Motivated by applications in protein function prediction, we consider a challenging supervised classification setting in which positive labels are scarce and there are no explicit negative labels. The learning algorithm must thus select which unlabeled examples to use as negative training points, possibly ending up with an unbalanced learning problem. We address these issues by proposing an algorithm that combines active learning (for selecting negative examples) with imbalance-aware learning (for mitigating the label imbalance). In our experiments we observe that these two techniques operate synergistically, outperforming state-of-the-art methods on standard protein function prediction benchmarks.
Positive Unlabeled (PU) learning is widely used in many applications, where a binary classifier is trained on the datasets consisting of only positive and unlabeled samples. In this paper, we improve PU learning over state-of-the-art from two aspects. Firstly, existing model evaluation methods for PU learning requires ground truth of unlabeled samples, which is unlikely to be obtained in practice. In order to release this restriction, we propose an asymptotic unbiased practical AUL (area under the lift) estimation method, which makes use of raw PU data without prior knowledge of unlabeled samp…
Uncertainty-aware Pseudo-label Selection for Positive-Unlabeled Learning
Ludwig-Maximilians-Universität München（慕尼黑大学）；Helmholtz Zentrum München—German Research Center for Environmental Health（亥姆霍兹慕尼黑中心——德国环境健康研究中心）；Munich Center for Machine Learning（慕尼黑机器学习中心）；Fraunhofer Institute for Integrated Circuits IIS（弗劳恩霍夫集成电路研究所）；Technical University of Munich（慕尼黑工业大学）
Existing semi-supervised learning (SSL) algorithms typically assume class-balanced datasets, although the class distributions of many real-world datasets are imbalanced. In general, classifiers trained on a class-imbalanced dataset are biased toward the majority classes. This issue becomes more problematic for SSL algorithms because they utilize the biased prediction of unlabeled data for training. However, traditional class-imbalanced learning techniques, which are designed for labeled data, cannot be readily combined with SSL algorithms. We propose a scalable class-imbalanced SSL algorithm t…
Learning from positive and unlabeled (PU) data is a setting where the learner only has access to positive and unlabeled samples while having no information on negative examples. Such PU setting is of great importance in various tasks such as medical diagnosis, social network analysis, financial markets analysis, and knowledge base completion, which also tend to be intrinsically imbalanced, i.e., where most examples are actually negatives. Most existing approaches for PU learning, however, only consider artificially balanced datasets and it is unclear how well they perform in the realistic scen…
Transductive graph-based semi-supervised learning methods usually build an undirected graph utilizing both labeled and unlabeled samples as vertices. Those methods propagate label information of labeled samples to neighbors through their edges in order to get the predicted labels of unlabeled samples. Most popular semi-supervised learning approaches are sensitive to initial label distribution happened in imbalanced labeled datasets. The class boundary will be severely skewed by the majority classes in an imbalanced classification. In this paper, we proposed a simple and effective approach to a…
Korea Advanced Institute of Science and Technology (KAIST)（韩国科学技术院）；Samsung Advanced Institute of Technology（三星综合技术院）；AItrics
While semi-supervised learning (SSL) has proven to be a promising way for leveraging unlabeled data when labeled data is scarce, the existing SSL algorithms typically assume that training class distributions are balanced. However, these SSL algorithms trained under imbalanced class distributions can severely suffer when generalizing to a balanced testing criterion, since they utilize biased pseudo-labels of unlabeled data toward majority classes. To alleviate this issue, we formulate a convex optimization problem to softly refine the pseudo-labels generated from the biased model, and develop a…
Data imbalance is a ubiquitous problem in machine learning. In large scale collected and annotated datasets, data imbalance is either mitigated manually by undersampling frequent classes and oversampling rare classes, or planned for with imputation and augmentation techniques. In both cases balancing data requires labels. In other words, only annotated data can be balanced. Collecting fully annotated datasets is challenging, especially for large scale satellite systems such as the unlabeled NASA's 35 PB Earth Imagery dataset. Although the NASA Earth Imagery dataset is unlabeled, there are impl…
RIKEN Center for Advanced Intelligence Project（理化学研究所先进智能中心）；Center for Artificial Intelligence, University of Technology Sydney（悉尼科技大学人工智能中心）；University of Tokyo（东京大学）
