Positive-unlabeled learning for open set domain adaptation

Conventional supervised binary classification algorithms have been widely applied to address significant research questions using biological and biomedical data. This classification scheme requires two fully labeled classes of data (e.g. positive and negative samples) to train a classification model. However, in many bioinformatics applications, labeling data is laborious, and the negative samples might be potentially mislabeled due to the limited sensitivity of the experimental equipment. The positive unlabeled (PU) learning scheme was therefore proposed to enable the classifier to learn directly from limited positive samples and a large number of unlabeled samples (i.e. a mixture of positive or negative samples). To date, several PU learning algorithms have been developed to address various biological questions, such as sequence identification, functional site characterization and interaction prediction. In this paper, we revisit a collection of 29 state-of-the-art PU learning bioinformatic applications to address various biological questions. Various important aspects are extensively discussed, including PU learning methodology, biological application, classifier design and evaluation strategy. We also comment on the existing issues of PU learning and offer our perspectives for the future development of PU learning applications. We anticipate that our work serves as an instrumental guideline for a better understanding of the PU learning framework in bioinformatics and further developing next-generation PU learning frameworks for critical biological applications.

Tax evasion detection has a crucial role in addressing tax revenue loss. In the real world, an accessed tax dataset only contains a small number of labeled taxpayers who evade tax (positive samples) and a large number of unlabeled taxpayers who either evade tax or do not evade tax. It is difficult to address this issue due to this nontraditional dataset. In addition, the basic features of taxpayers designed according to tax experts’ domain knowledge and experience are very limited to determining whether taxpayers evade tax. These limitations motivate the contribution of this work. In this paper, we argue that the tax evasion detection task in the real world should be formalized as a positive unlabeled (PU) learning problem. We propose a novel tax evasion detection method based on PU learning with Network Embedding features (PUNE). PUNE effectively detects tax evasion based on basic features and transaction network features that are extracted by a network embedding algorithm. Moreover, PUNE can work well even under label noise. To evaluate the effectiveness of PUNE, we conduct experimental tests on a real-world tax dataset. The results demonstrate that PUNE can significantly improve the performance of tax evasion detection.

Positive-unlabeled (PU) learning deals with the binary classification problem when only positive (P) and unlabeled (U) data are available, without negative (N) data. Existing PU methods perform well on the balanced dataset. However, in real applications such as financial fraud detection or medical diagnosis, data are always imbalanced. It remains unclear whether existing PU methods can perform well on imbalanced data. In this paper, we explore this problem and propose a general learning objective for PU learning targeting specially at imbalanced data. By this general learning objective, state-of-the-art PU methods based on optimizing a consistent risk can be adapted to conquer the imbalance. We theoretically show that in expectation, optimizing our learning objective is equivalent to learning a classifier on the oversampled balanced data with both P and N data available, and further provide an estimation error bound. Finally, experimental results validate the effectiveness of our proposal compared to state-of-the-art PU methods.

lncRNAs are involved in many biological processes, and their mutations and disorders are closely related to many diseases. Identification of LncRNA-Disease Associations (LDAs) helps us understand the pathogenesis of diseases and improve their diagnosis and treatment. However, experiments to determine LDAs are expensive, so it is essential to exploit effective computational methods to screen possible LDAs. In this study, we developed an LDA prediction model (LDA-DLPU) based on deep learning and positive-unlabeled (PU) learning. First, LDA-DLPU extracted features of lncRNAs and diseases based on singular value decomposition and regression model. Second, it selected negative LDAs based on PU learning and graph autoencoder. Finally, it classified unknown lncRNA-disease pairs based on deep neural network. LDA-DLPU obtained the best performance on two datasets. We predict that BCYRN1 and IFNG-AS1 may associate with leukemia.

