Author name cluster

Bowen Li

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

13 papers

1 author row

AAAI Conference 2026 Conference Paper

CLM-Access: A Specialized Foundation Model for High-Dimensional Single-Cell ATAC-Seq Analysis

Ziqiang Liu
Bowen Li
Zhenyu Xu
Yantao Li
Junwei Zhang
Chulin Sha
Xiaolin Li

Inspired by the success of large language models (LLMs) in natural language processing, cell language models (CLMs) have emerged as a promising paradigm to learn cell representations from high-dimensional single-cell data—particularly transcriptomic profiles from scRNA-seq. These foundation models have shown remarkable potential across a variety of downstream applications. However, there remains a lack of foundation models for scATAC-seq data, which measures chromatin accessibility at single-cell level and is critical for decoding epigenetic regulation. Developing such model is considerably more challenging due to the unique characteristics of scATAC-seq data, including the vast number of chromatin regions, lack of standardized annotations, extreme sparsity, and near-binary distributions. To address these challenges, we systematically explore various strategies and propose CLM-Access, a specialized foundation model for scATAC-seq data. CLM-Access incorporates three main innovations: (1) an unified data processing pipeline that maps 2.8 million cells onto an unified reference of over 1 million chromatin regions; (2) a specialized patching and embedding strategy to effectively manage high-dimensional inputs; and (3) a tailored masking and loss function design that preserves fine-grained regional information while enhancing training efficiency and representation quality. With comprehensive benchmarks, we show that CLM-Access significantly outperforms existing methods in key downstream tasks, including batch effect correction, cell type annotation, RNA expression prediction, and multi-modal integration. This work establishes a scalable and interpretable foundation model for single-cell epigenomic analysis and expands the application of CLMs in single-cell research.

PDF Details DOI

NeurIPS Conference 2025 Conference Paper

Gradient Alignment in Physics-informed Neural Networks: A Second-Order Optimization Perspective

Sifan Wang
Ananyae bhartari
Bowen Li
Paris Perdikaris

Physics-informed neural networks (PINNs) have shown significant promise in computational science and engineering, yet they often face optimization challenges and limited accuracy. In this work, we identify directional gradient conflicts during PINN training as a critical bottleneck. We introduce a novel gradient alignment score to systematically diagnose this issue through both theoretical analysis and empirical experiments. Building on these insights, we show that (quasi) second-order optimization methods inherently mitigate gradient conflicts, thereby consistently outperforming the widely used Adam optimizer. Among them, we highlight the effectiveness of SOAP \cite{vyas2024soap} by establishing its connection to Newton’s method. Empirically, SOAP achieves state-of-the-art results on 10 challenging PDE benchmarks, including the first successful application of PINNs to turbulent flows at Reynolds numbers up to 10, 000. It yields 2–10x accuracy improvements over existing methods while maintaining computational scalability, advancing the frontier of neural PDE solvers for real-world, multi-scale physical systems. All code and datasets used in this work are publicly available at: \url{https: //github. com/PredictiveIntelligenceLab/jaxpi/tree/pirate}. \end{abstract}