In the early history of positive-unlabeled (PU) learning, the sample selection approach, which heuristically selects negative (N) data from U data, was explored extensively. However, this approach was later dominated by the importance reweighting approach, which carefully treats all U data as N data. May there be a new sample selection method that can outperform the latest importance reweighting method in the deep learning age? This paper is devoted to answering this question affirmatively---we propose to label large-loss U data as P, based on the memorization properties of deep networks. Sinc…
From only positive (P) and unlabeled (U) data, a binary classifier could be trained with PU learning, in which the state of the art is unbiased PU learning. However, if its model is very flexible, empirical risks on training data will go negative, and we will suffer from serious overfitting. In this paper, we propose a non-negative risk estimator for PU learning: when getting minimized, it is more robust against overfitting, and thus we are able to use very flexible models (such as deep neural networks) given limited P data. Moreover, we analyze the bias, consistency, and mean-squared-error re…
The University of Tokyo（东京大学）；Boston University（波士顿大学）；RIKEN（日本理化学研究所）
In PU learning, a binary classifier is trained from positive (P) and unlabeled (U) data without negative (N) data. Although N data is missing, it sometimes outperforms PN learning (i.e., ordinary supervised learning). Hitherto, neither theoretical nor experimental analysis has been given to explain this phenomenon. In this paper, we theoretically compare PU (and NU) learning against PN learning based on the upper bounds on estimation errors. We find simple conditions when PU and NU learning are likely to outperform PN learning, and we prove that, in terms of the upper bounds, either PU or NU l…
École Normale Supérieure（巴黎高等师范学院）；RIKEN（理化学研究所）；The University of Tokyo（东京大学）
In binary classification, there are situations where negative (N) data are too diverse to be fully labeled and we often resort to positive-unlabeled (PU) learning in these scenarios. However, collecting a non-representative N set that contains only a small portion of all possible N data can often be much easier in practice. This paper studies a novel classification framework which incorporates such biased N (bN) data in PU learning. We provide a method based on empirical risk minimization to address this PUbN classification problem. Our approach can be regarded as a novel example-weighting alg…
Peking University（北京大学）；The University of Sydney（悉尼大学）；Huawei Noah’s Ark Lab（华为诺亚方舟实验室）；Peng Cheng Laboratory（鹏城实验室）
This paper defines a positive and unlabeled classification problem for standard GANs, which then leads to a novel technique to stabilize the training of the discriminator in GANs. Traditionally, real data are taken as positive while generated data are negative. This positive-negative classification criterion was kept fixed all through the learning process of the discriminator without considering the gradually improved quality of generated data, even if they could be more realistic than real data at times. In contrast, it is more reasonable to treat the generated data as unlabeled, which could …
Learning from positive and unlabeled data (PU learning) is prevalent in practical applications where only a couple of examples are positively labeled. Previous PU learning studies typically rely on existing samples such that the data distribution is not extensively explored. In this work, we propose a simple yet effective data augmentation method, coined~\algo, based on \emph{consistency regularization} which provides a new perspective of using PU data. In particular, the proposed~\algo~incorporates supervised and unsupervised consistency training to generate augmented data. To facilitate supe…
Positive-unlabeled (PU) learning trains a binary classifier using only positive and unlabeled data. A common simplifying assumption is that the positive data is representative of the target positive class. This assumption rarely holds in practice due to temporal drift, domain shift, and/or adversarial manipulation. This paper shows that PU learning is possible even with arbitrarily non-representative positive data given unlabeled data from the source and target distributions. Our key insight is that only the negative class's distribution need be fixed. We integrate this into two statistically …
The capability of the traditional semi-supervised learning (SSL) methods is far from real-world application due to severely biased pseudo-labels caused by (1) class imbalance and (2) class distribution mismatch between labeled and unlabeled data. This paper addresses such a relatively under-explored problem. First, we propose a general pseudo-labeling framework that class-adaptively blends the semantic pseudo-label from a similarity-based classifier to the linear one from the linear classifier, after making the observation that both types of pseudo-labels have complementary properties in terms…
