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This work addresses the challenging domain adaptation setting in which knowledge from the labelled source domain dataset is available only from the pretrained black-box segmentation model. The pretrained model's predictions for the target domain images are noisy because of the distributional differences between the source domain data and the target domain data. Since the model's predictions serve as pseudo labels during self-training, the noise in the predictions impose an upper bound on model performance. Therefore, we propose a simple yet novel image translation workflow, ReGEN, to address this problem. ReGEN comprises an image-to-image translation network and a segmentation network. Our workflow generates target-like images using the noisy predictions from the original target domain images. These target-like images are semantically consistent with the noisy model predictions and therefore can be used to train the segmentation network. In addition to being semantically consistent with the predictions from the original target domain images, the generated target-like images are also stylistically similar to the target domain images. This allows us to leverage the stylistic differences between the target-like images and the target domain image as an additional source of supervision while training the segmentation model. We evaluate our model with two benchmark domain adaptation settings and demonstrate that our approach performs favourably relative to recent state-of-the-art work. The source code will be made available.

Obtaining sufficient labeled data for training deep models is often challenging in real-life applications. To address this issue, we propose a novel solution for single-source domain generalized semantic segmentation. Recent approaches have explored data diversity enhancement using hallucination techniques. However, excessive hallucination can degrade performance, particularly for imbalanced datasets. As shown in our experiments, minority classes are more susceptible to performance reduction due to hallucination compared to majority classes. To tackle this challenge, we introduce a dual-stage Feature Transform (dFT) layer within the Adversarial Semantic Hallucination+ (ASH+) framework. The ASH+ framework performs a dual-stage manipulation of hallucination strength. By leveraging semantic information for each pixel, our approach adaptively adjusts the pixel-wise hallucination strength, thus providing fine-grained control over hallucination. We validate the effectiveness of our proposed method through comprehensive experiments on publicly available semantic segmentation benchmark datasets (Cityscapes and SYNTHIA). Quantitative and qualitative comparisons demonstrate that our approach is competitive with state-of-the-art methods for the Cityscapes dataset and surpasses existing solutions for the SYNTHIA dataset. Code for our framework will be made readily available to the research community.

Label-efficient time series representation learning, which aims to learn effective representations with limited labeled data, is crucial for deploying deep learning models in real-world applications. To address the scarcity of labeled time series data, various strategies, e.g., transfer learning, self-supervised learning, and semi-supervised learning, have been developed. In this survey, we introduce a novel taxonomy for the first time, categorizing existing approaches as in-domain or cross-domain, based on their reliance on external data sources or not. Furthermore, we present a review of the recent advances in each strategy, conclude the limitations of current methodologies, and suggest future research directions that promise further improvements in the field., Comment: Accepted in the IEEE Transactions on Artificial Intelligence (TAI) https://ieeexplore.ieee.org/document/10601520

Unsupervised Domain Adaptation (UDA) has emerged as a powerful solution for the domain shift problem via transferring the knowledge from a labeled source domain to a shifted unlabeled target domain. Despite the prevalence of UDA for visual applications, it remains relatively less explored for time-series applications. In this work, we propose a novel lightweight contrastive domain adaptation framework called CoTMix for time-series data. Unlike existing approaches that either use statistical distances or adversarial techniques, we leverage contrastive learning solely to mitigate the distribution shift across the different domains. Specifically, we propose a novel temporal mixup strategy to generate two intermediate augmented views for the source and target domains. Subsequently, we leverage contrastive learning to maximize the similarity between each domain and its corresponding augmented view. The generated views consider the temporal dynamics of time-series data during the adaptation process while inheriting the semantics among the two domains. Hence, we gradually push both domains towards a common intermediate space, mitigating the distribution shift across them. Extensive experiments conducted on five real-world time-series datasets show that our approach can significantly outperform all state-of-the-art UDA methods. The implementation code of CoTMix is available at \href{https://github.com/emadeldeen24/CoTMix}{github.com/emadeldeen24/CoTMix}., Comment: Accepted in the IEEE Transactions on Artificial Intelligence

The past few years have witnessed a remarkable advance in deep learning for EEG-based sleep stage classification (SSC). However, the success of these models is attributed to possessing a massive amount of labeled data for training, limiting their applicability in real-world scenarios. In such scenarios, sleep labs can generate a massive amount of data, but labeling these data can be expensive and time-consuming. Recently, the self-supervised learning (SSL) paradigm has shined as one of the most successful techniques to overcome the scarcity of labeled data. In this paper, we evaluate the efficacy of SSL to boost the performance of existing SSC models in the few-labels regime. We conduct a thorough study on three SSC datasets, and we find that fine-tuning the pretrained SSC models with only 5% of labeled data can achieve competitive performance to the supervised training with full labels. Moreover, self-supervised pretraining helps SSC models to be more robust to data imbalance and domain shift problems. The code is publicly available at https://github.com/emadeldeen24/eval_ssl_ssc., Comment: Under Review. This document contains 9 pages as a main text, and 2 pages for supplementary materials