PDF Details

TMLR Journal 2025 Journal Article

Large Language Model-Brained GUI Agents: A Survey

Chaoyun Zhang
Shilin He
Jiaxu Qian
Bowen Li
Liqun Li
Si Qin
Yu Kang
Minghua Ma

Graphical User Interfaces (GUIs) have long been central to human-computer interaction, providing an intuitive and visually-driven way to access and interact with digital systems. Traditionally, automating GUI interactions relied on script-based or rule-based approaches, which, while effective for fixed workflows, lacked the flexibility and adaptability required for dynamic, real-world applications. The advent of Large Language Models (LLMs), particularly multimodal models, has ushered in a new era of GUI automation. They have demonstrated exceptional capabilities in natural language understanding, code generation, task generalization, and visual processing. This has paved the way for a new generation of ''LLM-brained'' GUI agents capable of interpreting complex GUI elements and autonomously executing actions based on natural language instructions. These agents represent a paradigm shift, enabling users to perform intricate, multi-step tasks through simple conversational commands. Their applications span across web navigation, mobile app interactions, and desktop automation, offering a transformative user experience that revolutionizes how individuals interact with software. This emerging field is rapidly advancing, with significant progress in both research and industry. To provide a structured understanding of this trend, this paper presents a comprehensive survey of LLM-brained GUI agents, exploring their historical evolution, core components, and advanced techniques. We address critical research questions such as existing GUI agent frameworks, the collection and utilization of data for training specialized GUI agents, the development of large action models tailored for GUI tasks, and the evaluation metrics and benchmarks necessary to assess their effectiveness. Additionally, we examine emerging applications powered by these agents. Through a detailed analysis, this survey identifies key research gaps and outlines a roadmap for future advancements in the field. By consolidating foundational knowledge and state-of-the-art developments, this work aims to guide both researchers and practitioners in overcoming challenges and unlocking the full potential of LLM-brained GUI agents. We anticipate that this survey will serve both as a practical cookbook for constructing LLM-powered GUI agents, and as a definitive reference for advancing research in this rapidly evolving domain.

PDF Details

NeurIPS Conference 2025 Conference Paper

MMaDA: Multimodal Large Diffusion Language Models

Ling Yang
Ye Tian
Bowen Li
Xinchen Zhang
Ke Shen
Yunhai Tong
Mengdi Wang

We introduce MMaDA, a novel class of multimodal diffusion foundation models designed to achieve superior performance across diverse domains such as textual reasoning, multimodal understanding, and text-to-image generation. The approach is distinguished by three key innovations: (i) MMaDA adopts a unified diffusion architecture with a shared probabilistic formulation and a modality-agnostic design, eliminating the need for modality-specific components. This architecture ensures seamless integration and processing across different data types. (ii) We implement a mixed long chain-of-thought (CoT) fine-tuning strategy that curates a unified CoT format across modalities. By aligning reasoning processes between textual and visual domains, this strategy facilitates cold-start training for the final reinforcement learning (RL) stage, thereby enhancing the model's ability to handle complex tasks from the outset. (iii) We propose UniGRPO, a unified policy-gradient-based RL algorithm specifically tailored for diffusion foundation models. Utilizing diversified reward modeling, UniGRPO unifies post-training across both reasoning and generation tasks, ensuring consistent performance improvements. Experimental results demonstrate that MMaDA-8B exhibits strong generalization capabilities as a unified multimodal foundation model. It surpasses powerful models like LLaMA-3-7B and Qwen2-7B in textual reasoning, outperforms Show-o and SEED-X in multimodal understanding, and excels over SDXL and Janus in text-to-image generation. These achievements highlight MMaDA's effectiveness in bridging the gap between pretraining and post-training within unified diffusion architectures, providing a comprehensive framework for future research and development. We open-source our code and trained models at: https: //github. com/Gen-Verse/MMaDA

PDF Details

AAAI Conference 2025 Conference Paper

NumbOD: A Spatial-Frequency Fusion Attack Against Object Detectors

Ziqi Zhou
Bowen Li
Yufei Song
Zhifei Yu
Shengshan Hu
Wei Wan
Leo Yu Zhang
Dezhong Yao

With the advancement of deep learning, object detectors (ODs) with various architectures have achieved significant success in complex scenarios like autonomous driving. Previous adversarial attacks against ODs have been focused on designing customized attacks targeting their specific structures (eg, NMS and RPN), yielding some results but simultaneously constraining their scalability. Moreover, most efforts against ODs stem from image-level attacks originally designed for classification tasks, resulting in redundant computations and disturbances in object-irrelevant areas (eg, background). Consequently, how to design a model-agnostic efficient attack to comprehensively evaluate the vulnerabilities of ODs remains challenging and unresolved. In this paper, we propose NumbOD, a brand-new spatial-frequency fusion attack against various ODs, aimed at disrupting object detection within images. We directly leverage the features output by the OD without relying on its any internal structures to craft adversarial examples. Specifically, we first design a dual-track attack target selection strategy to select high-quality bounding boxes from OD outputs for targeting. Subsequently, we employ directional perturbations to shift and compress predicted boxes and change classification results to deceive ODs. Additionally, we focus on manipulating the high-frequency components of images to confuse ODs' attention on critical objects, thereby enhancing the attack efficiency. Our extensive experiments on nine ODs and two datasets show that NumbOD achieves powerful attack performance and high stealthiness.

