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Social Aspects · Accountability, Transparency and Interpretability

Alan Chen, Jack Merullo, Alessandro Stolfo, Ellie Pavlick

In this work, we demonstrate that affine mappings between residual streams of language models is a cheap way to effectively transfer represented features between models. We apply this technique to transfer the \textit{weights} of Sparse Autoencoders (SAEs) between models of different sizes to compare their representations. We find that small and large models learn highly similar representation spaces, which motivates training expensive components like SAEs on a smaller model and transferring to a larger model at a FLOPs savings. For example, using a small-to-large transferred SAE as initialization can lead to 50% cheaper training runs when training SAEs on larger models. Next, we show that transferred probes and steering vectors can effectively recover ground truth performance. Finally, we dive deeper into feature-level transferability, finding that semantic and structural features transfer noticeably differently while specific classes of functional features have their roles faithfully mapped. Overall, our findings illustrate similarities and differences in the linear representation spaces of small and large models and demonstrate a method for improving the training efficiency of SAEs.

Deep Learning · Generative Models and Autoencoders

Ziqiao Wang, Wangbo Zhao, Yuhao Zhou, Zekai Li, Zhiyuan Liang, Mingjia Shi, Xuanlei Zhao, Pengfei Zhou, Kaipeng Zhang, Zhangyang "Atlas" Wang 等

Diffusion Transformers (DiTs) deliver state-of-the-art image quality, yet their training remains notoriously slow. A recent remedy---representation alignment (REPA) that matches DiT hidden features to those of a non-generative teacher (e.g., DINO)---dramatically accelerates the early epochs but plateaus or even degrades performance later. We trace this failure to the capacity mismatch: once the generative student begins modeling the joint data distribution, the teacher's lower-dimensional embeddings and attention patterns become a straitjacket rather than a guide. We then introduce HASTE (Holistic Alignment with Stage-wise Termination for Efficient training), a two-phase schedule that keeps the help and drops the hindrance. Phase I applies a holistic alignment loss that simultaneously distills attention maps (relational priors) and feature projections (semantic anchors) from the teacher into mid-level layers of the DiT, yielding rapid convergence. Phase II then performs one-shot termination that deactivates the alignment loss, once a simple trigger such as a fixed iteration is hit, freeing the DiT to focus on denoising and exploit its generative capacity. HASTE speeds up training of diverse DiTs without architecture changes. On ImageNet 256×256, it reaches the vanilla SiT-XL/2 baseline FID in 50 epochs and matches REPA’s best FID in 500 epochs, amounting to a 28× reduction in optimization steps. HASTE also improves text-to-image DiTs on MS-COCO, proving to be a simple yet principled recipe for efficient diffusion training across various tasks.

Deep Learning · Generative Models and Autoencoders

Joonhyuk Park, Donghyun Lee, Yujee Song, Guorong Wu, Won Hwa Kim

Generating realistic graphs faces challenges in estimating accurate distribution of graphs in an embedding space while preserving structural characteristics. However, existing graph generation methods primarily focus on approximating the joint distribution of nodes and edges, often overlooking topological properties such as connected components and loops, hindering accurate representation of global structures. To address this issue, we propose a Topology-Aware diffusion-based Graph Generation (TAGG), which aims to sample synthetic graphs that closely resemble the structural characteristics of the original graph based on persistent homology. Specifically, we suggest two core components: 1) Persistence Diagram Matching (PDM) loss which ensures high topological fidelity of generated graphs, and 2) topology-aware attention module (TAM) which induces the denoising network to capture the homological characteristics of the original graphs. Extensive experiments on conventional graph benchmarks demonstrate the effectiveness of our approach demonstrating high generation performance across various metrics, while achieving closer alignment with the distribution of topological features observed in the original graphs. Furthermore, application to real brain network data showcases its potential for complex and real graph applications.

