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Qiwei Ye

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12 papers

2 author rows

AAAI Conference 2026 Conference Paper

EPO: Diverse and Realistic Protein Ensemble Generation via Energy Preference Optimization

Yuancheng Sun
Yuxuan Ren
Zhaoming Chen
Xu Han
Kang Liu
Qiwei Ye

Accurate exploration of protein conformational ensembles is essential for uncovering function but remains hard because molecular-dynamics (MD) simulations suffer from high computational costs and energy-barrier trapping. This paper presents Energy Preference Optimization (EPO), an online refinement algorithm that turns a pretrained protein ensemble generator into an energy-aware sampler without extra MD trajectories. Specifically, EPO leverages stochastic differential equation sampling to explore the conformational landscape and incorporates a novel energy-ranking mechanism based on list-wise preference optimization. Crucially, EPO introduces a practical upper bound to efficiently approximate the intractable probability of long sampling trajectories in continuous-time generative models, making it easily adaptable to existing pretrained generators. On Tetrapeptides, ATLAS, and Fast-Folding benchmarks, EPO successfully generates diverse and physically realistic ensembles, establishing a new state-of-the-art in nine evaluation metrics. These results demonstrate that energy-only preference signals can efficiently steer generative models toward thermodynamically consistent conformational ensembles, providing an alternative to long MD simulations and widening the applicability of learned potentials in structural biology and drug discovery.

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ICLR Conference 2025 Conference Paper

CryoGEN: Generative Energy-based Models for Cryogenic Electron Tomography Reconstruction

Yunfei Teng
Yuxuan Ren
Kai Chen
Xi Chen
Zhaoming Chen
Qiwei Ye

Cryogenic electron tomography (Cryo-ET) is a powerful technique for visualizing subcellular structures in their native states. Nonetheless, its effectiveness is compromised by anisotropic resolution artifacts caused by the missing-wedge effect. To address this, IsoNet, a deep learning-based method, proposes iteratively reconstructing the missing-wedge information. While successful, IsoNet's dependence on recursive prediction updates often leads to training instability and model divergence. In this study, we introduce CryoGEN—an energy-based probabilistic model that not only mitigates resolution anisotropy but also removes the need for recursive subtomogram averaging, delivering an approximate *10*$\times$ speedup for training. Evaluations across various biological datasets, including immature HIV-1 virions and ribosomes, demonstrate that CryoGEN significantly enhances structural completeness and interpretability of the reconstructed samples.

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NeurIPS Conference 2025 Conference Paper

IneqSearch: Hybrid Reasoning for Olympiad Inequality Proofs

Zhaoqun Li
Beishui Liao
Qiwei Ye

Mathematicians have long employed decomposition techniques to prove inequalities, yet automating this process remains a significant challenge in computational mathematics. We introduce IneqSearch, a hybrid reasoning system that integrates symbolic computation with large language models (LLMs) to address this challenge. IneqSearch reformulates inequality proving as a structured search problem: identifying appropriate combinations of theorems that decompose expressions into non-negative components. The system combines a symbolic solver for deductive reasoning with an LLM-based agent for constructive proof exploration, effectively implementing methodologies observed in formal mathematical practice. A key contribution of IneqSearch is its iterative learning mechanism that systematically incorporates newly proven results into its theorem database, enabling knowledge acquisition during practice that enhances its capabilities without requiring human intervention. In empirical evaluation on 437 Olympiad-level inequalities, IneqSearch successfully proves 342 problems, significantly outperforming existing methods and demonstrating the effectiveness of integrating symbolic and neural approaches for mathematical reasoning.

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ICLR Conference 2025 Conference Paper

Long Context Compression with Activation Beacon

Peitian Zhang
Zheng Liu 0011
Shitao Xiao
Ninglu Shao
Qiwei Ye
Zhicheng Dou

Long context compression is a critical research problem due to its significance in reducing the high computational and memory costs associated with LLMs. In this paper, we propose Activation Beacon, a plug-in module for transformer-based LLMs that targets effective, efficient, and flexible compression of long contexts. To achieve this, our method introduces the following technical designs. 1) We directly compress the activations (i.e. keys and values at every layer), rather than leveraging soft prompts to relay information (which constitute a major bottleneck to encapsulate the complex information within long contexts). 2) We tailor the compression workflow, where each fine-grained input unit is progressively compressed, enabling high-quality compression and efficient computation during both training and inference. 3) We train the model through compression-based auto-regression, making full use of plain texts and instructional data to optimize the model's compression performance. 4) During training, we randomly sample a compression ratio at each step, teaching the model to support a wide range of compression configurations. Extensive evaluations are conducted on various long-context tasks whose lengths (e.g., 128K) may far exceed the maximum training length (20K), such as document understanding, few-shot learning, and Needle-in-a-Haystack. Whilst existing methods struggle to handle these challenging tasks, Activation Beacon maintains a comparable performance to the uncompressed baseline across various scenarios, achieving a 2x acceleration in inference time and an 8x reduction of memory costs for KV cache.