PDF Details DOI

NeurIPS Conference 2025 Conference Paper

SWE-bench Goes Live!

LingHao Zhang
Shilin He
Chaoyun Zhang
Yu Kang
Bowen Li
Chengxing Xie
Junhao Wang
Maoquan Wang

The issue-resolving task, where a model generates patches to fix real-world bugs, has emerged as a key benchmark for evaluating the capabilities of large language models (LLMs). While SWE-bench has become the dominant benchmark in this domain, it suffers from several limitations: it has not been updated since its release, is restricted to only 12 repositories, and relies heavily on manual effort for constructing test instances and setting up executable environments, significantly limiting its scalability. We present SWE-bench-Live, a live-updatable benchmark designed to address these limitations. SWE-bench-Live currently includes 1, 890 tasks derived from real GitHub issues created since 2024, spanning 223 repositories. Each task is accompanied by a dedicated Docker image to ensure reproducible execution. Additionally, we introduce an automated curation pipeline that streamlines the entire process from instance creation to environment setup, removing manual bottlenecks and enabling scalability and continuous updates. We evaluate a range of state-of-the-art models and agent frameworks on SWE-bench-Live, offering detailed empirical insights into their real-world bug-fixing capabilities. By providing a fresh, diverse, and executable benchmark grounded in live repository activity, SWE-bench-Live supports reliable, large-scale assessment of code LLMs and code agents in realistic development settings.

PDF Details

NeurIPS Conference 2024 Conference Paper

LogiCity: Advancing Neuro-Symbolic AI with Abstract Urban Simulation

Bowen Li
Zhaoyu Li
Qiwei Du
Jinqi Luo
Wenshan Wang
Yaqi Xie
Simon Stepputtis
Chen Wang

Recent years have witnessed the rapid development of Neuro-Symbolic (NeSy) AI systems, which integrate symbolic reasoning into deep neural networks. However, most of the existing benchmarks for NeSy AI fail to provide long-horizon reasoning tasks with complex multi-agent interactions. Furthermore, they are usually constrained by fixed and simplistic logical rules over limited entities, making them far from real-world complexities. To address these crucial gaps, we introduce LogiCity, the first simulator based on customizable first-order logic (FOL) for an urban-like environment with multiple dynamic agents. LogiCity models diverse urban elements using semantic and spatial concepts, such as $\texttt{IsAmbulance}(\texttt{X})$ and $\texttt{IsClose}(\texttt{X}, \texttt{Y})$. These concepts are used to define FOL rules that govern the behavior of various agents. Since the concepts and rules are abstractions, they can be universally applied to cities with any agent compositions, facilitating the instantiation of diverse scenarios. Besides, a key feature of LogiCity is its support for user-configurable abstractions, enabling customizable simulation complexities for logical reasoning. To explore various aspects of NeSy AI, LogiCity introduces two tasks, one features long-horizon sequential decision-making, and the other focuses on one-step visual reasoning, varying in difficulty and agent behaviors. Our extensive evaluation reveals the advantage of NeSy frameworks in abstract reasoning. Moreover, we highlight the significant challenges of handling more complex abstractions in long-horizon multi-agent scenarios or under high-dimensional, imbalanced data. With its flexible design, various features, and newly raised challenges, we believe LogiCity represents a pivotal step forward in advancing the next generation of NeSy AI. All the code and data are open-sourced at our website.