Learning time-series representations when only unlabeled data or few labeled samples are available can be a challenging task. Recently, contrastive self-supervised learning has shown great improvement in extracting useful representations from unlabeled data via contrasting different augmented views of data. In this work, we propose a novel Time-Series representation learning framework via Temporal and Contextual Contrasting (TS-TCC) that learns representations from unlabeled data with contrastive learning. Specifically, we propose time-series-specific weak and strong augmentations and use their views to learn robust temporal relations in the proposed temporal contrasting module, besides learning discriminative representations by our proposed contextual contrasting module. Additionally, we conduct a systematic study of time-series data augmentation selection, which is a key part of contrastive learning. We also extend TS-TCC to the semi-supervised learning settings and propose a Class-Aware TS-TCC (CA-TCC) that benefits from the available few labeled data to further improve representations learned by TS-TCC. Specifically, we leverage the robust pseudo labels produced by TS-TCC to realize a class-aware contrastive loss. Extensive experiments show that the linear evaluation of the features learned by our proposed framework performs comparably with the fully supervised training. Additionally, our framework shows high efficiency in the few labeled data and transfer learning scenarios. The code is publicly available at \url{https://github.com/emadeldeen24/CA-TCC}., Comment: Accepted in the IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI). arXiv admin note: text overlap with arXiv:2106.14112

Unsupervised domain adaptation methods aim to generalize well on unlabeled test data that may have a different (shifted) distribution from the training data. Such methods are typically developed on image data, and their application to time series data is less explored. Existing works on time series domain adaptation suffer from inconsistencies in evaluation schemes, datasets, and backbone neural network architectures. Moreover, labeled target data are often used for model selection, which violates the fundamental assumption of unsupervised domain adaptation. To address these issues, we develop a benchmarking evaluation suite (AdaTime) to systematically and fairly evaluate different domain adaptation methods on time series data. Specifically, we standardize the backbone neural network architectures and benchmarking datasets, while also exploring more realistic model selection approaches that can work with no labeled data or just a few labeled samples. Our evaluation includes adapting state-of-the-art visual domain adaptation methods to time series data as well as the recent methods specifically developed for time series data. We conduct extensive experiments to evaluate 11 state-of-the-art methods on five representative datasets spanning 50 cross-domain scenarios. Our results suggest that with careful selection of hyper-parameters, visual domain adaptation methods are competitive with methods proposed for time series domain adaptation. In addition, we find that hyper-parameters could be selected based on realistic model selection approaches. Our work unveils practical insights for applying domain adaptation methods on time series data and builds a solid foundation for future works in the field. The code is available at \href{https://github.com/emadeldeen24/AdaTime}{github.com/emadeldeen24/AdaTime}., Comment: Accepted in the ACM Transactions on Knowledge Discovery from Data (TKDD)

Re-ranking models refine item recommendation lists generated by the prior global ranking model, which have demonstrated their effectiveness in improving the recommendation quality. However, most existing re-ranking solutions only learn from implicit feedback with a shared prediction model, which regrettably ignore inter-item relationships under diverse user intentions. In this paper, we propose a novel Intention-aware Re-ranking Model with Dynamic Transformer Encoder (RAISE), aiming to perform user-specific prediction for each individual user based on her intentions. Specifically, we first propose to mine latent user intentions from text reviews with an intention discovering module (IDM). By differentiating the importance of review information with a co-attention network, the latent user intention can be explicitly modeled for each user-item pair. We then introduce a dynamic transformer encoder (DTE) to capture user-specific inter-item relationships among item candidates by seamlessly accommodating the learned latent user intentions via IDM. As such, one can not only achieve more personalized recommendations but also obtain corresponding explanations by constructing RAISE upon existing recommendation engines. Empirical study on four public datasets shows the superiority of our proposed RAISE, with up to 13.95%, 9.60%, and 13.03% relative improvements evaluated by Precision@5, MAP@5, and NDCG@5 respectively., Comment: Accepted by IEEE TKDE