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ICLR Conference 2024 Conference Paper

Beyond Weisfeiler-Lehman: A Quantitative Framework for GNN Expressiveness

Bohang Zhang
Jingchu Gai
Yiheng Du
Qiwei Ye
Di He 0001
Liwei Wang 0001

Designing expressive Graph Neural Networks (GNNs) is a fundamental topic in the graph learning community. So far, GNN expressiveness has been primarily assessed via the Weisfeiler-Lehman (WL) hierarchy. However, such an expressivity measure has notable limitations: it is inherently coarse, qualitative, and may not well reflect practical requirements (e.g., the ability to encode substructures). In this paper, we introduce a novel framework for quantitatively studying the expressiveness of GNN architectures, addressing all the above limitations. Specifically, we identify a fundamental expressivity measure termed homomorphism expressivity, which quantifies the ability of GNN models to count graphs under homomorphism. Homomorphism expressivity offers a complete and practical assessment tool: the completeness enables direct expressivity comparisons between GNN models, while the practicality allows for understanding concrete GNN abilities such as subgraph counting. By examining four classes of prominent GNNs as case studies, we derive simple, unified, and elegant descriptions of their homomorphism expressivity for both invariant and equivariant settings. Our results provide novel insights into a series of previous work, unify the landscape of different subareas in the community, and settle several open questions. Empirically, extensive experiments on both synthetic and real-world tasks verify our theory, showing that the practical performance of GNN models aligns well with the proposed metric.

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ICML Conference 2024 Conference Paper

Do Efficient Transformers Really Save Computation?

Kai Yang
Jan Ackermann
Zhenyu He 0012
Guhao Feng
Bohang Zhang
Yunzhen Feng
Qiwei Ye
Di He 0001

As transformer-based language models are trained on increasingly large datasets and with vast numbers of parameters, finding more efficient alternatives to the standard Transformer has become very valuable. While many efficient Transformers and Transformer alternatives have been proposed, none provide theoretical guarantees that they are a suitable replacement for the standard Transformer. This makes it challenging to identify when to use a specific model and what directions to prioritize for further investigation. In this paper, we aim to understand the capabilities and limitations of efficient Transformers, specifically the Sparse Transformer and the Linear Transformer. We focus on their reasoning capability as exhibited by Chain-of-Thought (CoT) prompts and follow previous works to model them as Dynamic Programming (DP) problems. Our results show that while these models are expressive enough to solve general DP tasks, contrary to expectations, they require a model size that scales with the problem size. Nonetheless, we identify a class of DP problems for which these models can be more efficient than the standard Transformer. We confirm our theoretical results through experiments on representative DP tasks, adding to the understanding of efficient Transformers’ practical strengths and weaknesses.

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NeurIPS Conference 2023 Conference Paper

DSR: Dynamical Surface Representation as Implicit Neural Networks for Protein

Daiwen Sun
He Huang
Yao Li
Xinqi Gong
Qiwei Ye

We propose a novel neural network-based approach to modeling protein dynamics using an implicit representation of a protein’s surface in 3D and time. Our method utilizes the zero-level set of signed distance functions (SDFs) to represent protein surfaces, enabling temporally and spatially continuous representations of protein dynamics. Our experimental results demonstrate that our model accurately captures protein dynamic trajectories and can interpolate and extrapolate in 3D and time. Importantly, this is the first study to introduce this method and successfully model large-scale protein dynamics. This approach offers a promising alternative to current methods, overcoming the limitations of first-principles-based and deep learning methods, and provides a more scalable and efficient approach to modeling protein dynamics. Additionally, our surface representation approach simplifies calculations and allows identifying movement trends and amplitudes of protein domains, making it a useful tool for protein dynamics research. Codes are available at https: //github. com/Sundw-818/DSR, and we have a project webpage that shows some video results, https: //sundw-818. github. io/DSR/.

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ICRA Conference 2021 Conference Paper

Decentralized Circle Formation Control for Fish-like Robots in the Real-world via Reinforcement Learning

Tianhao Zhang
Yueheng Li
Shuai Li
Qiwei Ye
Chen Wang 0005
Guangming Xie

In this paper, the circle formation control problem is addressed for a group of cooperative underactuated fish-like robots involving unknown nonlinear dynamics and disturbances. Based on the reinforcement learning and cognitive consistency theory, we propose a decentralized controller without the knowledge of the dynamics of the fish-like robots. The proposed controller can be transferred from simulation to reality. It is only trained in our established simulation environment, and the trained controller can be deployed to real robots without any manual tuning. Simulation results confirm that the proposed model-free robust formation control method is scalable with respect to the group size of the robots and outperforms other representative RL algorithms. Several experiments in the real world verify the effectiveness of our RL-based approach for circle formation control.

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IJCAI Conference 2021 Conference Paper

MFVFD: A Multi-Agent Q-Learning Approach to Cooperative and Non-Cooperative Tasks

Tianhao Zhang
Qiwei Ye
Jiang Bian
Guangming Xie
Tie-Yan Liu

Value function decomposition (VFD) methods under the popular paradigm of centralized training and decentralized execution (CTDE) have promoted multi-agent reinforcement learning progress. However, existing VFD methods proceed from a group's value function decomposition to only solve cooperative tasks. With the individual value function decomposition, we propose MFVFD, a novel multi-agent Q-learning approach for solving cooperative and non-cooperative tasks based on mean-field theory. Our analysis on the Hawk-Dove and Nonmonotonic Cooperation matrix games evaluate MFVFD's convergent solution. Empirical studies on the challenging mixed cooperative-competitive tasks where hundreds of agents coexist demonstrate that MFVFD significantly outperforms existing baselines.