Deep Learning · Generative Models and Autoencoders

Gregory Barber, Todd Henry, Mulugeta Haile

We present TIDES, a text informed design approach for generating physically sound designs based on a textual description and a set of physical constraints. TIDES jointly optimizes structural (topology) and visual properties. A pre-trained text-image model is used to measure the design's visual alignment with a text prompt and a differentiable physics simulator is used to measure its physical performance. We evaluate TIDES on a series of structural optimization problems operating under different load and support conditions, at different resolutions, and experimentally in the lab by performing the 3-point bending test on 2D beam designs that are extruded and 3D printed. We find that it can jointly optimize the two objectives and return designs that satisfy engineering design requirements (compliance and density) while utilizing features specified by text.

Deep Learning · Generative Models and Autoencoders

Haoyan Yang, Runxue Bao, Cao (Danica) Xiao, Jun Ma, Parminder Bhatia, Shangqian Gao, Taha Kass-Hout

LLM-as-a-Judge has emerged as a promising tool for automatically evaluating generated outputs, but its reliability is often undermined by potential biases in judgment. Existing efforts to mitigate these biases face key limitations: in-context learning-based methods fail to address rooted biases due to the evaluator’s limited capacity for self-reflection, whereas fine-tuning is not applicable to all evaluator types, especially closed-source models. To address this challenge, we introduce the **R**easoning-based **B**ias **D**etector (RBD), which is a plug-in module that identifies biased evaluations and generates structured reasoning to guide evaluator self-correction. Rather than modifying the evaluator itself, RBD operates externally and engages in an iterative process of bias detection and feedback-driven revision. To support its development, we design a complete pipeline consisting of biased dataset construction, supervision collection, distilled reasoning-based fine-tuning of RBD, and integration with LLM evaluators. We fine-tune four sizes of RBD models, ranging from 1.5B to 14B, and observe consistent performance improvements across all scales. Experimental results on 4 bias types—verbosity, position, bandwagon, and sentiment—evaluated using 8 LLM evaluators demonstrate RBD’s strong effectiveness. For example, the RBD-8B model improves evaluation accuracy by an average of 18.5% and consistency by 10.9%, and surpasses prompting-based baselines and fine-tuned judges by 12.8% and 17.2%, respectively. These results highlight RBD’s effectiveness and scalability. Additional experiments further demonstrate its strong generalization across biases and domains, as well as its efficiency.

Theory · Learning Theory

Futoshi Futami, Masahiro Fujisawa

Latent variables (LVs) play a crucial role in encoder-decoder models by enabling effective data compression, prediction, and generation. Although their theoretical properties, such as generalization, have been extensively studied in supervised learning, similar analyses for unsupervised models such as variational autoencoders (VAEs) remain insufficiently underexplored. In this work, we extend information-theoretic generalization analysis to vector-quantized (VQ) VAEs with discrete latent spaces, introducing a novel data-dependent prior to rigorously analyze the relationship among LVs, generalization, and data generation. We derive a novel generalization error bound of the reconstruction loss of VQ-VAEs, which depends solely on the complexity of LVs and the encoder, independent of the decoder. Additionally, we provide the upper bound of the 2-Wasserstein distance between the distributions of the true data and the generated data, explaining how the regularization of the LVs contributes to the data generation performance.

Social Aspects · Accountability, Transparency and Interpretability

Mengyu Ye, Jun Suzuki, Tatsuro Inaba, Tatsuki Kuribayashi

Recent interpretability work on large language models (LLMs) has been increasingly dominated by a feature-discovery approach with the help of proxy modules. Then, the quality of features learned by, e.g., sparse auto-encoders (SAEs), is evaluated. This paradigm naturally raises a critical question: do such learned features have better properties than those already represented within the original model parameters, and unfortunately, only a few studies have made such comparisons systematically so far. In this work, we revisit the interpretability of feature vectors stored in feed-forward (FF) layers, given the perspective of FF as key-value memories, with modern interpretability benchmarks. Our extensive evaluation revealed that SAE and FFs exhibits a similar range of interpretability, although SAEs displayed an observable but minimal improvement in some aspects. Furthermore, in certain aspects, surprisingly, even vanilla FFs yielded better interpretability than the SAEs, and features discovered in SAEs and FFs diverged. These bring questions about the advantage of SAEs from both perspectives of feature quality and faithfulness, compared to directly interpreting FF feature vectors, and FF key-value parameters serve as a strong baseline in modern interpretability research.