Unsupervised domain adaptation (UDA) has successfully addressed the domain shift problem for visual applications. Yet, these approaches may have limited performance for time series data due to the following reasons. First, they mainly rely on large-scale dataset (i.e., ImageNet) for the source pretraining, which is not applicable for time-series data. Second, they ignore the temporal dimension on the feature space of the source and target domains during the domain alignment step. Last, most of prior UDA methods can only align the global features without considering the fine-grained class distribution of the target domain. To address these limitations, we propose a Self-supervised Autoregressive Domain Adaptation (SLARDA) framework. In particular, we first design a self-supervised learning module that utilizes forecasting as an auxiliary task to improve the transferability of the source features. Second, we propose a novel autoregressive domain adaptation technique that incorporates temporal dependency of both source and target features during domain alignment. Finally, we develop an ensemble teacher model to align the class-wise distribution in the target domain via a confident pseudo labeling approach. Extensive experiments have been conducted on three real-world time series applications with 30 cross-domain scenarios. Results demonstrate that our proposed SLARDA method significantly outperforms the state-of-the-art approaches for time series domain adaptation., Comment: Accepted for publication in IEEE Transactions on Neural Networks and Learning Systems

Sleep staging is of great importance in the diagnosis and treatment of sleep disorders. Recently, numerous data-driven deep learning models have been proposed for automatic sleep staging. They mainly train the model on a large public labeled sleep dataset and test it on a smaller one with subjects of interest. However, they usually assume that the train and test data are drawn from the same distribution, which may not hold in real-world scenarios. Unsupervised domain adaption (UDA) has been recently developed to handle this domain shift problem. However, previous UDA methods applied for sleep staging have two main limitations. First, they rely on a totally shared model for the domain alignment, which may lose the domain-specific information during feature extraction. Second, they only align the source and target distributions globally without considering the class information in the target domain, which hinders the classification performance of the model while testing. In this work, we propose a novel adversarial learning framework called ADAST to tackle the domain shift problem in the unlabeled target domain. First, we develop an unshared attention mechanism to preserve the domain-specific features in both domains. Second, we design an iterative self-training strategy to improve the classification performance on the target domain via target domain pseudo labels. We also propose dual distinct classifiers to increase the robustness and quality of the pseudo labels. The experimental results on six cross-domain scenarios validate the efficacy of our proposed framework and its advantage over state-of-the-art UDA methods. The source code is available at https://github.com/emadeldeen24/ADAST., Comment: Published in IEEE Transactions on Emerging Topics in Computational Intelligence

Learning decent representations from unlabeled time-series data with temporal dynamics is a very challenging task. In this paper, we propose an unsupervised Time-Series representation learning framework via Temporal and Contextual Contrasting (TS-TCC), to learn time-series representation from unlabeled data. First, the raw time-series data are transformed into two different yet correlated views by using weak and strong augmentations. Second, we propose a novel temporal contrasting module to learn robust temporal representations by designing a tough cross-view prediction task. Last, to further learn discriminative representations, we propose a contextual contrasting module built upon the contexts from the temporal contrasting module. It attempts to maximize the similarity among different contexts of the same sample while minimizing similarity among contexts of different samples. Experiments have been carried out on three real-world time-series datasets. The results manifest that training a linear classifier on top of the features learned by our proposed TS-TCC performs comparably with the supervised training. Additionally, our proposed TS-TCC shows high efficiency in few-labeled data and transfer learning scenarios. The code is publicly available at https://github.com/emadeldeen24/TS-TCC., Comment: Accepted in IJCAI-21 conference ... please cite the conference version

Representation learning-based recommendation models play a dominant role among recommendation techniques. However, most of the existing methods assume both historical interactions and embedding dimensions are independent of each other, and thus regrettably ignore the high-order interaction information among historical interactions and embedding dimensions. In this paper, we propose a novel representation learning-based model called COMET (COnvolutional diMEnsion inTeraction), which simultaneously models the high-order interaction patterns among historical interactions and embedding dimensions. To be specific, COMET stacks the embeddings of historical interactions horizontally at first, which results in two "embedding maps". In this way, internal interactions and dimensional interactions can be exploited by convolutional neural networks (CNN) with kernels of different sizes simultaneously. A fully-connected multi-layer perceptron (MLP) is then applied to obtain two interaction vectors. Lastly, the representations of users and items are enriched by the learnt interaction vectors, which can further be used to produce the final prediction. Extensive experiments and ablation studies on various public implicit feedback datasets clearly demonstrate the effectiveness and rationality of our proposed method., Comment: Accepted by ACM TIST

