problems, while performing on par with them on single-cell trajectory prediction, which showcases its versatility and scalability.

Mason Wang, Anna Huang

We introduce the Latent Fourier Transform (LatentFT), a framework that provides novel frequency-domain controls for generative music models. LatentFT combines a diffusion autoencoder with a latent-space Fourier transform to separate musical patterns by timescale. By masking latents in the frequency domain during training, our method yields representations that can be manipulated coherently at inference. This allows us to generate musical variations and blends from reference examples while preserving characteristics at desired timescales, which are specified as frequencies in the latent space. LatentFT parallels the role of the equalizer in music production: while traditional equalizers operates on audible frequencies to shape timbre, LatentFT operates on latent-space frequencies to shape musical structure. Experiments and listening tests show that LatentFT improves condition adherence and quality compared to baselines. We also present a technique for hearing frequencies in the latent space in isolation, and show different musical attributes reside in different regions of the latent spectrum. Our results show how frequency-domain control in latent space provides an intuitive, continuous frequency axis for conditioning and blending, advancing us toward more interpretable and interactive generative music models.

Deep Learning · Generative Models and Autoencoders

Mason Wang, Anna Huang

We introduce the Latent Fourier Transform (LatentFT), a framework that provides novel frequency-domain controls for generative music models. LatentFT combines a diffusion autoencoder with a latent-space Fourier transform to separate musical patterns by timescale. By masking latents in the frequency domain during training, our method yields representations that can be manipulated coherently at inference. This allows us to generate musical variations and blends from reference examples while preserving characteristics at desired timescales, which are specified as frequencies in the latent space. LatentFT parallels the role of the equalizer in music production: while traditional equalizers operates on audible frequencies to shape timbre, LatentFT operates on latent-space frequencies to shape musical structure. Experiments and listening tests show that LatentFT improves condition adherence and quality compared to baselines. We also present a technique for hearing frequencies in the latent space in isolation, and show different musical attributes reside in different regions of the latent spectrum. Our results show how frequency-domain control in latent space provides an intuitive, continuous frequency axis for conditioning and blending, advancing us toward more interpretable and interactive generative music models.

Deep Learning · Generative Models and Autoencoders

Haoye Lu, Yaoliang Yu, Darren Lo

In many real-world scenarios, obtaining fully observed samples is prohibitively expensive or even infeasible, while partial and noisy observations are comparatively easy to collect. In this work, we study distribution restoration with abundant noisy samples, assuming the corruption process is available as a black-box generator. We show that this task can be framed as a one-sided entropic optimal transport problem and solved via an EM-like algorithm. We further provide a test criterion to determine whether the true underlying distribution is recoverable under per-sample information loss, and show that in otherwise unrecoverable cases, a small number of clean samples can render the distribution largely recoverable. Building on these insights, we introduce SFBD-OMNI, a bridge model-based framework that maps corrupted sample distributions to the ground-truth distribution. Our method generalizes Stochastic Forward-Backward Deconvolution (SFBD; Lu et al., 2025) to handle arbitrary measurement models beyond Gaussian corruption. Experiments across benchmark datasets and diverse measurement settings demonstrate significant improvements in both qualitative and quantitative performance.