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Ziqi Pan

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6 papers

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JBHI Journal 2025 Journal Article

Decoding Drug Response With Structurized Gridding Map-Based Cell Representation

Jiayi Yin
Hanyu Zhang
Xiuna Sun
Nanxin You
Minjie Mou
Mingkun Lu
Ziqi Pan
Fengcheng Li

A thorough understanding of cell-line drug response mechanisms is crucial for drug development, repurposing, and resistance reversal. While targeted anticancer therapies have shown promise, not all cancers have well-established biomarkers to stratify drug response. Single-gene associations only explain a small fraction of the observed drug sensitivity, so a more comprehensive method is needed. However, while deep learning models have shown promise in predicting drug response in cell lines, they still face significant challenges when it comes to their application in clinical applications. Therefore, this study proposed a new strategy called DD-Response for cell-line drug response prediction. First, a limitation of narrow modeling horizons was overcome to expand the model training domain by integrating multiple datasets through source-specific label binarization. Second, a modified representation based on a two-dimensional structurized gridding map (SGM) was developed for cell lines & drugs, avoiding feature correlation neglect and potential information loss. Third, a dual-branch, multi-channel convolutional neural network-based model for pairwise response prediction was constructed, enabling accurate outcomes and improved exploration of underlying mechanisms. As a result, the DD-Response demonstrated superior performance, captured cell-line characteristic variations, and provided insights into key factors impacting cell-line drug response. In addition, DD-Response exhibited scalability in predicting clinical patient responses to drug therapy. Overall, because of DD-response's excellent ability to predict drug response and capture key molecules behind them, DD-response is expected to greatly facilitate drug discovery, repurposing, resistance reversal, and therapeutic optimization.

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AAAI Conference 2023 Conference Paper

Geometric Inductive Biases for Identifiable Unsupervised Learning of Disentangled Representations

Ziqi Pan
Li Niu
Liqing Zhang

The model identifiability is a considerable issue in the unsupervised learning of disentangled representations. The PCA inductive biases revealed recently for unsupervised disentangling in VAE-based models are shown to improve local alignment of latent dimensions with principal components of the data. In this paper, in additional to the PCA inductive biases, we propose novel geometric inductive biases from the manifold perspective for unsupervised disentangling, which induce the model to capture the global geometric properties of the data manifold with guaranteed model identifiability. We also propose a Geometric Disentangling Regularized AutoEncoder (GDRAE) that combines the PCA and the proposed geometric inductive biases in one unified framework. The experimental results show the usefulness of the geometric inductive biases in unsupervised disentangling and the effectiveness of our GDRAE in capturing the geometric inductive biases.

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AAAI Conference 2023 Conference Paper

Isometric Manifold Learning Using Hierarchical Flow

Ziqi Pan
Jianfu Zhang
Li Niu
Liqing Zhang

We propose the Hierarchical Flow (HF) model constrained by isometric regularizations for manifold learning that combines manifold learning goals such as dimensionality reduction, inference, sampling, projection and density estimation into one unified framework. Our proposed HF model is regularized to not only produce embeddings preserving the geometric structure of the manifold, but also project samples onto the manifold in a manner conforming to the rigorous definition of projection. Theoretical guarantees are provided for our HF model to satisfy the two desired properties. In order to detect the real dimensionality of the manifold, we also propose a two-stage dimensionality reduction algorithm, which is a time-efficient algorithm thanks to the hierarchical architecture design of our HF model. Experimental results justify our theoretical analysis, demonstrate the superiority of our dimensionality reduction algorithm in cost of training time, and verify the effect of the aforementioned properties in improving performances on downstream tasks such as anomaly detection.

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NeurIPS Conference 2022 Conference Paper

UniGAN: Reducing Mode Collapse in GANs using a Uniform Generator

Ziqi Pan
Li Niu
Liqing Zhang

Despite the significant progress that has been made in the training of Generative Adversarial Networks (GANs), the mode collapse problem remains a major challenge in training GANs, which refers to a lack of diversity in generative samples. In this paper, we propose a new type of generative diversity named uniform diversity, which relates to a newly proposed type of mode collapse named $u$-mode collapse where the generative samples distribute nonuniformly over the data manifold. From a geometric perspective, we show that the uniform diversity is closely related with the generator uniformity property, and the maximum uniform diversity is achieved if the generator is uniform. To learn a uniform generator, we propose UniGAN, a generative framework with a Normalizing Flow based generator and a simple yet sample efficient generator uniformity regularization, which can be easily adapted to any other generative framework. A new type of diversity metric named udiv is also proposed to estimate the uniform diversity given a set of generative samples in practice. Experimental results verify the effectiveness of our UniGAN in learning a uniform generator and improving uniform diversity.

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AAAI Conference 2021 Conference Paper

Disentangled Information Bottleneck

Ziqi Pan
Li Niu
Jianfu Zhang
Liqing Zhang

The information bottleneck (IB) method is a technique for extracting information that is relevant for predicting the target random variable from the source random variable, which is typically implemented by optimizing the IB Lagrangian that balances the compression and prediction terms. However, the IB Lagrangian is hard to optimize, and multiple trials for tuning values of Lagrangian multiplier are required. Moreover, we show that the prediction performance strictly decreases as the compression gets stronger during optimizing the IB Lagrangian. In this paper, we implement the IB method from the perspective of supervised disentangling. Specifically, we introduce Disentangled Information Bottleneck (DisenIB) that is consistent on compressing source maximally without target prediction performance loss (maximum compression). Theoretical and experimental results demonstrate that our method is consistent on maximum compression, and performs well in terms of generalization, robustness to adversarial attack, outof-distribution detection, and supervised disentangling.

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AAAI Conference 2020 Conference Paper

Exploiting Motion Information from Unlabeled Videos for Static Image Action Recognition

Yiyi Zhang
Li Niu
Ziqi Pan
Meichao Luo
Jianfu Zhang
Dawei Cheng
Liqing Zhang

Static image action recognition, which aims to recognize action based on a single image, usually relies on expensive human labeling effort such as adequate labeled action images and large-scale labeled image dataset. In contrast, abundant unlabeled videos can be economically obtained. Therefore, several works have explored using unlabeled videos to facilitate image action recognition, which can be categorized into the following two groups: (a) enhance visual representations of action images with a designed proxy task on unlabeled videos, which falls into the scope of self-supervised learning; (b) generate auxiliary representations for action images with the generator learned from unlabeled videos. In this paper, we integrate the above two strategies in a uniﬁed framework, which consists of Visual Representation Enhancement (VRE) module and Motion Representation Augmentation (MRA) module. Speciﬁcally, the VRE module includes a proxy task which imposes pseudo motion label constraint and temporal coherence constraint on unlabeled videos, while the MRA module could predict the motion information of a static action image by exploiting unlabeled videos. We demonstrate the superiority of our framework based on four benchmark human action datasets with limited labeled data.

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