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Yanqiao Zhu

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10 papers

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NeurIPS Conference 2025 Conference Paper

MMAR: A Challenging Benchmark for Deep Reasoning in Speech, Audio, Music, and Their Mix

Ziyang Ma
Yinghao Ma
Yanqiao Zhu
Chen Yang
Yi-Wen Chao
Ruiyang Xu
Wenxi Chen
Yuanzhe Chen

We introduce MMAR, a new benchmark designed to evaluate the deep reasoning capabilities of Audio-Language Models (ALMs) across massive multi-disciplinary tasks. MMAR comprises 1, 000 meticulously curated audio-question-answer triplets, collected from real-world internet videos and refined through iterative error corrections and quality checks to ensure high quality. Unlike existing benchmarks that are limited to specific domains of sound, music, or speech, MMAR extends them to a broad spectrum of real-world audio scenarios, including mixed-modality combinations of sound, music, and speech. Each question in MMAR is hierarchically categorized across four reasoning layers: Signal, Perception, Semantic, and Cultural, with additional sub-categories within each layer to reflect task diversity and complexity. To further foster research in this area, we annotate every question with a Chain-of-Thought (CoT) rationale to promote future advancements in audio reasoning. Each item in the benchmark demands multi-step deep reasoning beyond surface-level understanding. Moreover, a part of the questions requires graduate-level perceptual and domain-specific knowledge, elevating the benchmark's difficulty and depth. We evaluate MMAR using a broad set of models, including Large Audio-Language Models (LALMs), Large Audio Reasoning Models (LARMs), Omni Language Models (OLMs), Large Language Models (LLMs), and Large Reasoning Models (LRMs), with audio caption inputs. The performance of these models on MMAR highlights the benchmark's challenging nature, and our analysis further reveals critical limitations of understanding and reasoning capabilities among current models. These findings underscore the urgent need for greater research attention in audio-language reasoning, including both data and algorithm innovation. We hope MMAR will serve as a catalyst for future advances in this important but little-explored area.

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NeurIPS Conference 2025 Conference Paper

Symmetry-Preserving Conformer Ensemble Networks for Molecular Representation Learning

Yanqiao Zhu
Yidan Shi
Yuanzhou Chen
Fang Sun
Yizhou Sun
Wei Wang

Molecular representation learning has emerged as a promising approach for modeling molecules with deep learning in chemistry and beyond. While 3D geometric models effectively capture molecular structure, they typically process single static conformers, overlooking the inherent flexibility and dynamics of molecules. In reality, many molecular properties depend on distributions of thermodynamically accessible conformations rather than single structures. Recent works show that learning from conformer ensembles can improve molecular representations, but existing approaches either produce unphysical structures through averaging or require restrictive molecular alignment. In this paper, we propose SymmetryPreserving Conformer Ensemble networks (SPiCE), which introduces two key innovations: (1) geometric mixture-of-experts for selective processing of scalar and vector features, and (2) hierarchical ensemble encoding that combines ensemblelevel representation with cross-conformer integration. Crucially, SPiCE ensures physically meaningful representations by maintaining joint equivariance to geometric transformations of individual conformers and conformer permutations. Extensive experiments demonstrate that SPiCE consistently outperforms existing conformer ensemble methods and state-of-the-art structural aggregation models across quantum mechanical and biological property prediction tasks.

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IJCAI Conference 2023 Conference Paper

A Systematic Survey of Chemical Pre-trained Models

Jun Xia
Yanqiao Zhu
Yuanqi Du
Stan Z. Li

Deep learning has achieved remarkable success in learning representations for molecules, which is crucial for various biochemical applications, ranging from property prediction to drug design. However, training Deep Neural Networks (DNNs) from scratch often requires abundant labeled molecules, which are expensive to acquire in the real world. To alleviate this issue, tremendous efforts have been devoted to Chemical Pre-trained Models (CPMs), where DNNs are pre-trained using large-scale unlabeled molecular databases and then fine-tuned over specific downstream tasks. Despite the prosperity, there lacks a systematic review of this fast-growing field. In this paper, we present the first survey that summarizes the current progress of CPMs. We first highlight the limitations of training molecular representation models from scratch to motivate CPM studies. Next, we systematically review recent advances on this topic from several key perspectives, including molecular descriptors, encoder architectures, pre-training strategies, and applications. We also highlight the challenges and promising avenues for future research, providing a useful resource for both machine learning and scientific communities.

