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Qiwei Ye

15 accepted papers

2026

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

AAAI 2026technical

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

Cited by 0SourcePDFScholar
2025

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

ICLR 2025poster

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,…

Cited by 0SourcePDFScholar
2025

Long Context Compression with Activation Beacon

ICLR 2025poster

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 compressi…

2024

Beyond Weisfeiler-Lehman: A Quantitative Framework for GNN Expressiveness

ICLR 2024oral

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, qualitati…

2024

Do Efficient Transformers Really Save Computation?

ICML 2024poster

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 provi…

Cited by 16SourcePDFScholar
2024

FDIG: A Fine-Grained Data Integration Approach for Group Recommendation

ICASSP 2024accepted

Effective group recommendation systems play a pivotal role in enriching the information consumption of users from different groups. Existing group recommendation approaches face challenges such as the sparsity of the rating matrix and low specificity between user clusters, leading to cold-start issu…

Cited by 0SourceScholar
2023

DSR: Dynamical Surface Representation as Implicit Neural Networks for Protein

NeurIPS 2023poster

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…

2021

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

ICRA 2021poster

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 kn…

Cited by 27SourceScholar
2021

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

IJCAI 2021poster

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 task…

Cited by 16SourcePDFScholar
2021

Semi-Supervised Semantic Segmentation via Adaptive Equalization Learning

NeurIPS 2021spotlight

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…

2019

G-SGD: Optimizing ReLU Neural Networks in its Positively Scale-Invariant Space

ICLR 2019poster

It is well known that neural networks with rectified linear units (ReLU) activation functions are positively scale-invariant. Conventional algorithms like stochastic gradient descent optimize the neural networks in the vector space of weights, which is, however, not positively scale-invariant. This…

Cited by 35SourcePDFScholar
2017

LightGBM: A Highly Efficient Gradient Boosting Decision Tree

NeurIPS 2017poster

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 th…

2016

A Communication-Efficient Parallel Algorithm for Decision Tree

NeurIPS 2016poster

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…

Cited by 193SourcePDFScholar