arXiv subjects

Haiping Lu

Publications and source records attributed to Haiping Lu.

At least 37 records · Page 2Linked to original sources

arXiv2023

SkelEx and BoundEx: Natural Visualization of ReLU Neural Networks

Despite their limited interpretability, weights and biases are still the most popular encoding of the functions learned by ReLU Neural Networks (ReLU NNs). That is why we introduce SkelEx, an algorithm to extract a skeleton of the membership functions learned by ReLU NNs, making those functions easier to interpret and analyze. To the best of our knowledge, this is the first work that considers linear regions from the perspective of critical points. As a natural follow-up, we also introduce BoundEx, which is the first analytical method known to us to extract the decision boundary from the realization of a ReLU NN. Both of those methods introduce very natural visualization tool for ReLU NNs trained on low-dimensional data.

cs.LG↗

arXiv2023

Interpretable bilinear attention network with domain adaptation improves drug-target prediction

Predicting drug-target interaction is key for drug discovery. Recent deep learning-based methods show promising performance but two challenges remain: (i) how to explicitly model and learn local interactions between drugs and targets for better prediction and interpretation; (ii) how to generalize prediction performance on novel drug-target pairs from different distribution. In this work, we propose DrugBAN, a deep bilinear attention network (BAN) framework with domain adaptation to explicitly learn pair-wise local interactions between drugs and targets, and adapt on out-of-distribution data. DrugBAN works on drug molecular graphs and target protein sequences to perform prediction, with conditional domain adversarial learning to align learned interaction representations across different distributions for better generalization on novel drug-target pairs. Experiments on three benchmark datasets under both in-domain and cross-domain settings show that DrugBAN achieves the best overall performance against five state-of-the-art baselines. Moreover, visualizing the learned bilinear attention map provides interpretable insights from prediction results.

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arXiv2022

Uncertainty Estimation for Heatmap-based Landmark Localization

Automatic anatomical landmark localization has made great strides by leveraging deep learning methods in recent years. The ability to quantify the uncertainty of these predictions is a vital component needed for these methods to be adopted in clinical settings, where it is imperative that erroneous predictions are caught and corrected. We propose Quantile Binning, a data-driven method to categorize predictions by uncertainty with estimated error bounds. Our framework can be applied to any continuous uncertainty measure, allowing straightforward identification of the best subset of predictions with accompanying estimated error bounds. We facilitate easy comparison between uncertainty measures by constructing two evaluation metrics derived from Quantile Binning. We compare and contrast three epistemic uncertainty measures (two baselines, and a proposed method combining aspects of the two), derived from two heatmap-based landmark localization model paradigms (U-Net and patch-based). We show results across three datasets, including a publicly available Cephalometric dataset. We illustrate how filtering out gross mispredictions caught in our Quantile Bins significantly improves the proportion of predictions under an acceptable error threshold. Finally, we demonstrate that Quantile Binning remains effective on landmarks with high aleatoric uncertainty caused by inherent landmark ambiguity, and offer recommendations on which uncertainty measure to use and how to use it. The code and data are available at https://github.com/schobs/qbin.

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arXiv2022

Multimodal Learning for Multi-Omics: A Survey

With advanced imaging, sequencing, and profiling technologies, multiple omics data become increasingly available and hold promises for many healthcare applications such as cancer diagnosis and treatment. Multimodal learning for integrative multi-omics analysis can help researchers and practitioners gain deep insights into human diseases and improve clinical decisions. However, several challenges are hindering the development in this area, including the availability of easily accessible open-source tools. This survey aims to provide an up-to-date overview of the data challenges, fusion approaches, datasets, and software tools from several new perspectives. We identify and investigate various omics data challenges that can help us understand the field better. We categorize fusion approaches comprehensively to cover existing methods in this area. We collect existing open-source tools to facilitate their broader utilization and development. We explore a broad range of omics data modalities and a list of accessible datasets. Finally, we summarize future directions that can potentially address existing gaps and answer the pressing need to advance multimodal learning for multi-omics data analysis.

q-bio.GN↗

arXiv2022

Knowledge-aware Neural Collective Matrix Factorization for Cross-domain Recommendation

Cross-domain recommendation (CDR) can help customers find more satisfying items in different domains. Existing CDR models mainly use common users or mapping functions as bridges between domains but have very limited exploration in fully utilizing extra knowledge across domains. In this paper, we propose to incorporate the knowledge graph (KG) for CDR, which enables items in different domains to share knowledge. To this end, we first construct a new dataset AmazonKG4CDR from the Freebase KG and a subset (two domain pairs: movies-music, movie-book) of Amazon Review Data. This new dataset facilitates linking knowledge to bridge within- and cross-domain items for CDR. Then we propose a new framework, KG-aware Neural Collective Matrix Factorization (KG-NeuCMF), leveraging KG to enrich item representations. It first learns item embeddings by graph convolutional autoencoder to capture both domain-specific and domain-general knowledge from adjacent and higher-order neighbours in the KG. Then, we maximize the mutual information between item embeddings learned from the KG and user-item matrix to establish cross-domain relationships for better CDR. Finally, we conduct extensive experiments on the newly constructed dataset and demonstrate that our model significantly outperforms the best-performing baselines.

