论文检索

Applications · Health

Zepeng Frazier Huo, Jason Fries, Alejandro Lozano, Jeya Maria Jose Valanarasu, Ethan Steinberg, Louis Blankemeier, Akshay Chaudhari, Curtis Langlotz, Nigam Shah

With the rise of medical foundation models and the growing availability of imaging data, scalable pretraining techniques offer a promising way to identify imaging biomarkers predictive of future disease risk. While current self-supervised methods for 3D medical imaging models capture local structural features like organ morphology, they fail to link pixel biomarkers with long-term health outcomes due to a missing context problem. Current approaches lack the temporal context necessary to identify biomarkers correlated with disease progression, as they rely on supervision derived only from images and concurrent text descriptions. To address this, we introduce time-to-event pretraining, a pretraining framework for 3D medical imaging models that leverages large-scale temporal supervision from paired, longitudinal electronic health records (EHRs). Using a dataset of 18,945 CT scans (4.2 million 2D images) and time-to-event distributions across thousands of EHR-derived tasks, our method improves outcome prediction, achieving an average AUROC increase of 23.7% and a 29.4% gain in Harrell’s C-index across 8 benchmark tasks. Importantly, these gains are achieved without sacrificing diagnostic classification performance. This study lays the foundation for integrating longitudinal EHR and 3D imaging data to advance clinical risk prediction.

Deep Learning · Everything Else

Zhuoyi Peng, Yixuan Tang, Yi Yang

Machine unlearning is a critical area of research aimed at safeguarding data privacy by enabling the removal of sensitive information from machine learning models. One unique challenge in this field is catastrophic unlearning, where erasing specific data from a well-trained model unintentionally removes essential knowledge, causing the model to deviate significantly from a retrained one. To address this, we introduce a novel approach that regularizes the unlearning process by utilizing synthesized mixup samples, which simulate the data susceptible to catastrophic effects. At the core of our approach is a generator-unlearner framework, MixUnlearn, where a generator adversarially produces challenging mixup examples, and the unlearner effectively forgets target information based on these synthesized data. Specifically, we first introduce a novel contrastive objective to train the generator in an adversarial direction: generating examples that prompt the unlearner to reveal information that should be forgotten, while losing essential knowledge. Then the unlearner, guided by two other contrastive loss terms, processes the synthesized and real data jointly to ensure accurate unlearning without losing critical knowledge, overcoming catastrophic effects. Extensive evaluations across benchmark datasets demonstrate that our method significantly outperforms state-of-the-art approaches, offering a robust solution to machine unlearning. This work not only deepens understanding of unlearning mechanisms but also lays the foundation for effective machine unlearning with mixup augmentation.

Applications · Robotics

Xiangyu Wang, Donglin Yang, ziqin wang, Hohin Kwan, Jinyu Chen, wenjun wu, Hongsheng Li, Yue Liao, Si Liu

Developing agents capable of navigating to a target location based on language instructions and visual information, known as vision-language navigation (VLN), has attracted widespread interest. Most research has focused on ground-based agents, while UAV-based VLN remains relatively underexplored. Recent efforts in UAV vision-language navigation predominantly adopt ground-based VLN settings, relying on predefined discrete action spaces and neglecting the inherent disparities in agent movement dynamics and the complexity of navigation tasks between ground and aerial environments. To address these disparities and challenges, we propose solutions from three perspectives: platform, benchmark, and methodology. To enable realistic UAV trajectory simulation in VLN tasks, we propose the OpenUAV platform, which features diverse environments, realistic flight control, and extensive algorithmic support. We further construct a target-oriented VLN dataset consisting of approximately 12k trajectories on this platform, serving as the first dataset specifically designed for realistic UAV VLN tasks. To tackle the challenges posed by complex aerial environments, we propose an assistant-guided UAV object search benchmark called UAV-Need-Help, which provides varying levels of guidance information to help UAVs better accomplish realistic VLN tasks. We also propose a UAV navigation LLM that, given multi-view images, task descriptions, and assistant instructions, leverages the multimodal understanding capabilities of the MLLM to jointly process visual and textual information, and performs hierarchical trajectory generation. The evaluation results of our method significantly outperform the baseline models, while there remains a considerable gap between our results and those achieved by human operators, underscoring the challenge presented by the UAV-Need-Help task.

