arXiv subjects

Ziqi Gao

Publications and source records attributed to Ziqi Gao.

33 records · Page 2Linked to original sources

arXiv2025

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

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.

cs.LG↗

arXiv2025

Molecule Generation for Target Protein Binding with Hierarchical Consistency Diffusion Model

Effective generation of molecular structures, or new chemical entities, that bind to target proteins is crucial for lead identification and optimization in drug discovery. Despite advancements in atom- and motif-wise deep learning models for 3D molecular generation, current methods often struggle with validity and reliability. To address these issues, we develop the Atom-Motif Consistency Diffusion Model (AMDiff), utilizing a joint-training paradigm for multi-view learning. This model features a hierarchical diffusion architecture that integrates both atom- and motif-level views of molecules, allowing for comprehensive exploration of complementary information. By leveraging classifier-free guidance and incorporating binding site features as conditional inputs, AMDiff ensures robust molecule generation across diverse targets. Compared to existing approaches, AMDiff exhibits superior validity and novelty in generating molecules tailored to fit various protein pockets. Case studies targeting protein kinases, including Anaplastic Lymphoma Kinase (ALK) and Cyclin-dependent kinase 4 (CDK4), demonstrate the model's capability in structure-based de novo drug design. Overall, AMDiff bridges the gap between atom-view and motif-view drug discovery and speeds up the process of target-aware molecular generation.

cs.LG↗

arXiv2024

MS-Glance: Bio-Insipred Non-semantic Context Vectors and their Applications in Supervising Image Reconstruction

Non-semantic context information is crucial for visual recognition, as the human visual perception system first uses global statistics to process scenes rapidly before identifying specific objects. However, while semantic information is increasingly incorporated into computer vision tasks such as image reconstruction, non-semantic information, such as global spatial structures, is often overlooked. To bridge the gap, we propose a biologically informed non-semantic context descriptor, \textbf{MS-Glance}, along with the Glance Index Measure for comparing two images. A Global Glance vector is formulated by randomly retrieving pixels based on a perception-driven rule from an image to form a vector representing non-semantic global context, while a local Glance vector is a flattened local image window, mimicking a zoom-in observation. The Glance Index is defined as the inner product of two standardized sets of Glance vectors. We evaluate the effectiveness of incorporating Glance supervision in two reconstruction tasks: image fitting with implicit neural representation (INR) and undersampled MRI reconstruction. Extensive experimental results show that MS-Glance outperforms existing image restoration losses across both natural and medical images. The code is available at \url{https://github.com/Z7Gao/MSGlance}.

eess.IV↗

arXiv2024

MRPD: Undersampled MRI reconstruction by prompting a large latent diffusion model

Implicit visual knowledge in a large latent diffusion model (LLDM) pre-trained on natural images is rich and hypothetically universal to natural and medical images. To test this hypothesis from a practical perspective, we propose a novel framework for undersampled MRI Reconstruction by Prompting a large latent Diffusion model (MRPD). While the existing methods trained on MRI datasets are typically of limited generalizability toward diverse data acquisition scenarios, MRPD supports unsupervised and universally adaptive MRI reconstruction. For unsupervised reconstruction, MRSampler guides LLDM with a random-phase-modulated hard-to-soft control. With any single- or multiple-source MRI dataset, MRPD's performance is boosted universally by a lightweight MRAdapter that only finetunes the LLDM's autoencoder. Experiments on FastMRI and IXI show that MRPD is the only model that supports both MRI database-free and database-available scenarios and attains the best generalizability towards out-of-domain (OOD) samplings, contrasts, and organs among compared unsupervised, supervised, and MRI diffusion methods. To our knowledge, MRPD is the first method that empirically shows the universal prowess of an LLDM pre-trained on vast natural images for MRI. Our official implementation is at https://github.com/Z7Gao/MRPD.

eess.IV↗

arXiv2024

Deep Reinforcement Learning for Modelling Protein Complexes

AlphaFold can be used for both single-chain and multi-chain protein structure prediction, while the latter becomes extremely challenging as the number of chains increases. In this work, by taking each chain as a node and assembly actions as edges, we show that an acyclic undirected connected graph can be used to predict the structure of multi-chain protein complexes (a.k.a., protein complex modelling, PCM). However, there are still two challenges: 1) The huge combinatorial optimization space of $N^{N-2}$ ($N$ is the number of chains) for the PCM problem can easily lead to high computational cost. 2) The scales of protein complexes exhibit distribution shift due to variance in chain numbers, which calls for the generalization in modelling complexes of various scales. 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 PCM prediction. Specifically, GAPN learns to efficiently search through the immense assembly space and optimize the direct docking reward through policy gradient. Importantly, we design an adversarial reward function to enhance the receptive field of our model. In this way, GAPN will simultaneously focus on a specific batch of complexes and the global assembly rules learned from complexes with varied chain numbers. Empirically, we have achieved both significant accuracy (measured by RMSD and TM-Score) and efficiency improvements compared to leading PCM softwares.

cs.CE↗

arXiv2024

Parameter-Efficient Fine-Tuning with Discrete Fourier Transform

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., $ΔW=BA$. 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 $ΔW$ 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 $ΔW$. 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 \url{https://github.com/Chaos96/fourierft}.