cs.IR↗

arXiv2022

Graph Node-Feature Convolution for Representation Learning

Graph convolutional network (GCN) is an emerging neural network approach. It learns new representation of a node by aggregating feature vectors of all neighbors in the aggregation process without considering whether the neighbors or features are useful or not. Recent methods have improved solutions by sampling a fixed size set of neighbors, or assigning different weights to different neighbors in the aggregation process, but features within a feature vector are still treated equally in the aggregation process. In this paper, we introduce a new convolution operation on regular size feature maps constructed from features of a fixed node bandwidth via sampling to get the first-level node representation, which is then passed to a standard GCN to learn the second-level node representation. Experiments show that our method outperforms competing methods in semi-supervised node classification tasks. Furthermore, our method opens new doors for exploring new GCN architectures, particularly deeper GCN models.

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arXiv2021

Evaluating Transformers for Lightweight Action Recognition

In video action recognition, transformers consistently reach state-of-the-art accuracy. However, many models are too heavyweight for the average researcher with limited hardware resources. In this work, we explore the limitations of video transformers for lightweight action recognition. We benchmark 13 video transformers and baselines across 3 large-scale datasets and 10 hardware devices. Our study is the first to evaluate the efficiency of action recognition models in depth across multiple devices and train a wide range of video transformers under the same conditions. We categorize current methods into three classes and show that composite transformers that augment convolutional backbones are best at lightweight action recognition, despite lacking accuracy. Meanwhile, attention-only models need more motion modeling capabilities and stand-alone attention block models currently incur too much latency overhead. Our experiments conclude that current video transformers are not yet capable of lightweight action recognition on par with traditional convolutional baselines, and that the previously mentioned shortcomings need to be addressed to bridge this gap. Code to reproduce our experiments will be made publicly available.

cs.CV↗

arXiv2021

VideoLightFormer: Lightweight Action Recognition using Transformers

Efficient video action recognition remains a challenging problem. One large model after another takes the place of the state-of-the-art on the Kinetics dataset, but real-world efficiency evaluations are often lacking. In this work, we fill this gap and investigate the use of transformers for efficient action recognition. We propose a novel, lightweight action recognition architecture, VideoLightFormer. In a factorized fashion, we carefully extend the 2D convolutional Temporal Segment Network with transformers, while maintaining spatial and temporal video structure throughout the entire model. Existing methods often resort to one of the two extremes, where they either apply huge transformers to video features, or minimal transformers on highly pooled video features. Our method differs from them by keeping the transformer models small, but leveraging full spatiotemporal feature structure. We evaluate VideoLightFormer in a high-efficiency setting on the temporally-demanding EPIC-KITCHENS-100 and Something-Something-V2 (SSV2) datasets and find that it achieves a better mix of efficiency and accuracy than existing state-of-the-art models, apart from the Temporal Shift Module on SSV2.

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arXiv2021

Channel-Temporal Attention for First-Person Video Domain Adaptation

Unsupervised Domain Adaptation (UDA) can transfer knowledge from labeled source data to unlabeled target data of the same categories. However, UDA for first-person action recognition is an under-explored problem, with lack of datasets and limited consideration of first-person video characteristics. This paper focuses on addressing this problem. Firstly, we propose two small-scale first-person video domain adaptation datasets: ADL$_{small}$ and GTEA-KITCHEN. Secondly, we introduce channel-temporal attention blocks to capture the channel-wise and temporal-wise relationships and model their inter-dependencies important to first-person vision. Finally, we propose a Channel-Temporal Attention Network (CTAN) to integrate these blocks into existing architectures. CTAN outperforms baselines on the two proposed datasets and one existing dataset EPIC$_{cvpr20}$.