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NeurIPS Conference 2023 Conference Paper

GSLB: The Graph Structure Learning Benchmark

Zhixun Li
Xin Sun
Yifan Luo
Yanqiao Zhu
Dingshuo Chen
Yingtao Luo
Xiangxin Zhou
Qiang Liu

Graph Structure Learning (GSL) has recently garnered considerable attention due to its ability to optimize both the parameters of Graph Neural Networks (GNNs) and the computation graph structure simultaneously. Despite the proliferation of GSL methods developed in recent years, there is no standard experimental setting or fair comparison for performance evaluation, which creates a great obstacle to understanding the progress in this field. To fill this gap, we systematically analyze the performance of GSL in different scenarios and develop a comprehensive Graph Structure Learning Benchmark (GSLB) curated from 20 diverse graph datasets and 16 distinct GSL algorithms. Specifically, GSLB systematically investigates the characteristics of GSL in terms of three dimensions: effectiveness, robustness, and complexity. We comprehensively evaluate state-of-the-art GSL algorithms in node- and graph-level tasks, and analyze their performance in robust learning and model complexity. Further, to facilitate reproducible research, we have developed an easy-to-use library for training, evaluating, and visualizing different GSL methods. Empirical results of our extensive experiments demonstrate the ability of GSL and reveal its potential benefits on various downstream tasks, offering insights and opportunities for future research. The code of GSLB is available at: https: //github. com/GSL-Benchmark/GSLB.

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NeurIPS Conference 2023 Conference Paper

M$^2$Hub: Unlocking the Potential of Machine Learning for Materials Discovery

Yuanqi Du
Yingheng Wang
Yining Huang
Jianan Canal Li
Yanqiao Zhu
Tian Xie
Chenru Duan
John Gregoire

We introduce M$^2$Hub, a toolkit for advancing machine learning in materials discovery. Machine learning has achieved remarkable progress in modeling molecular structures, especially biomolecules for drug discovery. However, the development of machine learning approaches for modeling materials structures lag behind, which is partly due to the lack of an integrated platform that enables access to diverse tasks for materials discovery. To bridge this gap, M$^2$Hub will enable easy access to materials discovery tasks, datasets, machine learning methods, evaluations, and benchmark results that cover the entire workflow. Specifically, the first release of M$^2$Hub focuses on three key stages in materials discovery: virtual screening, inverse design, and molecular simulation, including 9 datasets that covers 6 types of materials with 56 tasks across 8 types of material properties. We further provide 2 synthetic datasets for the purpose of generative tasks on materials. In addition to random data splits, we also provide 3 additional data partitions to reflect the real-world materials discovery scenarios. State-of-the-art machine learning methods (including those are suitable for materials structures but never compared in the literature) are benchmarked on representative tasks. Our codes and library are publicly available at \url{https: //github. com/yuanqidu/M2Hub}.

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AAAI Conference 2023 Conference Paper

Neighborhood-Regularized Self-Training for Learning with Few Labels

Ran Xu
Yue Yu
Hejie Cui
Xuan Kan
Yanqiao Zhu
Joyce Ho
Chao Zhang
Carl Yang

Training deep neural networks (DNNs) with limited supervision has been a popular research topic as it can significantly alleviate the annotation burden. Self-training has been successfully applied in semi-supervised learning tasks, but one drawback of self-training is that it is vulnerable to the label noise from incorrect pseudo labels. Inspired by the fact that samples with similar labels tend to share similar representations, we develop a neighborhood-based sample selection approach to tackle the issue of noisy pseudo labels. We further stabilize self-training via aggregating the predictions from different rounds during sample selection. Experiments on eight tasks show that our proposed method outperforms the strongest self-training baseline with 1.83% and 2.51% performance gain for text and graph datasets on average. Our further analysis demonstrates that our proposed data selection strategy reduces the noise of pseudo labels by 36.8% and saves 57.3% of the time when compared with the best baseline. Our code and appendices will be uploaded to: https://github.com/ritaranx/NeST.