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NeurIPS Conference 2021 Conference Paper

Semi-Supervised Semantic Segmentation via Adaptive Equalization Learning

Hanzhe Hu
Fangyun Wei
Han Hu
Qiwei Ye
Jinshi Cui
Liwei Wang

Due to the limited and even imbalanced data, semi-supervised semantic segmentation tends to have poor performance on some certain categories, e. g. , tailed categories in Cityscapes dataset which exhibits a long-tailed label distribution. Existing approaches almost all neglect this problem, and treat categories equally. Some popular approaches such as consistency regularization or pseudo-labeling may even harm the learning of under-performing categories, that the predictions or pseudo labels of these categories could be too inaccurate to guide the learning on the unlabeled data. In this paper, we look into this problem, and propose a novel framework for semi-supervised semantic segmentation, named adaptive equalization learning (AEL). AEL adaptively balances the training of well and badly performed categories, with a confidence bank to dynamically track category-wise performance during training. The confidence bank is leveraged as an indicator to tilt training towards under-performing categories, instantiated in three strategies: 1) adaptive Copy-Paste and CutMix data augmentation approaches which give more chance for under-performing categories to be copied or cut; 2) an adaptive data sampling approach to encourage pixels from under-performing category to be sampled; 3) a simple yet effective re-weighting method to alleviate the training noise raised by pseudo-labeling. Experimentally, AEL outperforms the state-of-the-art methods by a large margin on the Cityscapes and Pascal VOC benchmarks under various data partition protocols. Code is available at https: //github. com/hzhupku/SemiSeg-AEL.

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NeurIPS Conference 2017 Conference Paper

LightGBM: A Highly Efficient Gradient Boosting Decision Tree

Guolin Ke
Qi Meng
Thomas Finley
Taifeng Wang
Wei Chen
Weidong Ma
Qiwei Ye
Tie-Yan Liu

Gradient Boosting Decision Tree (GBDT) is a popular machine learning algorithm, and has quite a few effective implementations such as XGBoost and pGBRT. Although many engineering optimizations have been adopted in these implementations, the efficiency and scalability are still unsatisfactory when the feature dimension is high and data size is large. A major reason is that for each feature, they need to scan all the data instances to estimate the information gain of all possible split points, which is very time consuming. To tackle this problem, we propose two novel techniques: \emph{Gradient-based One-Side Sampling} (GOSS) and \emph{Exclusive Feature Bundling} (EFB). With GOSS, we exclude a significant proportion of data instances with small gradients, and only use the rest to estimate the information gain. We prove that, since the data instances with larger gradients play a more important role in the computation of information gain, GOSS can obtain quite accurate estimation of the information gain with a much smaller data size. With EFB, we bundle mutually exclusive features (i. e. , they rarely take nonzero values simultaneously), to reduce the number of features. We prove that finding the optimal bundling of exclusive features is NP-hard, but a greedy algorithm can achieve quite good approximation ratio (and thus can effectively reduce the number of features without hurting the accuracy of split point determination by much). We call our new GBDT implementation with GOSS and EFB \emph{LightGBM}. Our experiments on multiple public datasets show that, LightGBM speeds up the training process of conventional GBDT by up to over 20 times while achieving almost the same accuracy.

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NeurIPS Conference 2016 Conference Paper

A Communication-Efficient Parallel Algorithm for Decision Tree

Qi Meng
Guolin Ke
Taifeng Wang
Wei Chen
Qiwei Ye
Zhi-Ming Ma
Tie-Yan Liu

Decision tree (and its extensions such as Gradient Boosting Decision Trees and Random Forest) is a widely used machine learning algorithm, due to its practical effectiveness and model interpretability. With the emergence of big data, there is an increasing need to parallelize the training process of decision tree. However, most existing attempts along this line suffer from high communication costs. In this paper, we propose a new algorithm, called \emph{Parallel Voting Decision Tree (PV-Tree)}, to tackle this challenge. After partitioning the training data onto a number of (e. g. , $M$) machines, this algorithm performs both local voting and global voting in each iteration. For local voting, the top-$k$ attributes are selected from each machine according to its local data. Then, the indices of these top attributes are aggregated by a server, and the globally top-$2k$ attributes are determined by a majority voting among these local candidates. Finally, the full-grained histograms of the globally top-$2k$ attributes are collected from local machines in order to identify the best (most informative) attribute and its split point. PV-Tree can achieve a very low communication cost (independent of the total number of attributes) and thus can scale out very well. Furthermore, theoretical analysis shows that this algorithm can learn a near optimal decision tree, since it can find the best attribute with a large probability. Our experiments on real-world datasets show that PV-Tree significantly outperforms the existing parallel decision tree algorithms in the tradeoff between accuracy and efficiency.

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