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Ziqi Gao

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11 papers

2 author rows

AAAI Conference 2026 Conference Paper

Unified Structural Factors for Transfer Learning Generalization with PAC-Bayesian Guarantees

Ziqi Gao

Understanding when a pre-trained model generalizes well to a new task remains a key challenge in transfer learning. Classical theories bound target risk using divergences such as total variation, MMD, or Wasserstein distance, yet tasks with similar divergences often show very different transfer performance. We propose a structural framework that explains transferability through two factors: the Feature Overlap Rate (FOR), measuring how much target representation lies in the source-induced subspace, and the Effective Task Complexity (ETC), quantifying the entropy of latent subtasks. We derive a PAC-Bayesian bound where target risk depends on FOR and ETC, and show that larger models attenuate their negative effects. Experiments on six GLUE transfer pairs estimate FOR and ETC from encoder representations and compare them to classical divergences. Results show that FOR and ETC together explain over 80% of transfer risk variance, while divergences fail to do so. Our findings provide a geometry-aware perspective for diagnosing and guiding transfer learning.

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ICLR Conference 2025 Conference Paper

InversionGNN: A Dual Path Network for Multi-Property Molecular Optimization

Yifan Niu
Ziqi Gao
Tingyang Xu
Yang Liu 0165
Yatao An Bian
Yu Rong 0001
Junzhou Huang
Jia Li 0009

Exploring chemical space to find novel molecules that simultaneously satisfy multiple properties is crucial in drug discovery. However, existing methods often struggle with trading off multiple properties due to the conflicting or correlated nature of chemical properties. To tackle this issue, we introduce InversionGNN framework, an effective yet sample-efficient dual-path graph neural network (GNN) for multi-objective drug discovery. In the direct prediction path of InversionGNN, we train the model for multi-property prediction to acquire knowledge of the optimal combination of functional groups. Then the learned chemical knowledge helps the inversion generation path to generate molecules with required properties. In order to decode the complex knowledge of multiple properties in the inversion path, we propose a gradient-based Pareto search method to balance conflicting properties and generate Pareto optimal molecules. Additionally, InversionGNN is able to search the full Pareto front approximately in discrete chemical space. Comprehensive experimental evaluations show that InversionGNN is both effective and sample-efficient in various discrete multi-objective settings including drug discovery.

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ICLR Conference 2024 Conference Paper

Deep Reinforcement Learning for Modelling Protein Complexes

Ziqi Gao
Tao Feng
Jiaxuan You
Chenyi Zi
Yan Zhou
Chen Zhang
Jia Li 0009

Structure prediction of large protein complexes (a.k.a., protein multimer mod- elling, PMM) can be achieved through the one-by-one assembly using provided dimer structures and predicted docking paths. However, existing PMM methods struggle with vast search spaces and generalization challenges: (1) The assembly of a N -chain multimer can be depicted using graph structured data, with each chain represented as a node and assembly actions as edges. Thus the assembly graph can be arbitrary acyclic undirected connected graph, leading to the com- binatorial optimization space of N^(N −2) for the PMM problem. (2) Knowledge transfer in the PMM task is non-trivial. The gradually limited data availability as the chain number increases necessitates PMM models that can generalize across multimers of various chains. To address these challenges, we propose GAPN, a Generative Adversarial Policy Network powered by domain-specific rewards and adversarial loss through policy gradient for automatic PMM prediction. Specifi- cally, GAPN learns to efficiently search through the immense assembly space and optimize the direct docking reward through policy gradient. Importantly, we de- sign a adversarial reward function to enhance the receptive field of our model. In this way, GAPN will simultaneously focus on a specific batch of multimers and the global assembly rules learned from multimers with varying chain numbers. Empirically, we have achieved both significant accuracy (measured by RMSD and TM-Score) and efficiency improvements compared to leading complex mod- eling software. GAPN outperforms the state-of-the-art method (MoLPC) with up to 27% improvement in TM-Score, with a speed-up of 600×.

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ICML Conference 2024 Conference Paper

Parameter-Efficient Fine-Tuning with Discrete Fourier Transform

Ziqi Gao
Qichao Wang
Aochuan Chen
Zijing Liu
Bingzhe Wu
Liang Chen 0001
Jia Li 0009

Low-rank adaptation (LoRA) has recently gained much interest in fine-tuning foundation models. It effectively reduces the number of trainable parameters by incorporating low-rank matrices $A$ and $B$ to represent the weight change, i. e. , $\Delta W=BA$. Despite LoRA’s progress, it faces storage challenges when handling extensive customization adaptations or larger base models. In this work, we aim to further compress trainable parameters by enjoying the powerful expressiveness of the Fourier transform. Specifically, we introduce FourierFT, which treats $\Delta W$ as a matrix in the spatial domain and learns only a small fraction of its spectral coefficients. With the trained spectral coefficients, we implement the inverse discrete Fourier transform to recover $\Delta W$. Empirically, our FourierFT method shows comparable or better performance with fewer parameters than LoRA on various tasks, including natural language understanding, natural language generation, instruction tuning, and image classification. For example, when performing instruction tuning on the LLaMA2-7B model, FourierFT surpasses LoRA with only 0. 064M trainable parameters, compared to LoRA’s 33. 5M. Our code is released at this link.