Positive-unlabeled (PU) learning deals with the circumstances where only a portion of positive instances are labeled, while the rest and all negative instances are unlabeled, and due to this confusion, the class prior can not be directly available. Existing PU learning methods usually estimate the class prior by training a nontraditional probabilistic classifier, which is prone to give an overestimation. Moreover, these methods learn the decision boundary by optimizing the minimum margin, which is not suitable in PU learning due to its sensitivity to label noise. In this paper, we enhance PU learning methods from the above two aspects. More specifically, we first explicitly learn a transformation from unlabeled data to positive data by entropy regularized optimal transport to achieve a much more precise estimation for class prior. Then we switch to optimizing the margin distribution, rather than the minimum margin, to obtain a label noise insensitive classifier. Extensive empirical studies on both synthetic and real-world data sets demonstrate the superiority of our proposed method.

Open-set domain adaptation (OSDA) seeks to transfer knowledge from a labeled source domain to an unlabeled target domain containing novel classes. Traditional OSDA methods rarely account for the uncertainty in predictions and typically require additional training overhead. Evidential deep learning (EDL) transforms the model's predictions from point estimates to distributions over the probability simplex by replacing the standard softmax output of classification neural networks with Dirichlet distributions. Considering the presence of out-of-distribution novel classes in OSDA and the additional overhead of existing methods, we propose EDL for open-set active domain adaptation (EOSADA). Leveraging EDL, we construct an open-set classifier and employ a two-round selection strategy guided by the data uncertainty of target domain samples and semantic similarity scores with known classes. This strategy balances the selection of samples from known and novel classes while identifying informative samples, thereby maximizing the performance of the model in OSDA scenarios without modifying the model structure and utilizing a limited annotation budget. Extensive experiments demonstrate the superiority of our approach.

Deceptive reviews detection has attracted significant attention from both business and research communities. However, due to the difficulty of human labeling needed for supervised learning, the problem remains to be highly challenging. This paper proposed a novel angle to the problem by modeling PU (positive unlabeled) learning. A semi-supervised model, called mixing population and individual property PU learning (MPIPUL), is proposed. Firstly, some reliable negative examples are identified from the unlabeled dataset. Secondly, some representative positive examples and negative examples are generated based on LDA (Latent Dirichlet Allocation). Thirdly, for the remaining unlabeled examples (we call them spy examples), which can not be explicitly identified as positive and negative, two similarity weights are assigned, by which the probability of a spy example belonging to the positive class and the negative class are displayed. Finally, spy examples and their similarity weights are incorporated into SVM (Support Vector Machine) to build an accurate classifier. Experiments on gold-standard dataset demonstrate the effectiveness of MPIPUL which outperforms the state-of-the-art baselines.

Unsupervised domain adaptation (UDA) involves a supervised loss in a labeled source domain and an unsupervised loss in an unlabeled target domain, which often faces more severe overfitting (than classical supervised learning) as the supervised source loss has clear domain gap and the unsupervised target loss is often noisy due to the lack of annotations. This paper presents RDA, a robust domain adaptation technique that introduces adversarial attacking to mitigate overfitting in UDA. We achieve robust domain adaptation by a novel Fourier adversarial attacking (FAA) method that allows large magnitude of perturbation noises but has minimal modification of image semantics, the former is critical to the effectiveness of its generated adversarial samples due to the existence of ‘domain gaps’. Specifically, FAA decomposes images into multiple frequency components (FCs) and generates adversarial samples by just perturbating certain FCs that capture little semantic information. With FAA-generated samples, the training can continue the ‘random walk’ and drift into an area with a flat loss landscape, leading to more robust domain adaptation. Extensive experiments over multiple domain adaptation tasks show that RDA can work with different computer vision tasks with superior performance.

Epilepsy is a chronic disorder of the brain. Intracranial electroencephalogram (iEEG) recorded from cortex is the most popular measurement for not only the diagnosis of epilepsy, but also the focus localization that is crucial for the surgery. In recent years, the machine learning methods have been rapidly developed and applied successfully to various real world problems. Given sufficient number of samples, the powerful deep learning methods can achieve high performance for epileptic focus localization. However, it is a challenging task to obtain large amount of labeled iEEG regarding focal/non-focal channels, since the annotations must be performed by multiple clinical experts through visual judgment on the long term iEEG signals. In order to reduce the necessary number of labeled training samples, we introduce the positive unlabeled (PU) learning method for classification of focal and non-focal epileptic iEEG signals. The proposed method enables us to learn a binary classifier by using small amount of labeled data containing only one class (i.e., focal signals) and unlabeled data containing two classes (i.e., focal and non-focal signals), which greatly reduces the workload of clinical experts for annotations. Experimental results on Bern dataset and iEEG recorded from Juntendo University Hospital demonstrate the effectiveness of our method.