Optimization · Learning for Optimization

Sirui Li, Janardhan Kulkarni, Ishai Menache, Cathy Wu, Beibin Li

Mixed Integer Linear Programming (MILP) is essential for modeling complex decision-making problems but faces challenges in computational tractability and interpretability. Current deep learning approaches for MILP focus on specific problem classes and do not generalize to unseen classes. To address this shortcoming, we take a foundation model training approach, where we train a single deep learning model on a diverse set of MILP problems to generalize across problem classes. As existing datasets for MILP lack diversity and volume, we introduce MILP-Evolve, a novel LLM-based evolutionary framework that is capable of generating a large set of diverse MILP classes with an unlimited amount of instances. We study our methodology on three key learning tasks that capture diverse aspects of MILP: (1) integrality gap prediction, (2) learning to branch, and (3) a new task of aligning MILP instances with natural language descriptions. Our empirical results show that models trained on the data generated by MILP-Evolve achieve significant improvements on unseen problems, including MIPLIB benchmarks. Our work highlights the potential of moving towards a foundation model approach for MILP that can generalize to a broad range of MILP problem classes. Our code and data are publicly available at https://github.com/microsoft/OptiGuide.

Applications · Chemistry and Drug Discovery

Gang Liu, Michael Sun, Wojciech Matusik, Meng Jiang, Jie Chen

While large language models (LLMs) have integrated images, adapting them to graphs remains challenging, limiting their applications in materials and drug design. This difficulty stems from the need for coherent autoregressive generation across texts and graphs. To address this, we introduce Llamole, the first multimodal LLM capable of interleaved text and graph generation, enabling molecular inverse design with retrosynthetic planning. Llamole integrates a base LLM with the Graph Diffusion Transformer and Graph Neural Networks for multi-conditional molecular generation and reaction inference within texts, while the LLM, with enhanced molecular understanding, flexibly controls activation among the different graph modules. Additionally, Llamole integrates A* search with LLM-based cost functions for efficient retrosynthetic planning. We create benchmarking datasets and conduct extensive experiments to evaluate Llamole against in-context learning and supervised fine-tuning. Llamole significantly outperforms 14 adapted LLMs across 12 metrics for controllable molecular design and retrosynthetic planning. Code and model at https://github.com/liugangcode/Llamole.

Theory · Domain Adaptation and Transfer Learning

Gezheng Xu, Hui GUO, Li Yi, Charles Ling, Boyu Wang, Grace Yi

Source-Free Domain Adaptation (SFDA) seeks to adapt a pre-trained source model to the target domain using only unlabeled target data, without access to the original source data. While current state-of-the-art (SOTA) methods rely on leveraging weak supervision from the source model to extract reliable information for self-supervised adaptation, they often overlook the uncertainty that arises during the transfer process. In this paper, we conduct a systematic and theoretical analysis of the uncertainty inherent in existing SFDA methods and demonstrate its impact on transfer performance through the lens of Distributionally Robust Optimization (DRO). Building upon the theoretical results, we propose a novel instance-dependent uncertainty control algorithm for SFDA. Our method is designed to quantify and exploit the uncertainty during the adaptation process, significantly improving the model performance. Extensive experiments on benchmark datasets and empirical analyses confirm the validity of our theoretical findings and the effectiveness of the proposed method. This work offers new insights into understanding and advancing SFDA performance.

Deep Learning · Large Language Models

Zhangheng LI, Keen You, Haotian Zhang, Di Feng, Harsh Agrawal, Xiujun Li, Mohana Moorthy, Jeffrey Nichols, Yinfei Yang, Zhe Gan

Building a generalist model for user interface (UI) understanding is challenging due to various foundational issues, such as platform diversity, resolution variation, and data limitation. In this paper, we introduce Ferret-UI 2, a multimodal large language model (MLLM) designed for universal UI understanding across a wide range of platforms, including iPhone, Android, iPad, Webpage, and AppleTV. Building on the foundation of Ferret-UI, Ferret-UI 2 introduces three key innovations: support for multiple platform types, high-resolution perception through adaptive scaling, and advanced task training data generation powered by GPT-4o with set-of-mark visual prompting. These advancements enable Ferret-UI 2 to perform complex, user-centered interactions, making it highly versatile and adaptable for the expanding diversity of platform ecosystems. Extensive empirical experiments on referring, grounding, user-centric advanced tasks (comprising 9 subtasks $\times$ 5 platforms), GUIDE next-action prediction dataset, and GUI-World multi-platform benchmark demonstrate that Ferret-UI 2 significantly outperforms Ferret-UI, and also shows strong cross-platform transfer capabilities.