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ICLR Conference 2024 Conference Paper

Protein Multimer Structure Prediction via Prompt Learning

Ziqi Gao
Xiangguo Sun
Zijing Liu
Yu Li 0003
Hong Cheng 0001
Jia Li 0009

Understanding the 3D structures of protein multimers is crucial, as they play a vital role in regulating various cellular processes. It has been empirically confirmed that the multimer structure prediction (MSP) can be well handled in a step-wise assembly fashion using provided dimer structures and predicted protein-protein interactions (PPIs). However, due to the biological gap in the formation of dimers and larger multimers, directly applying PPI prediction techniques can often cause a poor generalization to the MSP task. To address this challenge, we aim to extend the PPI knowledge to multimers of different scales (i.e., chain numbers). Specifically, we propose PromptMSP, a pre-training and Prompt tuning framework for Multimer Structure Prediction. First, we tailor the source and target tasks for effective PPI knowledge learning and efficient inference, respectively. We design PPI-inspired prompt learning to narrow the gaps of two task formats and generalize the PPI knowledge to multimers of different scales. We provide a meta-learning strategy to learn a reliable initialization of the prompt model, enabling our prompting framework to effectively adapt to limited data for large-scale multimers. Empirically, we achieve both significant accuracy (RMSD and TM-Score) and efficiency improvements compared to advanced MSP models.

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YNICL Journal 2024 Journal Article

Temporal evolution of microstructural integrity in cerebellar peduncles in Parkinson’s disease: Stage-specific patterns and dopaminergic correlates

Chentao He
Rui Yang
Siming Rong
Piao Zhang
Xi Chen
Qi Qi
Ziqi Gao
Yan Li

BACKGROUND: Previous research revealed differences in cerebellar white matter integrity by disease stages, indicating a compensatory role in Parkinson's disease (PD). However, the temporal evolution of cerebellar white matter microstructure in patients with PD (PwPD) remains unclear. OBJECTIVE: To unravel temporal evolution of cerebellar white matter and its dopaminergic correlates in PD. METHODS: We recruited 124 PwPD from the PPMI study. The participants were divided into two subsets: Subset 1 (n = 41) had three MRI scans (baseline, 2 years, and 4 years), and Subset 2 (n = 106) had at least two MRI scans at baseline, 1 year, and/or 2 years. Free water-corrected diffusion metrics were used to measure the microstructural integrity in cerebellar peduncles (CP), the main white matter tracts connecting to and from the cerebellum. The ACAPULCO processing pipeline was used to assess cerebellar lobules volumes. Linear mixed-effect models were used to study longitudinal changes. We also examined the relationships between microstructural integrity in CP, striatal dopamine transporter specific binding ratio (SBR), and clinical symptoms. RESULTS: Microstructural changes in CP showed a non-linear pattern in PwPD. Free water-corrected fractional anisotropy (FAt) increased in the first two years but declined from 2 to 4 years, while free water-corrected mean diffusivity exhibited the opposite trend. The initial increased FAt in CP correlated with cerebellar regional volume atrophy, striatal dopaminergic SBR decline, and worsening clinical symptoms, but this correlation varied across disease stages. CONCLUSIONS: Our findings suggest a non-linear evolution of microstructural integrity in CP throughout the course of PD, indicating the adaptive structural reorganization of the cerebellum simultaneously with progressive striatal dopaminergic degeneration in PD.

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NeurIPS Conference 2024 Conference Paper

Towards Stable Representations for Protein Interface Prediction

Ziqi Gao
Zijing Liu
Yu Li
Jia Li

The knowledge of protein interactions is crucial but challenging for drug discovery applications. This work focuses on protein interface prediction, which aims to determine whether a pair of residues from different proteins interact. Existing data-driven methods have made significant progress in effectively learning protein structures. Nevertheless, they overlook the conformational changes (i. e. , flexibility) within proteins upon binding, leading to poor generalization ability. In this paper, we regard the protein flexibility as an attack on the trained model and aim to defend against it for improved generalization. To fulfill this purpose, we propose ATProt, an adversarial training framework for protein representations to robustly defend against the attack of protein flexibility. ATProt can theoretically guarantee protein representation stability under complicated protein flexibility. Experiments on various benchmarks demonstrate that ATProt consistently improves the performance for protein interface prediction. Moreover, our method demonstrates broad applicability, performing the best even when provided with testing structures from structure prediction models like ESMFold and AlphaFold2.