PDF Details DOI

JMLR Journal 2024 Journal Article

PirateNets: Physics-informed Deep Learning with Residual Adaptive Networks

Sifan Wang
Bowen Li
Yuhan Chen
Paris Perdikaris

While physics-informed neural networks (PINNs) have become a popular deep learning framework for tackling forward and inverse problems governed by partial differential equations (PDEs), their performance is known to degrade when larger and deeper neural network architectures are employed. Our study identifies that the root of this counter-intuitive behavior lies in the use of multi-layer perceptron (MLP) architectures with non-suitable initialization schemes, which result in poor trainablity for the network derivatives, and ultimately lead to an unstable minimization of the PDE residual loss. To address this, we introduce Physics-Informed Residual Adaptive Networks (PirateNets), a novel architecture that is designed to facilitate stable and efficient training of deep PINN models. PirateNets leverage a novel adaptive residual connection, which allows the networks to be initialized as shallow networks that progressively deepen during training. We also show that the proposed initialization scheme allows us to encode appropriate inductive biases corresponding to a given PDE system into the network architecture. We provide comprehensive empirical evidence showing that PirateNets are easier to optimize and can gain accuracy from considerably increased depth, ultimately achieving state-of-the-art results across various benchmarks. All code and data accompanying this manuscript will be made publicly available at https://github.com/PredictiveIntelligenceLab/jaxpi/tree/pirate. [abs] [ pdf ][ bib ] [ code ] &copy JMLR 2024. ( edit, beta )

PDF Details

NeurIPS Conference 2023 Conference Paper

Can LLM Already Serve as A Database Interface? A BIg Bench for Large-Scale Database Grounded Text-to-SQLs

Jinyang Li
Binyuan Hui
Ge Qu
Jiaxi Yang
Binhua Li
Bowen Li
Bailin Wang
Bowen Qin

Text-to-SQL parsing, which aims at converting natural language instructions into executable SQLs, has gained increasing attention in recent years. In particular, GPT-4 and Claude-2 have shown impressive results in this task. However, most of the prevalent benchmarks, i. e. , Spider, and WikiSQL, focus on database schema with few rows of database contents leaving the gap between academic study and real-world applications. To mitigate this gap, we present BIRD, a BIg benchmark for laRge-scale Database grounded in text-to-SQL tasks, containing 12, 751 pairs of text-to-SQL data and 95 databases with a total size of 33. 4 GB, spanning 37 professional domains. Our emphasis on database values highlights the new challenges of dirty database contents, external knowledge between NL questions and database contents, and SQL efficiency, particularly in the context of massive databases. To solve these problems, text-to-SQL models must feature database value comprehension in addition to semantic parsing. The experimental results demonstrate the significance of database values in generating accurate text-to-SQLs for big databases. Furthermore, even the most popular and effective text-to-SQL models, i. e. GPT-4, only achieve 54. 89% in execution accuracy, which is still far from the human result of 92. 96%, proving that challenges still stand. We also provide an efficiency analysis to offer insights into generating text-to-efficient-SQLs that are beneficial to industries. We believe that BIRD will contribute to advancing real-world applications of text-to-SQL research. The leaderboard and source code are available: https: //bird-bench. github. io/.