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NeurIPS Conference 2023 Conference Paper

Uncovering Neural Scaling Laws in Molecular Representation Learning

Dingshuo Chen
Yanqiao Zhu
Jieyu Zhang
Yuanqi Du
Zhixun Li
Qiang Liu
Shu Wu
Liang Wang

Molecular Representation Learning (MRL) has emerged as a powerful tool for drug and materials discovery in a variety of tasks such as virtual screening and inverse design. While there has been a surge of interest in advancing model-centric techniques, the influence of both data quantity and quality on molecular representations is not yet clearly understood within this field. In this paper, we delve into the neural scaling behaviors of MRL from a data-centric viewpoint, examining four key dimensions: (1) data modalities, (2) dataset splitting, (3) the role of pre-training, and (4) model capacity. Our empirical studies confirm a consistent power-law relationship between data volume and MRL performance across these dimensions. Additionally, through detailed analysis, we identify potential avenues for improving learning efficiency. To challenge these scaling laws, we adapt seven popular data pruning strategies to molecular data and benchmark their performance. Our findings underline the importance of data-centric MRL and highlight possible directions for future research.

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TIST Journal 2023 Journal Article

Unsupervised Graph Representation Learning with Cluster-aware Self-training and Refining

Yanqiao Zhu
Yichen Xu
Feng Yu
Qiang Liu
Shu Wu

Unsupervised graph representation learning aims to learn low-dimensional node embeddings without supervision while preserving graph topological structures and node attributive features. Previous Graph Neural Networks (GNN) require a large number of labeled nodes, which may not be accessible in real-world applications. To this end, we present a novel unsupervised graph neural network model with Cluster-aware Self-training and Refining ( CLEAR ). Specifically, in the proposed CLEAR model, we perform clustering on the node embeddings and update the model parameters by predicting the cluster assignments. To avoid degenerate solutions of clustering, we formulate the graph clustering problem as an optimal transport problem and leverage a balanced clustering strategy. Moreover, we observe that graphs often contain inter-class edges, which mislead the GNN model to aggregate noisy information from neighborhood nodes. Therefore, we propose to refine the graph topology by strengthening intra-class edges and reducing node connections between different classes based on cluster labels, which better preserves cluster structures in the embedding space. We conduct comprehensive experiments on two benchmark tasks using real-world datasets. The results demonstrate the superior performance of the proposed model over baseline methods. Notably, our model gains over 7% improvements in terms of accuracy on node clustering over state-of-the-arts.

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NeurIPS Conference 2021 Conference Paper

An Empirical Study of Graph Contrastive Learning

Yanqiao Zhu
Yichen Xu
Qiang Liu
Shu Wu

Graph Contrastive Learning (GCL) establishes a new paradigm for learning graph representations without human annotations. Although remarkable progress has been witnessed recently, the success behind GCL is still left somewhat mysterious. In this work, we first identify several critical design considerations within a general GCL paradigm, including augmentation functions, contrasting modes, contrastive objectives, and negative mining strategies. Then, to understand the interplay of different GCL components, we conduct comprehensive, controlled experiments over benchmark tasks on datasets across various domains. Our empirical studies suggest a set of general receipts for effective GCL, e. g. , simple topology augmentations that produce sparse graph views bring promising performance improvements; contrasting modes should be aligned with the granularities of end tasks. In addition, to foster future research and ease the implementation of GCL algorithms, we develop an easy-to-use library PyGCL, featuring modularized CL components, standardized evaluation, and experiment management. We envision this work to provide useful empirical evidence of effective GCL algorithms and offer several insights for future research.

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AAAI Conference 2019 Conference Paper

Session-Based Recommendation with Graph Neural Networks

Shu Wu
Yuyuan Tang
Yanqiao Zhu
Liang Wang
Xing Xie
Tieniu Tan

The problem of session-based recommendation aims to predict user actions based on anonymous sessions. Previous methods model a session as a sequence and estimate user representations besides item representations to make recommendations. Though achieved promising results, they are insufficient to obtain accurate user vectors in sessions and neglect complex transitions of items. To obtain accurate item embedding and take complex transitions of items into account, we propose a novel method, i. e. Session-based Recommendation with Graph Neural Networks, SR-GNN for brevity. In the proposed method, session sequences are modeled as graphstructured data. Based on the session graph, GNN can capture complex transitions of items, which are difficult to be revealed by previous conventional sequential methods. Each session is then represented as the composition of the global preference and the current interest of that session using an attention network. Extensive experiments conducted on two real datasets show that SR-GNN evidently outperforms the state-of-the-art session-based recommendation methods consistently.

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