cs.LG↗

arXiv2024

DuDoUniNeXt: Dual-domain unified hybrid model for single and multi-contrast undersampled MRI reconstruction

Multi-contrast (MC) Magnetic Resonance Imaging (MRI) reconstruction aims to incorporate a reference image of auxiliary modality to guide the reconstruction process of the target modality. Known MC reconstruction methods perform well with a fully sampled reference image, but usually exhibit inferior performance, compared to single-contrast (SC) methods, when the reference image is missing or of low quality. To address this issue, we propose DuDoUniNeXt, a unified dual-domain MRI reconstruction network that can accommodate to scenarios involving absent, low-quality, and high-quality reference images. DuDoUniNeXt adopts a hybrid backbone that combines CNN and ViT, enabling specific adjustment of image domain and k-space reconstruction. Specifically, an adaptive coarse-to-fine feature fusion module (AdaC2F) is devised to dynamically process the information from reference images of varying qualities. Besides, a partially shared shallow feature extractor (PaSS) is proposed, which uses shared and distinct parameters to handle consistent and discrepancy information among contrasts. Experimental results demonstrate that the proposed model surpasses state-of-the-art SC and MC models significantly. Ablation studies show the effectiveness of the proposed hybrid backbone, AdaC2F, PaSS, and the dual-domain unified learning scheme.

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arXiv2024

Protein Multimer Structure Prediction via Prompt Learning

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 \textit{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 \textbf{\textsc{PromptMSP}}, a pre-training and \textbf{Prompt} tuning framework for \textbf{M}ultimer \textbf{S}tructure \textbf{P}rediction. 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. The code, data and checkpoints are released at \url{https://github.com/zqgao22/PromptMSP}.

cs.CE↗

arXiv2024

Rethinking Dual-Domain Undersampled MRI reconstruction: domain-specific design from the perspective of the receptive field

Undersampled MRI reconstruction is crucial for accelerating clinical scanning. Dual-domain reconstruction network is performant among SoTA deep learning methods. In this paper, we rethink dual-domain model design from the perspective of the receptive field, which is needed for image recovery and K-space interpolation problems. Further, we introduce domain-specific modules for dual-domain reconstruction, namely k-space global initialization and image-domain parallel local detail enhancement. We evaluate our modules by translating a SoTA method DuDoRNet under different conventions of MRI reconstruction including image-domain, dual-domain, and reference-guided reconstruction on the public IXI dataset. Our model DuDoRNet+ achieves significant improvements over competing deep learning methods.

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arXiv2023

GADBench: Revisiting and Benchmarking Supervised Graph Anomaly Detection

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 ($\sim$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.

cs.LG↗

arXiv2023

MMTSA: Multimodal Temporal Segment Attention Network for Efficient Human Activity Recognition

Multimodal sensors provide complementary information to develop accurate machine-learning methods for human activity recognition (HAR), but introduce significantly higher computational load, which reduces efficiency. This paper proposes an efficient multimodal neural architecture for HAR using an RGB camera and inertial measurement units (IMUs) called Multimodal Temporal Segment Attention Network (MMTSA). MMTSA first transforms IMU sensor data into a temporal and structure-preserving gray-scale image using the Gramian Angular Field (GAF), representing the inherent properties of human activities. MMTSA then applies a multimodal sparse sampling method to reduce data redundancy. Lastly, MMTSA adopts an inter-segment attention module for efficient multimodal fusion. Using three well-established public datasets, we evaluated MMTSA's effectiveness and efficiency in HAR. Results show that our method achieves superior performance improvements 11.13% of cross-subject F1-score on the MMAct dataset than the previous state-of-the-art (SOTA) methods. The ablation study and analysis suggest that MMTSA's effectiveness in fusing multimodal data for accurate HAR. The efficiency evaluation on an edge device showed that MMTSA achieved significantly better accuracy, lower computational load, and lower inference latency than SOTA methods.

cs.CV↗

arXiv2023

ImGCL: Revisiting Graph Contrastive Learning on Imbalanced Node Classification

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.

cs.LG↗

arXiv2022

Handling Missing Data via Max-Entropy Regularized Graph Autoencoder

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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arXiv2022

ImDrug: A Benchmark for Deep Imbalanced Learning in AI-aided Drug Discovery

The last decade has witnessed a prosperous development of computational methods and dataset curation for AI-aided drug discovery (AIDD). However, real-world pharmaceutical datasets often exhibit highly imbalanced distribution, which is overlooked by the current literature but may severely compromise the fairness and generalization of machine learning applications. Motivated by this observation, we introduce ImDrug, a comprehensive benchmark with an open-source Python library which consists of 4 imbalance settings, 11 AI-ready datasets, 54 learning tasks and 16 baseline algorithms tailored for imbalanced learning. It provides an accessible and customizable testbed for problems and solutions spanning a broad spectrum of the drug discovery pipeline such as molecular modeling, drug-target interaction and retrosynthesis. We conduct extensive empirical studies with novel evaluation metrics, to demonstrate that the existing algorithms fall short of solving medicinal and pharmaceutical challenges in the data imbalance scenario. We believe that ImDrug opens up avenues for future research and development, on real-world challenges at the intersection of AIDD and deep imbalanced learning.

cs.LG↗

arXiv2022

Rethinking Graph Neural Networks for Anomaly Detection

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

cs.LG↗