GCL-OSDA: Uncertainty prediction-based graph collaborative learning for open-set domain adaptation

The open set domain adaptation problem was rarely studied and its existing solutions are mostly based on learning a joint latent space which may encounter issues when the domains differ significantly from each other. This work is driven by the question whether or not it is beneficial to operate the source images to another image domain as close to the target as possible. We propose to address the open set domain adaptation problem by aligning sample at both feature space and pixel space. Our approach, called Open Set Translation and Adaptation Network (Ostan), consists of two main components: translation and adaptation. The translation model is a cycle-consistent generative adversarial network, which translates any source sample to the style of a target domain. The adaptation network is built upon OpenBP, an open set domain adaptation framework, and trained using both (labeled) translated source images and (unlabeled) target images. The proposed Ostan model significantly outperforms the state-of-the-art open set domain adaptation methods on multiple public datasets. Our experiment also demonstrates that an image-to-image translation component can further improve the decision boundaries for both known and unknown classes.

C-PUGP: A cluster-based positive unlabeled learning method for disease gene prediction and prioritization

Unsupervised domain adaptation (UDA) is an important solution to reduce the bias between the labeled source domain and the unlabeled target domain. It has attracted more attention for optical remote sensing image scene classification and retrieval. Currently, most of the previous work is devoted to closed-set UDA. In fact, the target domain often contains unknown classes. Moreover, some open UDA methods mine structural information of the target domain directly from the type knowledge of the source domain, and less directly from the unlabeled data of the target domain. In this paper, we propose a new self-supervised-driven open-set UDA method combining contrastive self-supervised learning with consistency self-training for optical remote sensing scene classification and retrieval. Specifically, a contrastive self-supervised learning network is introduced to learn discriminative features from the unlabeled target domain data. Moreover, a novel open-set class learning module is developed based on two-level confidence rules and the consistency self-training strategy, which can obtain reliable unknown class samples for co-training. Finally, an open-set dataset including six cross-domain scenarios is constructed based on three public datasets and several experiments are conducted with eleven state-of-the-art domain adaptation methods. Experimental results demonstrate that our proposed method achieves superior performances on the six open-set cross-domain scenarios in both scene classification and retrieval. Especially, our method improves the overall classification accuracies by 9.72% to 24.06% and improve mean average retrieval precisions by 8.06% to 16.21% on the complex UCMD (source domain) → NWPU (target domain) scenario, compared with the other eleven state-of-the-art methods.

A meta-learning framework using representation learning to predict drug-drug interaction

Unsupervised domain adaptation (UDA) aims to mitigate the domain shift that occurs when transferring knowledge from a labeled source domain to an unlabeled target domain. While it has been studied for application in unsupervised person re-identification (ReID), the relations of feature distribution across the source and target domains remain underexplored, as they either ignore the local relations or omit the in-depth consideration of negative transfer when two domains do not share identical label spaces. In light of the above, this paper presents an innovative part-aware progressive adaptation network (PPAN) that exploits global and local relations for UDA-based ReID across domains. A multi-branch network is developed that explicitly learns discriminative feature representation from both whole-body images and body-part images under the supervision of a labeled source domain. Within each network branch, an independent UDA constraint is designed that aligns the global and local feature distributions from a labeled source domain with those of an unlabeled target domain. In addition, a novel progressive adaptation strategy (PAS) is designed that effectively alleviates the negative influence of outlier source identities. The proposed unsupervised ReID model is evaluated on five widely used datasets (Market-1501, DukeMTMC-reID, CUHK03, VIPeR and PRID), and experimental results demonstrate its superior robustness and effectiveness relative to state-of-the-art approaches.