Miscellaneous Aspects of Machine Learning · Unsupervised and Semi-supervised Learning

Yingwen Wu, Ruiji Yu, Xinwen Cheng, Zhengbao He, Xiaolin Huang

In the open world, detecting out-of-distribution (OOD) data, whose labels are disjoint with those of in-distribution (ID) samples, is important for reliable deep neural networks (DNNs). To achieve better detection performance, one type of approach proposes to fine-tune the model with auxiliary OOD datasets to amplify the difference between ID and OOD data through a separation loss defined on model outputs. However, none of these studies consider enlarging the feature disparity, which should be more effective compared to outputs. The main difficulty lies in the diversity of OOD samples, which makes it hard to describe their feature distribution, let alone design losses to separate them from ID features. In this paper, we neatly fence off the problem based on an aggregation property of ID features named Neural Collapse (NC). NC means that the penultimate features of ID samples within a class are nearly identical to the last layer weight of the corresponding class. Based on this property, we propose a simple but effective loss called Separation Loss, which binds the features of OOD data in a subspace orthogonal to the principal subspace of ID features formed by NC. In this way, the features of ID and OOD samples are separated by different dimensions. By optimizing the feature separation loss rather than purely enlarging output differences, our detection achieves SOTA performance on CIFAR10, CIFAR100 and ImageNet benchmarks without any additional data augmentation or sampling, demonstrating the importance of feature separation in OOD detection. Code is availableat https://github.com/Wuyingwen/Pursuing-Feature-Separation-for-OOD-Detection.

Renrui Zhang, Xinyu Wei, Dongzhi Jiang, Ziyu Guo, Yichi Zhang, Chengzhuo Tong, Jiaming Liu, Aojun Zhou, Shanghang Zhang, Gao Peng 等

Multi-modal Large Language Models (MLLMs) have recently showcased superior proficiency in general visual scenarios. However, we identify their mathematical capabilities remain under-explored with three areas to be improved: visual encoding of math diagrams, diagram-language alignment, and chain-of-thought (CoT) reasoning. This draws forth an urgent demand for an effective training paradigm and a large-scale, comprehensive dataset with detailed CoT rationales, which is challenging to collect and costly to annotate manually. To tackle this issue, we propose MAVIS, a MAthematical VISual instruction tuning pipeline for MLLMs, featuring an automatic data engine to efficiently create mathematical visual datasets.We design the data generation process to be entirely independent of human intervention or GPT API usage, while ensuring the diagram-caption correspondence, question-answer correctness, and CoT reasoning quality. With this approach, we curate two datasets, MAVIS-Caption (558K diagram-caption pairs) and MAVIS-Instruct (834K visual math problems with CoT rationales), and propose four progressive stages for training MLLMs from scratch.First, we utilize MAVIS-Caption to fine-tune a math-specific vision encoder (CLIP-Math) through contrastive learning, tailored for improved diagram visual encoding. Second, we also leverage MAVIS-Caption to align the CLIP-Math with a large language model (LLM) by a projection layer, enhancing vision-language alignment in mathematical domains. Third, we adopt MAVIS-Instruct to perform the instruction tuning for robust problem-solving skills, and term the resulting model as MAVIS-7B. Fourth, we apply Direct Preference Optimization (DPO) to enhance the CoT capabilities of our model, further refining its step-wise reasoning performance.On various mathematical benchmarks, our MAVIS-7B achieves leading results among open-source MLLMs, e.g., surpassing other 7B models by +9.3% and the second-best LLaVA-NeXT (110B) by +6.9%, demonstrating the effectiveness of our method.

Applications · Physics

Mingquan Feng, Yixin Huang, Yizhou Liu, Bofang Jiang, Junchi Yan

Despite extensive research, recovering PDE expressions from experimental observations often involves symbolic regression. This method generally lacks the incorporation of meaningful physical insights, resulting in outcomes lacking clear physical interpretations. Recognizing that the primary interest of Machine Learning for Science (ML4Sci) often lies in understanding the underlying physical mechanisms or even discovering new physical laws rather than simply obtaining mathematical expressions, this paper introduces a novel ML4Sci task paradigm. This paradigm focuses on interpreting experimental data within the framework of prior physical hypotheses and theories, thereby guiding and constraining the discovery of PDE expressions. We have formulated this approach as a nonlinear mixed-integer programming (MIP) problem, addressed through an efficient search scheme developed for this purpose. Our experiments on newly designed Fluid Mechanics and Laser Fusion datasets demonstrate the interpretability and feasibility of this method.