Pseudo-labels are confident predictions made on unlabeled target data by a classifier trained on labeled source data. They are widely used for adapting a model to unlabeled data, e.g., in a semi-supervised learning setting. Our key insight is that pseudo-labels are naturally imbalanced due to intrinsic data similarity, even when a model is trained on balanced source data and evaluated on balanced target data. If we address this previously unknown imbalanced classification problem arising from pseudo-labels instead of ground-truth training labels, we could remove model biases towards false majo…
People learn to discriminate between classes without explicit exposure to negative examples. On the contrary, traditional machine learning algorithms often rely on negative examples, otherwise the model would be prone to collapse and always-true predictions. Therefore, it is crucial to design the learning objective which leads the model to converge and to perform predictions unbiasedly without explicit negative signals. In this paper, we propose a Collectively loss function to learn from only Positive and Unlabeled data (cPU). We theoretically elicit the loss function from the setting of PU le…
Graduate School of Frontier Sciences, The University of Tokyo（东京大学前沿科学研究生院）；Center for Advanced Intelligence Project, RIKEN（理化学研究所高级智能项目中心）
Maximizing the area under the receiver operating characteristic curve (AUC) is a standard approach to imbalanced classification. So far, various supervised AUC optimization methods have been developed and they are also extended to semi-supervised scenarios to cope with small sample problems. However, existing semi-supervised AUC optimization methods rely on strong distributional assumptions, which are rarely satisfied in real-world problems. In this paper, we propose a novel semi-supervised AUC optimization method that does not require such restrictive assumptions. We first develop an AUC opti…
The recently proposed unlabeled-unlabeled (UU) classification method allows us to train a binary classifier only from two unlabeled datasets with different class priors. Since this method is based on the empirical risk minimization, it works as if it is a supervised classification method, compatible with any model and optimizer. However, this method sometimes suffers from severe overfitting, which we would like to prevent in this paper. Our empirical finding in applying the original UU method is that overfitting often co-occurs with the empirical risk going negative, which is not legitimate. T…
A common approach in positive-unlabeled learning is to train a classification model between labeled and unlabeled data. This strategy is in fact known to give an optimal classifier under mild conditions; however, it results in biased empirical estimates of the classifier performance. In this work, we show that the typically used performance measures such as the receiver operating characteristic curve, or the precision-recall curve obtained on such data can be corrected with the knowledge of class priors; i.e., the proportions of the positive and negative examples in the unlabeled data. We exte…
National Research University Higher School of Economics（国立研究型大学高等经济学院）；JetBrains Research（JetBrains研究院）
Positive-Unlabeled (PU) learning is an analog to supervised binary classification for the case when only the positive sample is clean, while the negative sample is contaminated with latent instances of positive class and hence can be considered as an unlabeled mixture. The objectives are to classify the unlabeled sample and train an unbiased PN classifier, which generally requires to identify the mixing proportions of positives and negatives first. Recently, unbiased risk estimation framework has achieved state-of-the-art performance in PU learning. This approach, however, exhibits two major b…
MIT（麻省理工学院）；University of Chicago（芝加哥大学）；Pennsylvania State University（宾夕法尼亚州立大学）
Datacenters execute large computational jobs, which are composed of smaller tasks. A job completes when all its tasks finish, so stragglers -- rare, yet extremely slow tasks -- are a major impediment to datacenter performance. Accurately predicting stragglers would enable proactive intervention, allowing datacenter operators to mitigate stragglers before they delay a job. While much prior work applies machine learning to predict computer system performance, these approaches rely on complete labels -- i.e., sufficient examples of all possible behaviors, including straggling and non-straggling -…