Deep Learning · Generative Models and Autoencoders

Jiaxiang Tang, Ruijie Lu, Max Li, Zekun Hao, Xuan Li, Fangyin Wei, Shuran Song, Gang Zeng, Ming-Yu Liu, Tsung-Yi Lin

Recent progress in 3D object generation has greatly improved both the quality and efficiency. However, most existing methods generate a single mesh with all parts fused together, which limits the ability to edit or manipulate individual parts. A key challenge is that different objects may have a varying number of parts. To address this, we propose a new end-to-end framework for part-level 3D object generation. Given a single input image, our method generates high-quality 3D objects with an arbitrary number of complete and semantically meaningful parts. We introduce a dual volume packing strategy that organizes all parts into two complementary volumes, allowing for the creation of complete and interleaved parts that assemble into the final object. Experiments show that our model achieves better quality, diversity, and generalization than previous image-based part-level generation methods. Our project page is at \url{https://research.nvidia.com/labs/dir/partpacker/}.

Applications · Time Series

Uros Zivanovic, Serafina Di Gioia, Andre Scaffidi, Martín de los Rios, Gabriella Contardo, Roberto Trotta

Applying Transformers to irregular time-series typically requires specializations to their baseline architecture, which can result in additional computational overhead and increased method complexity. We present the Rotary Masked Autoencoder (RoMAE), which utilizes the popular Rotary Positional Embedding (RoPE) method for continuous positions. RoMAE is an extension to the Masked Autoencoder (MAE) that enables interpolation and representation learning with multidimensional continuous positional information while avoiding any time-series-specific architectural specializations. We showcase RoMAE's performance on a variety of modalities including irregular and multivariate time-series, images, and audio, demonstrating that RoMAE surpasses specialized time-series architectures on difficult datasets such as the DESC ELAsTiCC Challenge while maintaining MAE's usual performance across other modalities. In addition, we investigate RoMAE's ability to reconstruct the embedded continuous positions, demonstrating that including learned embeddings in the input sequence breaks RoPE's relative position property.

Deep Learning · Generative Models and Autoencoders

Lu Gao, Wenlan Chen, Daoyuan Wang, Fei Guo, Cheng Liang

Cross-modal representation learning aims to extract semantically aligned representations from heterogeneous modalities such as images and text. Existing multimodal VAE-based models often suffer from limited capability to align heterogeneous modalities or lack sufficient structural constraints to clearly separate the modality-specific and shared factors. In this work, we propose a novel framework, termed **D**isentangled **C**ross-**M**odal Representation Learning with **E**nhanced **M**utual Supervision (DCMEM). Specifically, our model disentangles the common and distinct information across modalities and regularizes the shared representation learned from each modality in a mutually supervised manner. Moreover, we incorporate the information bottleneck principle into our model to ensure that the shared and modality-specific factors encode exclusive yet complementary information. Notably, our model is designed to be trainable on both complete and partial multimodal datasets with a valid Evidence Lower Bound. Extensive experimental results demonstrate significant improvements of our model over existing methods on various tasks including cross-modal generation, clustering, and classification.

Deep Learning · Generative Models and Autoencoders

Oussama Zekri, Nicolas Boulle

Discrete diffusion models have recently gained significant attention due to their ability to process complex discrete structures for language modeling. However, fine-tuning these models with policy gradient methods, as is commonly done in Reinforcement Learning from Human Feedback (RLHF), remains a challenging task. We propose an efficient, broadly applicable, and theoretically justified policy gradient algorithm, called Score Entropy Policy Optimization (SEPO), for fine-tuning discrete diffusion models over non-differentiable rewards. Our numerical experiments across several discrete generative tasks demonstrate the scalability and efficiency of our method.