Graph-based recommendation models work well for top-N recommender systems due to their capability to capture the potential relationships between entities. However, most of the existing methods only construct a single global item graph shared by all the users and regrettably ignore the diverse tastes between different user groups. Inspired by the success of local models for recommendation, this paper provides the first attempt to investigate multiple local item graphs along with a global item graph for graph-based recommendation models. We argue that recommendation on global and local graphs outperforms that on a single global graph or multiple local graphs. Specifically, we propose a novel graph-based recommendation model named GLIMG (Global and Local IteM Graphs), which simultaneously captures both the global and local user tastes. By integrating the global and local graphs into an adapted semi-supervised learning model, users' preferences on items are propagated globally and locally. Extensive experimental results on real-world datasets show that our proposed method consistently outperforms the state-of-the art counterparts on the top-N recommendation task.

Accurate estimation of remaining useful life (RUL) of industrial equipment can enable advanced maintenance schedules, increase equipment availability and reduce operational costs. However, existing deep learning methods for RUL prediction are not completely successful due to the following two reasons. First, relying on a single objective function to estimate the RUL will limit the learned representations and thus affect the prediction accuracy. Second, while longer sequences are more informative for modelling the sensor dynamics of equipment, existing methods are less effective to deal with very long sequences, as they mainly focus on the latest information. To address these two problems, we develop a novel attention-based sequence to sequence with auxiliary task (ATS2S) model. In particular, our model jointly optimizes both reconstruction loss to empower our model with predictive capabilities (by predicting next input sequence given current input sequence) and RUL prediction loss to minimize the difference between the predicted RUL and actual RUL. Furthermore, to better handle longer sequence, we employ the attention mechanism to focus on all the important input information during training process. Finally, we propose a new dual-latent feature representation to integrate the encoder features and decoder hidden states, to capture rich semantic information in data. We conduct extensive experiments on four real datasets to evaluate the efficacy of the proposed method. Experimental results show that our proposed method can achieve superior performance over 13 state-of-the-art methods consistently.

Disease-gene association through Genome-wide association study (GWAS) is an arduous task for researchers. Investigating single nucleotide polymorphisms (SNPs) that correlate with specific diseases needs statistical analysis of associations. Considering the huge number of possible mutations, in addition to its high cost, another important drawback of GWAS analysis is the large number of false-positives. Thus, researchers search for more evidence to cross-check their results through different sources. To provide the researchers with alternative low-cost disease-gene association evidence, computational approaches come into play. Since molecular networks are able to capture complex interplay among molecules in diseases, they become one of the most extensively used data for disease-gene association prediction. In this survey, we aim to provide a comprehensive and an up-to-date review of network-based methods for disease gene prediction. We also conduct an empirical analysis on 14 state-of-the-art methods. To summarize, we first elucidate the task definition for disease gene prediction. Secondly, we categorize existing network-based efforts into network diffusion methods, traditional machine learning methods with handcrafted graph features and graph representation learning methods. Thirdly, an empirical analysis is conducted to evaluate the performance of the selected methods across seven diseases. We also provide distinguishing findings about the discussed methods based on our empirical analysis. Finally, we highlight potential research directions for future studies on disease gene prediction., Comment: Published in Briefings in Bioinformatics, 05 December 2020

Real-world networks often exist with multiple views, where each view describes one type of interaction among a common set of nodes. For example, on a video-sharing network, while two user nodes are linked if they have common favorite videos in one view, they can also be linked in another view if they share common subscribers. Unlike traditional single-view networks, multiple views maintain different semantics to complement each other. In this paper, we propose MANE, a multi-view network embedding approach to learn low-dimensional representations. Similar to existing studies, MANE hinges on diversity and collaboration - while diversity enables views to maintain their individual semantics, collaboration enables views to work together. However, we also discover a novel form of second-order collaboration that has not been explored previously, and further unify it into our framework to attain superior node representations. Furthermore, as each view often has varying importance w.r.t. different nodes, we propose MANE+, an attention-based extension of MANE to model node-wise view importance. Finally, we conduct comprehensive experiments on three public, real-world multi-view networks, and the results demonstrate that our models consistently outperform state-of-the-art approaches., Comment: Accepted for publication in the ACM Transactions on Knowledge Discovery from Data, TKDD