Data imbalance remains one of the factors negatively affecting the performance of contemporary machine learning algorithms. One of the most common approaches to reducing the negative impact of data imbalance is preprocessing the original dataset with data-level strategies. In this paper we propose a unified framework for imbalanced data over- and undersampling. The proposed approach utilizes radial basis functions to preserve the original shape of the underlying class distributions during the resampling process. This is done by optimizing the positions of generated synthetic observations with …
Many pairwise classification tasks, such as paraphrase detection and open-domain question answering, naturally have extreme label imbalance (e.g., $99.99\%$ of examples are negatives). In contrast, many recent datasets heuristically choose examples to ensure label balance. We show that these heuristics lead to trained models that generalize poorly: State-of-the art models trained on QQP and WikiQA each have only $2.4\%$ average precision when evaluated on realistically imbalanced test data. We instead collect training data with active learning, using a BERT-based embedding model to efficiently…
University of Chinese Academy of Sciences（中国科学院大学）；Institute of Computing Technology, CAS（中国科学院计算技术研究所）；Institute of Information Engineering, CAS（中国科学院信息工程研究所）
Positive-Unlabeled (PU) learning tries to learn binary classifiers from a few labeled positive examples with many unlabeled ones. Compared with ordinary semi-supervised learning, this task is much more challenging due to the absence of any known negative labels. While existing cost-sensitive-based methods have achieved state-of-the-art performances, they explicitly minimize the risk of classifying unlabeled data as negative samples, which might result in a negative-prediction preference of the classifier. To alleviate this issue, we resort to a label distribution perspective for PU learning in…
King Abdullah University of Science and Technology（阿卜杜拉国王科技大学）；Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）；Institute of Artificial Intelligence, Beihang University（北京航空航天大学人工智能研究院）；School of Computer Science, Beihang University（北京航空航天大学计算机学院）；University of Notre Dame（圣母大学）
Most real-world knowledge graphs (KG) are far from complete and comprehensive. This problem has motivated efforts in predicting the most plausible missing facts to complete a given KG, i.e., knowledge graph completion (KGC). However, existing KGC methods suffer from two main issues, 1) the false negative issue, i.e., the sampled negative training instances may include potential true facts; and 2) the data sparsity issue, i.e., true facts account for only a tiny part of all possible facts. To this end, we propose positive-unlabeled learning with adversarial data augmentation (PUDA) for KGC. In …
We study the problem of learning from positive and unlabeled (PU) data in the federated setting, where each client only labels a little part of their dataset due to the limitation of resources and time. Different from the settings in traditional PU learning where the negative class consists of a single class, the negative samples which cannot be identified by a client in the federated setting may come from multiple classes which are unknown to the client. Therefore, existing PU learning methods can be hardly applied in this situation. To address this problem, we propose a novel framework, name…
University of Rochester（罗切斯特大学）；Baylor College of Medicine（贝勒医学院）；University of Texas Health Science Center at Houston（休斯顿德克萨斯大学健康科学中心）；University of Washington（华盛顿大学）
The positive-unlabeled (PU) classification is a common scenario in real-world applications such as healthcare, text classification, and bioinformatics, in which we only observe a few samples labeled as "positive" together with a large volume of "unlabeled" samples that may contain both positive and negative samples. Building robust classifier for the PU problem is very challenging, especially for complex data where the negative samples overwhelm and mislabeled samples or corrupted features exist. To address these three issues, we propose a robust learning framework that unifies AUC maximizatio…
Huawei Noah’s Ark Lab（华为诺亚方舟实验室）；Peking University（北京大学）；The University of Sydney（悉尼大学）
Many attempts have been done to extend the great success of convolutional neural networks (CNNs) achieved on high-end GPU servers to portable devices such as smart phones. Providing compression and acceleration service of deep learning models on the cloud is therefore of significance and is attractive for end users. However, existing network compression and acceleration approaches usually fine-tuning the svelte model by requesting the entire original training data (\eg ImageNet), which could be more cumbersome than the network itself and cannot be easily uploaded to the cloud. In this paper, w…