Deep Learning · Large Language Models

Jinlong Pang, Jiaheng Wei, Ankit Parag Shah, Zhaowei Zhu, Yaxuan Wang, Chen Qian, Yang Liu, Yujia Bao, Wei Wei

Instruction tuning is critical for adapting large language models (LLMs) to downstream tasks, and recent studies have demonstrated that small amounts of human-curated data can outperform larger datasets, challenging traditional data scaling laws. While LLM-based data quality rating systems offer a cost-effective alternative to human annotation, they often suffer from inaccuracies and biases, even in powerful models like GPT-4. In this work, we introduce $DS^2$, a **D**iversity-aware **S**core curation method for **D**ata **S**election. By systematically modeling error patterns through a score transition matrix, $DS^2$ corrects LLM-based scores and promotes diversity in the selected data samples. Our approach shows that a curated subset (just 3.3\% of the original dataset) outperforms full-scale datasets (300k samples) across various machine-alignment benchmarks, and matches or surpasses human-aligned datasets such as LIMA with the same sample size (1k samples). These findings challenge conventional data scaling assumptions, highlighting that redundant, low-quality samples can degrade performance and reaffirming that ``more can be less''.

Deep Learning · Robustness

Alexander Li, Ananya Kumar, Deepak Pathak

Discriminative approaches to classification often learn shortcuts that hold in-distribution but fail even under minor distribution shift. This failure mode stems from an overreliance on features that are spuriously correlated with the label. We show that generative classifiers, which use class-conditional generative models, can avoid this issue by modeling all features, both core and spurious, instead of mainly spurious ones. These generative classifiers are simple to train, avoiding the need for specialized augmentations, strong regularization, extra hyperparameters, or knowledge of the specific spurious correlations to avoid. We find that diffusion-based and autoregressive generative classifiers achieve state-of-the-art performance on five standard image and text distribution shift benchmarks and reduce the impact of spurious correlations in realistic applications, such as medical or satellite datasets. Finally, we carefully analyze a Gaussian toy setting to understand the inductive biases of generative classifiers, as well as the data properties that determine when generative classifiers outperform discriminative ones.

Deep Learning · Large Language Models

Chengwen Qi, Ren Ma, Bowen Li, he du, Binyuan Hui, Jinwang Wu, Yuanjun Laili, Conghui He

First-order logic (FOL) reasoning, which involves sequential deduction, is pivotal for intelligent systems and serves as a valuable task for evaluating reasoning capabilities, particularly in chain-of-thought (CoT) contexts. Existing benchmarks often rely on extensive human annotation or handcrafted templates, making it difficult to achieve the necessary complexity, scalability, and diversity for robust evaluation. To address these limitations, we propose a novel framework called ProverGen that synergizes the generative strengths of Large Language Models (LLMs) with the rigor and precision of symbolic provers, enabling the creation of a scalable, diverse, and high-quality FOL reasoning dataset, ProverQA. ProverQA is also distinguished by its inclusion of accessible and logically coherent intermediate reasoning steps for each problem. Our evaluation shows that state-of-the-art LLMs struggle to solve ProverQA problems, even with CoT prompting, highlighting the dataset's challenging nature. We also finetune Llama3.1-8B-Instruct on a separate training set generated by our framework.The finetuned model demonstrates consistent improvements on both in-distribution and out-of-distribution test sets, suggesting the value of our proposed data generation framework. Code available at: \url{https://github.com/opendatalab/ProverGen}

Theory · Deep Learning

Binh Nguyen, Minh-Duong Nguyen, Jinsun Park, Viet Pham, Won-Joo Hwang

Domain Generalization (DG) aims to learn from multiple known source domains a model that can generalize well to unknown target domains. One of the key approaches in DG is training an encoder which generates domain-invariant representations. However, this approach is not applicable in Federated Domain Generalization (FDG), where data from various domains are distributed across different clients. In this paper, we introduce a novel approach, dubbed Federated Learning via On-server Matching Gradient (FedOMG), which can efficiently leverage domain information from distributed domains. Specifically, we utilize the local gradients as information about the distributed models to find an invariant gradient direction across all domains through gradient inner product maximization. The advantages are two-fold: 1) FedOMG can aggregate the characteristics of distributed models on the centralized server without incurring any additional communication cost, and 2) FedOMG is orthogonal to many existing FL/FDG methods, allowing for additional performance improvements by being seamlessly integrated with them. Extensive experimental evaluations on various settings demonstrate the robustness of FedOMG compared to other FL/FDG baselines. Our method outperforms recent SOTA baselines on four FL benchmark datasets (MNIST, EMNIST, CIFAR-10, and CIFAR-100), and three FDG benchmark datasets (PACS, VLCS, and OfficeHome). The reproducible code is publicly available~\footnote[1]{\url{https://github.com/skydvn/fedomg}}.