This paper focuses on scalability and robustness of spectral clustering for extremely large-scale datasets with limited resources. Two novel algorithms are proposed, namely, ultra-scalable spectral clustering (U-SPEC) and ultra-scalable ensemble clustering (U-SENC). In U-SPEC, a hybrid representative selection strategy and a fast approximation method for K-nearest representatives are proposed for the construction of a sparse affinity sub-matrix. By interpreting the sparse sub-matrix as a bipartite graph, the transfer cut is then utilized to efficiently partition the graph and obtain the clustering result. In U-SENC, multiple U-SPEC clusterers are further integrated into an ensemble clustering framework to enhance the robustness of U-SPEC while maintaining high efficiency. Based on the ensemble generation via multiple U-SEPC's, a new bipartite graph is constructed between objects and base clusters and then efficiently partitioned to achieve the consensus clustering result. It is noteworthy that both U-SPEC and U-SENC have nearly linear time and space complexity, and are capable of robustly and efficiently partitioning ten-million-level nonlinearly-separable datasets on a PC with 64GB memory. Experiments on various large-scale datasets have demonstrated the scalability and robustness of our algorithms. The MATLAB code and experimental data are available at https://www.researchgate.net/publication/330760669., Comment: To appear in IEEE Transactions on Knowledge and Data Engineering, 2019

Ensemble clustering has been a popular research topic in data mining and machine learning. Despite its significant progress in recent years, there are still two challenging issues in the current ensemble clustering research. First, most of the existing algorithms tend to investigate the ensemble information at the object-level, yet often lack the ability to explore the rich information at higher levels of granularity. Second, they mostly focus on the direct connections (e.g., direct intersection or pair-wise co-occurrence) in the multiple base clusterings, but generally neglect the multi-scale indirect relationship hidden in them. To address these two issues, this paper presents a novel ensemble clustering approach based on fast propagation of cluster-wise similarities via random walks. We first construct a cluster similarity graph with the base clusters treated as graph nodes and the cluster-wise Jaccard coefficient exploited to compute the initial edge weights. Upon the constructed graph, a transition probability matrix is defined, based on which the random walk process is conducted to propagate the graph structural information. Specifically, by investigating the propagating trajectories starting from different nodes, a new cluster-wise similarity matrix can be derived by considering the trajectory relationship. Then, the newly obtained cluster-wise similarity matrix is mapped from the cluster-level to the object-level to achieve an enhanced co-association (ECA) matrix, which is able to simultaneously capture the object-wise co-occurrence relationship as well as the multi-scale cluster-wise relationship in ensembles. Finally, two novel consensus functions are proposed to obtain the consensus clustering result. Extensive experiments on a variety of real-world datasets have demonstrated the effectiveness and efficiency of our approach., Comment: To appear in IEEE Transactions on Systems, Man, and Cybernetics: Systems. The MATLAB source code of this work is available at: http://www.researchgate.net/publication/328581758

The rapid emergence of high-dimensional data in various areas has brought new challenges to current ensemble clustering research. To deal with the curse of dimensionality, recently considerable efforts in ensemble clustering have been made by means of different subspace-based techniques. However, besides the emphasis on subspaces, rather limited attention has been paid to the potential diversity in similarity/dissimilarity metrics. It remains a surprisingly open problem in ensemble clustering how to create and aggregate a large population of diversified metrics, and furthermore, how to jointly investigate the multi-level diversity in the large populations of metrics, subspaces, and clusters in a unified framework. To tackle this problem, this paper proposes a novel multidiversified ensemble clustering approach. In particular, we create a large number of diversified metrics by randomizing a scaled exponential similarity kernel, which are then coupled with random subspaces to form a large set of metric-subspace pairs. Based on the similarity matrices derived from these metric-subspace pairs, an ensemble of diversified base clusterings can thereby be constructed. Further, an entropy-based criterion is utilized to explore the cluster-wise diversity in ensembles, based on which three specific ensemble clustering algorithms are presented by incorporating three types of consensus functions. Extensive experiments are conducted on 30 high-dimensional datasets, including 18 cancer gene expression datasets and 12 image/speech datasets, which demonstrate the superiority of our algorithms over the state-of-the-art. The source code is available at https://github.com/huangdonghere/MDEC., Comment: Accepted by IEEE Transactions on Cybernetics. The MATLAB source code is available at https://github.com/huangdonghere/MDEC

Classification is one of the most popular and widely used supervised learning tasks, which categorizes objects into predefined classes based on known knowledge. Classification has been an important research topic in machine learning and data mining. Different classification methods have been proposed and applied to deal with various real-world problems. Unlike unsupervised learning such as clustering, a classifier is typically trained with labeled data before being used to make prediction, and usually achieves higher accuracy than unsupervised one. In this paper, we first define classification and then review several representative methods. After that, we study in details the application of classification to a critical problem in drug discovery, i.e., drug-target prediction, due to the challenges in predicting possible interactions between drugs and targets.