PDF Details

NeurIPS Conference 2023 Conference Paper

VoxDet: Voxel Learning for Novel Instance Detection

Bowen Li
Jiashun Wang
Yaoyu Hu
Chen Wang
Sebastian Scherer

Detecting unseen instances based on multi-view templates is a challenging problem due to its open-world nature. Traditional methodologies, which primarily rely on $2 \mathrm{D}$ representations and matching techniques, are often inadequate in handling pose variations and occlusions. To solve this, we introduce VoxDet, a pioneer 3D geometry-aware framework that fully utilizes the strong 3D voxel representation and reliable voxel matching mechanism. VoxDet first ingeniously proposes template voxel aggregation (TVA) module, effectively transforming multi-view 2D images into 3D voxel features. By leveraging associated camera poses, these features are aggregated into a compact 3D template voxel. In novel instance detection, this voxel representation demonstrates heightened resilience to occlusion and pose variations. We also discover that a $3 \mathrm{D}$ reconstruction objective helps to pre-train the 2D-3D mapping in TVA. Second, to quickly align with the template voxel, VoxDet incorporates a Query Voxel Matching (QVM) module. The 2D queries are first converted into their voxel representation with the learned 2D-3D mapping. We find that since the 3D voxel representations encode the geometry, we can first estimate the relative rotation and then compare the aligned voxels, leading to improved accuracy and efficiency. In addition to method, we also introduce the first instance detection benchmark, RoboTools, where 20 unique instances are video-recorded with camera extrinsic. RoboTools also provides 24 challenging cluttered scenarios with more than $9 \mathrm{k}$ box annotations. Exhaustive experiments are conducted on the demanding LineMod-Occlusion, YCB-video, and RoboTools benchmarks, where VoxDet outperforms various $2 \mathrm{D}$ baselines remarkably with faster speed. To the best of our knowledge, VoxDet is the first to incorporate implicit 3D knowledge for 2D novel instance detection tasks.

PDF Details

NeurIPS Conference 2020 Conference Paper

Lightweight Generative Adversarial Networks for Text-Guided Image Manipulation

Bowen Li
Xiaojuan Qi
Philip Torr
Thomas Lukasiewicz

We propose a novel lightweight generative adversarial network for efficient image manipulation using natural language descriptions. To achieve this, a new word-level discriminator is proposed, which provides the generator with fine-grained training feedback at word-level, to facilitate training a lightweight generator that has a small number of parameters, but can still correctly focus on specific visual attributes of an image, and then edit them without affecting other contents that are not described in the text. Furthermore, thanks to the explicit training signal related to each word, the discriminator can also be simplified to have a lightweight structure. Compared with the state of the art, our method has a much smaller number of parameters, but still achieves a competitive manipulation performance. Extensive experimental results demonstrate that our method can better disentangle different visual attributes, then correctly map them to corresponding semantic words, and thus achieve a more accurate image modification using natural language descriptions.

PDF Details

NeurIPS Conference 2019 Conference Paper

Controllable Text-to-Image Generation

Bowen Li
Xiaojuan Qi
Thomas Lukasiewicz
Philip Torr

In this paper, we propose a novel controllable text-to-image generative adversarial network (ControlGAN), which can effectively synthesise high-quality images and also control parts of the image generation according to natural language descriptions. To achieve this, we introduce a word-level spatial and channel-wise attention-driven generator that can disentangle different visual attributes, and allow the model to focus on generating and manipulating subregions corresponding to the most relevant words. Also, a word-level discriminator is proposed to provide fine-grained supervisory feedback by correlating words with image regions, facilitating training an effective generator which is able to manipulate specific visual attributes without affecting the generation of other content. Furthermore, perceptual loss is adopted to reduce the randomness involved in the image generation, and to encourage the generator to manipulate specific attributes required in the modified text. Extensive experiments on benchmark datasets demonstrate that our method outperforms existing state of the art, and is able to effectively manipulate synthetic images using natural language descriptions.

PDF Details

AAAI Conference 2019 Conference Paper

Dependency Grammar Induction with a Neural Variational Transition-Based Parser

Bowen Li
Jianpeng Cheng
Yang Liu
Frank Keller

Dependency grammar induction is the task of learning dependency syntax without annotated training data. Traditional graph-based models with global inference achieve state-ofthe-art results on this task but they require O(n3 ) run time. Transition-based models enable faster inference with O(n) time complexity, but their performance still lags behind. In this work, we propose a neural transition-based parser for dependency grammar induction, whose inference procedure utilizes rich neural features with O(n) time complexity. We train the parser with an integration of variational inference, posterior regularization and variance reduction techniques. The resulting framework outperforms previous unsupervised transition-based dependency parsers and achieves performance comparable to graph-based models, both on the English Penn Treebank and on the Universal Dependency Treebank. In an empirical comparison, we show that our approach substantially increases parsing speed over graphbased models.

PDF Details