Chengyue Huang, Junjiao Tian, Brisa Maneechotesuwan, Shivang Chopra, Zsolt Kira

Robust fine-tuning aims to adapt large foundation models to downstream tasks while preserving their robustness to distribution shifts. Existing methods primarily focus on constraining and projecting current model towards the pre-trained initialization based on the magnitudes between fine-tuned and pre-trained weights, which often require extensive hyper-parameter tuning and can sometimes result in underfitting. In this work, we propose $\textbf{Di}$rectional $\textbf{Gra}$dient $\textbf{P}$rojection (DiGraP), a novel layer-wise trainable method that incorporates directional information from gradients to bridge regularization and multi-objective optimization. Besides demonstrating our method on image classification, as another contribution we generalize this area to the multi-modal evaluation settings for robust fine-tuning. Specifically, we first bridge the uni-modal and multi-modal gap by performing analysis on Image Classification reformulated Visual Question Answering (VQA) benchmarks and further categorize ten out-of-distribution (OOD) VQA datasets by distribution shift types and degree (i.e. near versus far OOD). Experimental results show that DiGraP consistently outperforms existing baselines across Image Classfication and VQA tasks with discriminative and generative backbones, improving both in-distribution (ID) generalization and OOD robustness.

Applications · Neuroscience, Cognitive Science

Drew Linsley, Peisen Zhou, Alekh Ashok, Akash Nagaraj, Gaurav Suhas Gaonkar, Francis Lewis, Zygmunt Pizlo, Thomas Serre

Visual perspective taking (VPT) is the ability to perceive and reason about the perspectives of others. It is an essential feature of human intelligence, which develops over the first decade of life and requires an ability to process the 3D structure of visual scenes. A growing number of reports have indicated that deep neural networks (DNNs) become capable of analyzing 3D scenes after training on large image datasets. We investigated if this emergent ability for 3D analysis in DNNs is sufficient for VPT with the 3D perception challenge (3D-PC): a novel benchmark for 3D perception in humans and DNNs. The 3D-PC is comprised of three 3D-analysis tasks posed within natural scene images: (i.) a simple test of object depth order, (ii.) a basic VPT task (VPT-basic), and (iii.) a more challenging version of VPT (VPT-perturb) designed to limit the effectiveness of "shortcut" visual strategies. We tested human participants (N=33) and linearly probed or text-prompted over 300 DNNs on the challenge and found that nearly all of the DNNs approached or exceeded human accuracy in analyzing object depth order. Surprisingly, DNN accuracy on this task correlated with their object recognition performance. In contrast, there was an extraordinary gap between DNNs and humans on VPT-basic. Humans were nearly perfect, whereas most DNNs were near chance. Fine-tuning DNNs on VPT-basic brought them close to human performance, but they, unlike humans, dropped back to chance when tested on VPT-perturb. Our challenge demonstrates that the training routines and architectures of today's DNNs are well-suited for learning basic 3D properties of scenes and objects but are ill-suited for reasoning about these properties like humans do. We release our 3D-PC datasets and code to help bridge this gap in 3D perception between humans and machines.

Deep Learning · Generative Models and Autoencoders

Xiaofeng Lin, Chenheng Xu, Matthew Yang, Guang Cheng

Generative Foundation Models (GFMs) have achieved remarkable success in producing high-quality synthetic data for images and text. However, their application to tabular data presents significant challenges due to the heterogeneous nature of table features. Current cross-table learning frameworks struggle because they lack a generative model backbone and an effective mechanism to decode heterogeneous feature values. To address these challenges, we propose the Cross-Table Synthesizer (CTSyn), a diffusion-based generative foundation model for tabular data generation. CTSyn comprises two key components. The first is an autoencoder network that consolidates diverse tables into a unified latent space. It dynamically reconstructs table values using a table schema embedding, allowing adaptation to heterogeneous datasets. The second is a conditional latent diffusion model that generates samples from the learned latent space, conditioned on the table schema. Through large-scale pre-training, CTSyn outperforms existing table synthesizers on standard benchmarks in both utility and diversity. These results position CTSyn as a promising framework for synthetic table generation and lay the groundwork for developing large-scale tabular foundation models.