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arXiv2021

Team PyKale (xy9) Submission to the EPIC-Kitchens 2021 Unsupervised Domain Adaptation Challenge for Action Recognition

This report describes the technical details of our submission to the EPIC-Kitchens 2021 Unsupervised Domain Adaptation Challenge for Action Recognition. The EPIC-Kitchens dataset is more difficult than other video domain adaptation datasets due to multi-tasks with more modalities. Firstly, to participate in the challenge, we employ a transformer to capture the spatial information from each modality. Secondly, we employ a temporal attention module to model temporal-wise inter-dependency. Thirdly, we employ the adversarial domain adaptation network to learn the general features between labeled source and unlabeled target domain. Finally, we incorporate multiple modalities to improve the performance by a three-stream network with late fusion. Our network achieves the comparable performance with the state-of-the-art baseline T$A^3$N and outperforms the baseline on top-1 accuracy for verb class and top-5 accuracies for all three tasks which are verb, noun and action. Under the team name xy9, our submission achieved 5th place in terms of top-1 accuracy for verb class and all top-5 accuracies.

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arXiv2021

PyKale: Knowledge-Aware Machine Learning from Multiple Sources in Python

Machine learning is a general-purpose technology holding promises for many interdisciplinary research problems. However, significant barriers exist in crossing disciplinary boundaries when most machine learning tools are developed in different areas separately. We present Pykale - a Python library for knowledge-aware machine learning on graphs, images, texts, and videos to enable and accelerate interdisciplinary research. We formulate new green machine learning guidelines based on standard software engineering practices and propose a novel pipeline-based application programming interface (API). PyKale focuses on leveraging knowledge from multiple sources for accurate and interpretable prediction, thus supporting multimodal learning and transfer learning (particularly domain adaptation) with latest deep learning and dimensionality reduction models. We build PyKale on PyTorch and leverage the rich PyTorch ecosystem. Our pipeline-based API design enforces standardization and minimalism, embracing green machine learning concepts via reducing repetitions and redundancy, reusing existing resources, and recycling learning models across areas. We demonstrate its interdisciplinary nature via examples in bioinformatics, knowledge graph, image/video recognition, and medical imaging.

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arXiv2020

Unifying Homophily and Heterophily Network Transformation via Motifs

Higher-order proximity (HOP) is fundamental for most network embedding methods due to its significant effects on the quality of node embedding and performance on downstream network analysis tasks. Most existing HOP definitions are based on either homophily to place close and highly interconnected nodes tightly in embedding space or heterophily to place distant but structurally similar nodes together after embedding. In real-world networks, both can co-exist, and thus considering only one could limit the prediction performance and interpretability. However, there is no general and universal solution that takes both into consideration. In this paper, we propose such a simple yet powerful framework called homophily and heterophliy preserving network transformation (H2NT) to capture HOP that flexibly unifies homophily and heterophily. Specifically, H2NT utilises motif representations to transform a network into a new network with a hybrid assumption via micro-level and macro-level walk paths. H2NT can be used as an enhancer to be integrated with any existing network embedding methods without requiring any changes to latter methods. Because H2NT can sparsify networks with motif structures, it can also improve the computational efficiency of existing network embedding methods when integrated. We conduct experiments on node classification, structural role classification and motif prediction to show the superior prediction performance and computational efficiency over state-of-the-art methods. In particular, DeepWalk-based H2 NT achieves 24% improvement in terms of precision on motif prediction, while reducing 46% computational time compared to the original DeepWalk.

cs.SI↗

arXiv2020

Hop-Hop Relation-aware Graph Neural Networks

Graph Neural Networks (GNNs) are widely used in graph representation learning. However, most GNN methods are designed for either homogeneous or heterogeneous graphs. In this paper, we propose a new model, Hop-Hop Relation-aware Graph Neural Network (HHR-GNN), to unify representation learning for these two types of graphs. HHR-GNN learns a personalized receptive field for each node by leveraging knowledge graph embedding to learn relation scores between the central node's representations at different hops. In neighborhood aggregation, our model simultaneously allows for hop-aware projection and aggregation. This mechanism enables the central node to learn a hop-wise neighborhood mixing that can be applied to both homogeneous and heterogeneous graphs. Experimental results on five benchmarks show the competitive performance of our model compared to state-of-the-art GNNs, e.g., up to 13K faster in terms of time cost per training epoch on large heterogeneous graphs.

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arXiv2020

Neuropsychiatric Disease Classification Using Functional Connectomics -- Results of the Connectomics in NeuroImaging Transfer Learning Challenge