Deep Learning · Generative Models and Autoencoders

Yining Shi, Kun Jiang, Qiang Meng, Ke Wang, JiaBao Wang, Wenchao Sun, Tuopu Wen, mengmeng yang, diange yang

World models are critical for autonomous driving to simulate environmental dynamics and generate synthetic data. Existing methods struggle to disentangle ego-vehicle motion (perspective shifts) from scene evolvement (agent interactions), leading to suboptimal predictions. Instead, we propose to separate environmental changes from ego-motion by leveraging the scene-centric coordinate systems. In this paper, we introduce COME: a framework that integrates scene-centric forecasting Control into the Occupancy world ModEl. Specifically, COME first generates ego-irrelevant, spatially consistent future features through a scene-centric prediction branch, which are then converted into scene condition using a tailored ControlNet. These condition features are subsequently injected into the occupancy world model, enabling more accurate and controllable future occupancy predictions. Experimental results on the nuScenes-Occ3D dataset show that COME achieves consistent and significant improvements over state-of-the-art (SOTA) methods across diverse configurations, including different input sources (ground-truth, camera-based, fusion-based occupancy) and prediction horizons (3s and 8s). For example, under the same settings, COME achieves 26.3% better mIoU metric than DOME and 23.7% better mIoU metric than UniScene. These results highlight the efficacy of disentangled representation learning in enhancing spatio-temporal prediction fidelity for world models. Code is available at https://github.com/synsin0/COME.

Deep Learning · Generative Models and Autoencoders

Jiayi Yuan, Hao Li, Xinheng Ding, Wenya Xie, Yu-Jhe Li, Wentian Zhao, Kun Wan, Jing Shi, Xia Hu, Zirui Liu

Large Language Models (LLMs) are now integral across various domains and have demonstrated impressive performance. Progress, however, rests on the premise that benchmark scores are both accurate and reproducible. We demonstrate that the reproducibility of LLM performance is fragile: changing system configuration, such as evaluation batch size, GPU count, and GPU version, can introduce significant differences in the generated responses. This issue is especially pronounced in reasoning models, where minor rounding differences in early tokens can cascade into divergent chains of thought, ultimately affecting accuracy. For instance, under bfloat16 precision with greedy decoding, a reasoning model like DeepSeek-R1-Distill-Qwen-7B can exhibit up to 9\% variation in accuracy and 9,000 tokens difference in response length due to differences in GPU count, type, and evaluation batch size. We trace the root cause of this variability to the non-associative nature of floating-point arithmetic under limited numerical precision. This work presents the first systematic investigation into how numerical precision affects reproducibility in LLM inference. Through carefully controlled experiments across various hardware, software, and precision settings, we quantify when and how model outputs diverge. Our analysis reveals that floating-point precision—while critical for reproducibility—is often neglected in evaluation practices. Inspired by this, we develop a lightweight inference pipeline, dubbed LayerCast, that stores weights in 16-bit precision but performs all computations in FP32, balancing memory efficiency with numerical stability. Code is available at https://github.com/nanomaoli/llm_reproducibility.

Deep Learning · Generative Models and Autoencoders

Michael Cardei, Jacob K Christopher, Bhavya Kailkhura, Tom Hartvigsen, Ferdinando Fioretto

Discrete diffusion models are a class of generative models that construct sequences by progressively denoising samples from a categorical noise distribution. Beyond their rapidly growing ability to generate coherent natural language, these models present a new and important opportunity to enforce sequence-level constraints, a capability that current autoregressive models cannot natively provide. This paper capitalizes on this opportunity by introducing $\textit{Constrained Discrete Diffusion}$ (CDD), a novel integration of differentiable constraint optimization within the diffusion process to ensure adherence to constraints, logic rules, or safety requirements for generated sequences. Unlike conventional text generators that often rely on post-hoc filtering or model retraining for controllable generation, CDD directly imposes constraints into the discrete diffusion sampling process, resulting in a training-free and effective approach. Experiments in toxicity-controlled text generation, property-constrained molecule design, and instruction-constrained text completion demonstrate that CDD achieves $\textit{zero constraint violations}$ in a diverse array of tasks while preserving fluency, novelty, and coherence, and outperforming autoregressive and existing discrete diffusion approaches.