Learning binary classifiers only from positive and unlabeled (PU) data is an important and challenging task in many real-world applications, including web text classification, disease gene identification and fraud detection, where negative samples are difficult to verify experimentally. Most recent PU learning methods are developed based on the conventional misclassification risk of the supervised learning type, and they require to solve the intractable risk estimation problem by approximating the negative data distribution or the class prior. In this paper, we introduce a variational principl…
Stanford University（斯坦福大学）；Toyota Research Institute（丰田研究所）
Self-supervised learning (SSL) is a scalable way to learn general visual representations since it learns without labels. However, large-scale unlabeled datasets in the wild often have long-tailed label distributions, where we know little about the behavior of SSL. In this work, we systematically investigate self-supervised learning under dataset imbalance. First, we find out via extensive experiments that off-the-shelf self-supervised representations are already more robust to class imbalance than supervised representations. The performance gap between balanced and imbalanced pre-training with…
Cost-Sensitive Unbiased Risk Estimation for Multi-Class Positive-Unlabeled Learning
Engineering Research Center of the Ministry of Education for Intelligent Control System and Intelligent Equipment, Yanshan University, Qinhuangdao, China（教育部智能控制与智能装备工程研究中心，燕山大学，秦皇岛，中国）
The University of Queensland（昆士兰大学）；The University of Adelaide（阿德莱德大学）；RIKEN（理化学研究所）
Positive-unlabeled (PU) learning deals with binary classification problems when only positive (P) and unlabeled (U) data are available. Many recent PU methods are based on neural networks, but little has been done to develop boosting algorithms for PU learning, despite boosting algorithms' strong performance on many fully supervised classification problems. In this paper, we propose a novel boosting algorithm, AdaPU, for PU learning. Similarly to AdaBoost, AdaPU aims to optimize an empirical exponential loss, but the loss is based on the PU data, rather than on positive-negative (PN) data. As …
The University of Sydney（悉尼大学）；Hong Kong Baptist University（香港浸会大学）；The University of Melbourne（墨尔本大学）；RIKEN AIP（理化学研究所先进智能项目中心）；The University of Tokyo（东京大学）；JD Explore Academy（京东探索研究院）
Given only positive (P) and unlabeled (U) data, PU learning can train a binary classifier without any negative data. It has two building blocks: PU class-prior estimation (CPE) and PU classification; the latter has been well studied while the former has received less attention. Hitherto, the distributional-assumption-free CPE methods rely on a critical assumption that the support of the positive data distribution cannot be contained in the support of the negative data distribution. If this is violated, those CPE methods will systematically overestimate the class prior; it is even worse that we…
Class imbalanced datasets are common in real-world applications that range from credit card fraud detection to rare disease diagnostics. Several popular classification algorithms assume that classes are approximately balanced, and hence build the accompanying objective function to maximize an overall accuracy rate. In these situations, optimizing the overall accuracy will lead to highly skewed predictions towards the majority class. Moreover, the negative business impact resulting from false positives (positive samples incorrectly classified as negative) can be detrimental. Many methods have b…
Learning from positive and unlabeled data or PU learning is the setting where a learner only has access to positive examples and unlabeled data. The assumption is that the unlabeled data can contain both positive and negative examples. This setting has attracted increasing interest within the machine learning literature as this type of data naturally arises in applications such as medical diagnosis and knowledge base completion. This article provides a survey of the current state of the art in PU learning. It proposes seven key research questions that commonly arise in this field and provides …
University of Hildesheim（希尔德斯海姆大学）；Volkwagen Financial Services（大众金融服务）
Domain Adaptation methodologies have shown to effectively generalize from a labeled source domain to a label scarce target domain. Previous research has either focused on unlabeled domain adaptation without any target supervision or semi-supervised domain adaptation with few labeled target examples per class. On the other hand Positive-Unlabeled (PU-) Learning has attracted increasing interest in the weakly supervised learning literature since in quite some real world applications positive labels are much easier to obtain than negative ones. In this work we are the first to introduce the chall…