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NeurIPS Conference 2023 Conference Paper

GADBench: Revisiting and Benchmarking Supervised Graph Anomaly Detection

Jianheng Tang
Fengrui Hua
Ziqi Gao
Peilin Zhao
Jia Li

With a long history of traditional Graph Anomaly Detection (GAD) algorithms and recently popular Graph Neural Networks (GNNs), it is still not clear (1) how they perform under a standard comprehensive setting, (2) whether GNNs can outperform traditional algorithms such as tree ensembles, and (3) how about their efficiency on large-scale graphs. In response, we introduce GADBench---a benchmark tool dedicated to supervised anomalous node detection in static graphs. GADBench facilitates a detailed comparison across 29 distinct models on ten real-world GAD datasets, encompassing thousands to millions (~6M) nodes. Our main finding is that tree ensembles with simple neighborhood aggregation can outperform the latest GNNs tailored for the GAD task. We shed light on the current progress of GAD, setting a robust groundwork for subsequent investigations in this domain. GADBench is open-sourced at https: //github. com/squareRoot3/GADBench.

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AAAI Conference 2023 Conference Paper

Handling Missing Data via Max-Entropy Regularized Graph Autoencoder

Ziqi Gao
Yifan Niu
Jiashun Cheng
Jianheng Tang
Lanqing Li
Tingyang Xu
Peilin Zhao
Fugee Tsung

Graph neural networks (GNNs) are popular weapons for modeling relational data. Existing GNNs are not specified for attribute-incomplete graphs, making missing attribute imputation a burning issue. Until recently, many works notice that GNNs are coupled with spectral concentration, which means the spectrum obtained by GNNs concentrates on a local part in spectral domain, e.g., low-frequency due to oversmoothing issue. As a consequence, GNNs may be seriously flawed for reconstructing graph attributes as graph spectral concentration tends to cause a low imputation precision. In this work, we present a regularized graph autoencoder for graph attribute imputation, named MEGAE, which aims at mitigating spectral concentration problem by maximizing the graph spectral entropy. Notably, we first present the method for estimating graph spectral entropy without the eigen-decomposition of Laplacian matrix and provide the theoretical upper error bound. A maximum entropy regularization then acts in the latent space, which directly increases the graph spectral entropy. Extensive experiments show that MEGAE outperforms all the other state-of-the-art imputation methods on a variety of benchmark datasets.

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AAAI Conference 2023 Conference Paper

ImGCL: Revisiting Graph Contrastive Learning on Imbalanced Node Classification

Liang Zeng
Lanqing Li
Ziqi Gao
Peilin Zhao
Jian Li

Graph contrastive learning (GCL) has attracted a surge of attention due to its superior performance for learning node/graph representations without labels. However, in practice, the underlying class distribution of unlabeled nodes for the given graph is usually imbalanced. This highly imbalanced class distribution inevitably deteriorates the quality of learned node representations in GCL. Indeed, we empirically find that most state-of-the-art GCL methods cannot obtain discriminative representations and exhibit poor performance on imbalanced node classification. Motivated by this observation, we propose a principled GCL framework on Imbalanced node classification (ImGCL), which automatically and adaptively balances the representations learned from GCL without labels. Specifically, we first introduce the online clustering based progressively balanced sampling (PBS) method with theoretical rationale, which balances the training sets based on pseudo-labels obtained from learned representations in GCL. We then develop the node centrality based PBS method to better preserve the intrinsic structure of graphs, by upweighting the important nodes of the given graph. Extensive experiments on multiple imbalanced graph datasets and imbalanced settings demonstrate the effectiveness of our proposed framework, which significantly improves the performance of the recent state-of-the-art GCL methods. Further experimental ablations and analyses show that the ImGCL framework consistently improves the representation quality of nodes in under-represented (tail) classes.

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ICML Conference 2022 Conference Paper

Rethinking Graph Neural Networks for Anomaly Detection

Jianheng Tang
Jiajin Li
Ziqi Gao
Jia Li 0009

Graph Neural Networks (GNNs) are widely applied for graph anomaly detection. As one of the key components for GNN design is to select a tailored spectral filter, we take the first step towards analyzing anomalies via the lens of the graph spectrum. Our crucial observation is the existence of anomalies will lead to the ‘right-shift’ phenomenon, that is, the spectral energy distribution concentrates less on low frequencies and more on high frequencies. This fact motivates us to propose the Beta Wavelet Graph Neural Network (BWGNN). Indeed, BWGNN has spectral and spatial localized band-pass filters to better handle the ‘right-shift’ phenomenon in anomalies. We demonstrate the effectiveness of BWGNN on four large-scale anomaly detection datasets. Our code and data are released at https: //github. com/squareRoot3/Rethinking-Anomaly-Detection.

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