Probabilistic Methods · Bayesian Models and Methods

Hadi Vafaii, Dekel Galor, Jacob Yates

Inference in both brains and machines can be formalized by optimizing a shared objective: maximizing the evidence lower bound (ELBO) in machine learning, or minimizing variational free energy ($\mathcal{F}$) in neuroscience (ELBO = $-\mathcal{F}$). While this equivalence suggests a unifying framework, it leaves open how inference is implemented in neural systems. Here, we introduce FOND (*Free energy Online Natural-gradient Dynamics*), a framework that derives neural inference dynamics from three principles: (1) natural gradients on $\mathcal{F}$, (2) online belief updating, and (3) iterative refinement. We apply FOND to derive iP-VAE (*iterative Poisson variational autoencoder*), a recurrent spiking neural network that performs variational inference through membrane potential dynamics, replacing amortized encoders with iterative inference updates. Theoretically, iP-VAE yields several desirable features such as emergent normalization via lateral competition, and hardware-efficient integer spike count representations. Empirically, iP-VAE outperforms both standard VAEs and Gaussian-based predictive coding models in sparsity, reconstruction, and biological plausibility, and scales to complex color image datasets such as CelebA. iP-VAE also exhibits strong generalization to out-of-distribution inputs, exceeding hybrid iterative-amortized VAEs. These results demonstrate how deriving inference algorithms from first principles can yield concrete architectures that are simultaneously biologically plausible and empirically effective.

Deep Learning · Generative Models and Autoencoders

Xi Chen, Kaituo Feng, Changsheng Li, Xunhao Lai, Xiangyu Yue, Ye Yuan, Guoren Wang

Low-rank training has emerged as a promising approach for reducing memory usage in training Large Language Models (LLMs). Previous methods either rely on decomposing weight matrices (e.g., LoRA), or seek to decompose gradient matrices (e.g., GaLore) to ensure reduced memory consumption. However, both of them constrain the training in a low-rank subspace, thus inevitably leading to sub-optimal performance. To resolve this, we propose a new plug-and-play training framework for LLMs called Fira, as the first attempt to consistently preserve the low-rank constraint for memory efficiency, while achieving full-rank training (i.e., training with full-rank gradients of full-rank weights) to avoid inferior outcomes. First, we observe an interesting phenomenon during LLM training: the scaling impact of adaptive optimizers (e.g., Adam) on the gradient norm remains similar from low-rank to full-rank training. In light of this, we propose a \textit{norm-based scaling} method, which utilizes the scaling impact of low-rank optimizers as substitutes for that of original full-rank optimizers to achieve this goal. Moreover, we find that there are potential loss spikes during training. To address this, we further put forward a norm-growth limiter to smooth the gradient. Extensive experiments on the pre-training and fine-tuning of LLMs show that Fira outperforms both LoRA and GaLore. Notably, for pre-training LLaMA 7B, our Fira uses $8\times$ smaller memory of optimizer states than Galore, yet outperforms it by a large margin.

Deep Learning · Generative Models and Autoencoders

Wenze Liu, Xiangyu Yue

To accelerate diffusion model inference, numerical solvers perform poorly at extremely small steps, while distillation techniques often introduce complexity and instability. This work presents an intermediate strategy, balancing performance and cost, by learning ODE integration using loss functions derived from the derivative-integral relationship, inspired by Monte Carlo integration and Picard iteration. From a geometric perspective, the losses operate by gradually extending the tangent to the secant, thus are named as secant losses. The target of secant losses is the same as that of diffusion models, or the diffusion model itself, leading to great training stability. By fine-tuning or distillation, the secant version of EDM achieves a $10$-step FID of $2.14$ on CIFAR-10, while the secant version of SiT-XL/2 attains a $4$-step FID of $2.27$ and an $8$-step FID of $1.96$ on ImageNet-$256\times256$. Code is available at \url{https://github.com/poppuppy/secant_expectation}.