Social Aspects · Fairness, Equity, Justice and Safety

Tinghao Xie, Xiangyu Qi, Yi Zeng, Yangsibo Huang, Udari Sehwag, Kaixuan Huang, Luxi He, Boyi Wei, Dacheng Li, Ying Sheng 等

Evaluating aligned large language models' (LLMs) ability to recognize and reject unsafe user requests is crucial for safe, policy-compliant deployments. Existing evaluation efforts, however, face three limitations that we address with **SORRY-Bench**, our proposed benchmark. **First**, existing methods often use coarse-grained taxonomies of unsafe topics, and are over-representing some fine-grained topics. For example, among the ten existing datasets that we evaluated, tests for refusals of self-harm instructions are over 3x less represented than tests for fraudulent activities. SORRY-Bench improves on this by using a fine-grained taxonomy of 44 potentially unsafe topics, and 440 class-balanced unsafe instructions, compiled through human-in-the-loop methods. **Second**, evaluations often overlook the linguistic formatting of prompts, like different languages, dialects, and more --- which are only implicitly considered in many evaluations. We supplement SORRY-bench with 20 diverse linguistic augmentations to systematically examine these effects. **Third**, existing evaluations rely on large LLMs (e.g., GPT-4) for evaluation, which can be computationally expensive. We investigate design choices for creating a fast, accurate automated safety evaluator. By collecting 7K+ human annotations and conducting a meta-evaluation of diverse LLM-as-a-judge designs, we show that fine-tuned 7B LLMs can achieve accuracy comparable to GPT-4 scale LLMs, with lower computational cost. Putting these together, we evaluate over 50 proprietary and open-weight LLMs on SORRY-Bench, analyzing their distinctive safety refusal behaviors. We hope our effort provides a building block for systematic evaluations of LLMs' safety refusal capabilities, in a balanced, granular, and efficient manner. Benchmark demo, data, code, and models are available through [https://sorry-bench.github.io](https://sorry-bench.github.io).

Ruiyi Fang, Bingheng Li, zhao kang, Qiuhao Zeng, Nima Hosseini Dashtbayaz, Ruizhi Pu, Charles Ling, Boyu Wang

Graph Domain Adaptation (GDA) addresses a pressing challenge in cross-network learning, particularly pertinent due to the absence of labeled data in real-world graph datasets. Recent studies attempted to learn domain invariant representations by eliminating structural shifts between graphs. In this work, we show that existing methodologies have overlooked the significance of the graph node attribute, a pivotal factor for graph domain alignment. Specifically, we first reveal the impact of node attributes for GDA by theoretically proving that in addition to the graph structural divergence between the domains, the node attribute discrepancy also plays a critical role in GDA. Moreover, we also empirically show that the attribute shift is more substantial than the topology shift, which further underscore the importance of node attribute alignment in GDA. Inspired by this finding, a novel cross-channel module is developed to fuse and align both views between the source and target graphs for GDA. Experimental results on a variety of benchmark verify the effectiveness of our method.

Xiang Xu 0008, Joseph G. Lambourne, Pradeep Kumar Jayaraman, Zhengqing Wang, Karl D. D. Willis, Yasutaka Furukawa

This paper presents BrepGen, a diffusion-based generative approach that directly outputs a Boundary representation (B-rep) Computer-Aided Design (CAD) model. BrepGen represents a B-rep model as a novel structured latent geometry in a hierarchical tree. With the root node representing a whole CAD solid, each element of a B-rep model (i.e., a face, an edge, or a vertex) progressively turns into a child-node from top to bottom. B-rep geometry information goes into the nodes as the global bounding box of each primitive along with a latent code describing the local geometric shape. The B-rep topology information is implicitly represented by node duplication. When two faces share an edge, the edge curve will appear twice in the tree, and a T-junction vertex with three incident edges appears six times in the tree with identical node features. Starting from the root and progressing to the leaf, BrepGen employs Transformer-based diffusion models to sequentially denoise node features while duplicated nodes are detected and merged, recovering the B-Rep topology information. Extensive experiments show that BrepGen advances the task of CAD B-rep generation, surpassing existing methods on various benchmarks. Results on our newly collected furniture dataset further showcase its exceptional capability in generating complicated geometry. While previous methods were limited to generating simple prismatic shapes, BrepGen incorporates free-form and doubly-curved surfaces for the first time. Additional applications of BrepGen include CAD autocomplete and design interpolation. The code, pretrained models, and dataset are available at https://github.com/samxuxiang/BrepGen.