Large, open-source consortium datasets have spurred the development of new and increasingly powerful machine learning approaches in brain connectomics. However, one key question remains: are we capturing biologically relevant and generalizable information about the brain, or are we simply overfitting to the data? To answer this, we organized a scientific challenge, the Connectomics in NeuroImaging Transfer Learning Challenge (CNI-TLC), held in conjunction with MICCAI 2019. CNI-TLC included two classification tasks: (1) diagnosis of Attention-Deficit/Hyperactivity Disorder (ADHD) within a pre-adolescent cohort; and (2) transference of the ADHD model to a related cohort of Autism Spectrum Disorder (ASD) patients with an ADHD comorbidity. In total, 240 resting-state fMRI time series averaged according to three standard parcellation atlases, along with clinical diagnosis, were released for training and validation (120 neurotypical controls and 120 ADHD). We also provided demographic information of age, sex, IQ, and handedness. A second set of 100 subjects (50 neurotypical controls, 25 ADHD, and 25 ASD with ADHD comorbidity) was used for testing. Models were submitted in a standardized format as Docker images through ChRIS, an open-source image analysis platform. Utilizing an inclusive approach, we ranked the methods based on 16 different metrics. The final rank was calculated using the rank product for each participant across all measures. Furthermore, we assessed the calibration curves of each method. Five participants submitted their model for evaluation, with one outperforming all other methods in both ADHD and ASD classification. However, further improvements are needed to reach the clinical translation of functional connectomics. We are keeping the CNI-TLC open as a publicly available resource for developing and validating new classification methodologies in the field of connectomics.

q-bio.NC↗

arXiv2020

GripNet: Graph Information Propagation on Supergraph for Heterogeneous Graphs

Heterogeneous graph representation learning aims to learn low-dimensional vector representations of different types of entities and relations to empower downstream tasks. Existing methods either capture semantic relationships but indirectly leverage node/edge attributes in a complex way, or leverage node/edge attributes directly without taking semantic relationships into account. When involving multiple convolution operations, they also have poor scalability. To overcome these limitations, this paper proposes a flexible and efficient Graph information propagation Network (GripNet) framework. Specifically, we introduce a new supergraph data structure consisting of supervertices and superedges. A supervertex is a semantically-coherent subgraph. A superedge defines an information propagation path between two supervertices. GripNet learns new representations for the supervertex of interest by propagating information along the defined path using multiple layers. We construct multiple large-scale graphs and evaluate GripNet against competing methods to show its superiority in link prediction, node classification, and data integration.

cs.LG↗

arXiv2020

Tri-graph Information Propagation for Polypharmacy Side Effect Prediction

The use of drug combinations often leads to polypharmacy side effects (POSE). A recent method formulates POSE prediction as a link prediction problem on a graph of drugs and proteins, and solves it with Graph Convolutional Networks (GCNs). However, due to the complex relationships in POSE, this method has high computational cost and memory demand. This paper proposes a flexible Tri-graph Information Propagation (TIP) model that operates on three subgraphs to learn representations progressively by propagation from protein-protein graph to drug-drug graph via protein-drug graph. Experiments show that TIP improves accuracy by 7%+, time efficiency by 83$\times$, and space efficiency by 3$\times$.

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arXiv2019

Domain Independent SVM for Transfer Learning in Brain Decoding

Brain imaging data are important in brain sciences yet expensive to obtain, with big volume (i.e., large p) but small sample size (i.e., small n). To tackle this problem, transfer learning is a promising direction that leverages source data to improve performance on related, target data. Most transfer learning methods focus on minimizing data distribution mismatch. However, a big challenge in brain imaging is the large domain discrepancies in cognitive experiment designs and subject-specific structures and functions. A recent transfer learning approach minimizes domain dependence to learn common features across domains, via the Hilbert-Schmidt Independence Criterion (HSIC). Inspired by this method, we propose a new Domain Independent Support Vector Machine (DI-SVM) for transfer learning in brain condition decoding. Specifically, DI-SVM simultaneously minimizes the SVM empirical risk and the dependence on domain information via a simplified HSIC. We use public data to construct 13 transfer learning tasks in brain decoding, including three interesting multi-source transfer tasks. Experiments show that DI-SVM's superior performance over eight competing methods on these tasks, particularly an improvement of more than 24% on multi-source transfer tasks.

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arXiv2018

Mixed-Order Spectral Clustering for Networks

Clustering is fundamental for gaining insights from complex networks, and spectral clustering (SC) is a popular approach. Conventional SC focuses on second-order structures (e.g., edges connecting two nodes) without direct consideration of higher-order structures (e.g., triangles and cliques). This has motivated SC extensions that directly consider higher-order structures. However, both approaches are limited to considering a single order. This paper proposes a new Mixed-Order Spectral Clustering (MOSC) approach to model both second-order and third-order structures simultaneously, with two MOSC methods developed based on Graph Laplacian (GL) and Random Walks (RW). MOSC-GL combines edge and triangle adjacency matrices, with theoretical performance guarantee. MOSC-RW combines first-order and second-order random walks for a probabilistic interpretation. We automatically determine the mixing parameter based on cut criteria or triangle density, and construct new structure-aware error metrics for performance evaluation. Experiments on real-world networks show 1) the superior performance of two MOSC methods over existing SC methods, 2) the effectiveness of the mixing parameter determination strategy, and 3) insights offered by the structure-aware error metrics.

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