Semi-supervised learning (SSL) is the branch of machine learning that aims to improve learning performance by leveraging unlabeled data when labels are insufficient. Recently, SSL with deep models has proven to be successful on standard benchmark tasks. However, they are still vulnerable to various robustness threats in real-world applications as these benchmarks provide perfect unlabeled data, while in realistic scenarios, unlabeled data could be corrupted. Many researchers have pointed out that after exploiting corrupted unlabeled data, SSL suffers severe performance degradation problems. Th…
IBM Research（IBM研究院）；University of Texas at Austin（德克萨斯大学奥斯汀分校）；University of Rochester（罗切斯特大学）
Identifying significant location categories visited by mobile users is the key to a variety of applications. This is an extremely challenging task due to the possible deviation between the estimated location coordinate and the actual location, which could be on the order of kilometers. To estimate the actual location category more precisely, we propose a novel tensor factorization framework, through several key observations including the intrinsic correlations between users, to infer the most likely location categories within the location uncertainty circle. In addition, the proposed algorithm…
University of Michigan（密歇根大学）；Syracuse University（雪城大学）
In supervised machine learning for author name disambiguation, negative training data are often dominantly larger than positive training data. This paper examines how the ratios of negative to positive training data can affect the performance of machine learning algorithms to disambiguate author names in bibliographic records. On multiple labeled datasets, three classifiers - Logistic Regression, Naïve Bayes, and Random Forest - are trained through representative features such as coauthor names, and title words extracted from the same training data but with various positive-negative training d…
We consider the problem of estimating the class prior in an unlabeled dataset. Under the assumption that an additional labeled dataset is available, the class prior can be estimated by fitting a mixture of class-wise data distributions to the unlabeled data distribution. However, in practice, such an additional labeled dataset is often not available. In this paper, we show that, with additional samples coming only from the positive class, the class prior of the unlabeled dataset can be estimated correctly. Our key idea is to use properly penalized divergences for model fitting to cancel the er…
Bottlenecks of binary classification from positive and unlabeled data (PU classification) are the requirements that given unlabeled patterns are drawn from the test marginal distribution, and the penalty of the false positive error is identical to the false negative error. However, such requirements are often not fulfilled in practice. In this paper, we generalize PU classification to the class prior shift and asymmetric error scenarios. Based on the analysis of the Bayes optimal classifier, we show that given a test class prior, PU classification under class prior shift is equivalent to PU cl…
AllMatch: Exploiting All Unlabeled Data for Semi-Supervised Learning
National Key Laboratory of General Artificial Intelligence（通用人工智能国家重点实验室）；School of Intelligence Science and Technology, Peking University（北京大学智能科学与技术学院）
Ludwig Maximilian Universität München（路德维希-马克西米利安-慕尼黑大学）；Helmholtz Zentrum München（慕尼黑亥姆霍兹中心）；Technical University of Munich（慕尼黑工业大学）
Accurate in silico modeling of the antigen processing pathway is crucial to enable personalized epitope vaccine design for cancer. An important step of such pathway is the degradation of the vaccine into smaller peptides by the proteasome, some of which are going to be presented to T cells by the MHC complex. While predicting MHC-peptide presentation has received a lot of attention recently, proteasomal cleavage prediction remains a relatively unexplored area in light of recent advancesin high-throughput mass spectrometry-based MHC ligandomics. Moreover, as such experimental techniques do not …
Angular Regularization for Positive-Unlabeled Learning on the Hypersphere
Athena RC Democritus University of Thrace（阿塔尼亚RC德摩克利特大学）；Athena RC University Campus Kimmeria（阿塔尼亚RC大学校园基米里亚）；Democritus University of Thrace Dept. Production and Management Engineering（德摩克利特大学生产与管理工程系）
Laboratoire Hubert Curien UMR 5516（于贝尔·居里安实验室 UMR 5516）；Univ Lyon（里昂大学）；UJM（让·莫内大学）
A key element of any machine learning algorithm is the use of a function that measures the dis/similarity between data points. Given a task, such a function can be optimized with a metric learning algorithm. Although this research field has received a lot of attention during the past decade, very few approaches have focused on learning a metric in an imbalanced scenario where the number of positive examples is much smaller than the negatives. Here, we address this challenging task by designing a new Mahalanobis metric learning algorithm (IML) which deals with class imbalance. The empirical stu…