Deep Learning · Generative Models and Autoencoders

Haoran Zhao, Yuchen Yan, Yongliang Shen, Haolei Xu, Wenqi Zhang, Kaitao Song, Jian Shao, Weiming Lu, Jun Xiao, Yueting Zhuang

Large reasoning models (LRMs), such as OpenAI o1 and DeepSeek-R1, have significantly enhanced their reasoning capabilities by generating longer chains of thought, demonstrating outstanding performance across a variety of tasks. However, this performance gain comes at the cost of a substantial increase in redundant reasoning during the generation process, leading to high computational overhead and exacerbating the issue of overthinking. Although numerous existing approaches aim to address the problem of overthinking, they often rely on external interventions. In this paper, we propose a novel framework, **Self-Braking Tuning**(SBT), which tackles overthinking from the perspective of allowing the model to regulate its own reasoning process, thus eliminating the reliance on external control mechanisms. We construct a set of overthinking identification metrics based on standard answers and design a systematic method to detect redundant reasoning. This method accurately identifies unnecessary steps within the reasoning trajectory and generates training signals for learning self-regulation behaviors. Building on this foundation, we develop a complete strategy for constructing data with adaptive reasoning lengths and introduce an innovative braking prompt mechanism that enables the model to naturally learn when to terminate reasoning at an appropriate point. Experiments across mathematical benchmarks (AIME, AMC, MATH500, GSM8K) demonstrate that our method reduces token consumption by up to 60\% while maintaining comparable accuracy to unconstrained models.

Applications · Chemistry and Drug Discovery

Zitao Chen, Yinjun Jia, Zitong Tian, Wei-Ying Ma, Yanyan Lan

Medicinal chemists often optimize drugs considering their 3D structures and designing structurally distinct molecules that retain key features, such as shapes, pharmacophores, or chemical properties. Previous deep learning approaches address this through supervised tasks like molecule inpainting or property-guided optimization. In this work, we propose a flexible zero-shot molecule manipulation method by navigating in a shared latent space of 3D molecules. We introduce a Variational AutoEncoder (VAE) for 3D molecules, named MolFLAE, which learns a fixed-dimensional, E(3)-equivariant latent space independent of atom counts. MolFLAE encodes 3D molecules using an E(3)-equivariant neural network into fixed number of latent nodes, distinguished by learned embeddings. The latent space is regularized, and molecular structures are reconstructed via a Bayesian Flow Network (BFN) conditioned on the encoder’s latent output. MolFLAE achieves competitive performance on standard unconditional 3D molecule generation benchmarks. Moreover, the latent space of MolFLAE enables zero-shot molecule manipulation, including atom number editing, structure reconstruction, and coordinated latent interpolation for both structure and properties. We further demonstrate our approach on a drug optimization task for the human glucocorticoid receptor, generating molecules with improved hydrophilicity while preserving key interactions, under computational evaluations. These results highlight the flexibility, robustness, and real-world utility of our method, opening new avenues for molecule editing and optimization.

Zhihao Li, Yufei Wang, Heliang Zheng, Yihao Luo, Bihan Wen

High-fidelity 3D object synthesis remains significantly more challenging than 2D image generation due to the unstructured nature of mesh data and the cubic complexity of dense volumetric grids. Existing two-stage pipelines—compressing meshes with a VAE (using either 2D or 3D supervision), followed by latent diffusion sampling—often suffer from severe detail loss caused by inefficient representations and modality mismatches introduced in VAE. We introduce Sparc3D, a unified framework that combines a sparse deformable marching cubes representation Sparcubes with a novel encoder Sparconv-VAE. Sparcubes converts raw meshes into high-resolution ($1024^3$) surfaces with arbitrary topology by scattering signed distance and deformation fields onto a sparse cube, allowing differentiable optimization. Sparconv-VAE is the first modality-consistent variational autoencoder built entirely upon sparse convolutional networks, enabling efficient and near-lossless 3D reconstruction suitable for high-resolution generative modeling through latent diffusion. Sparc3D achieves state-of-the-art reconstruction fidelity on challenging inputs, including open surfaces, disconnected components, and intricate geometry. It preserves fine-grained shape details, reduces training and inference cost, and integrates naturally with latent diffusion models for scalable, high-resolution 3D generation.