Predicting G protein-coupled receptor (GPCR) -ligand binding affinity plays a crucial role in drug development. However, determining GPCR-ligand binding affinities is time-consuming and resource-intensive. Although many studies used data-driven methods to predict binding affinity, most of these methods required protein 3D structure, which was often unknown. Moreover, part of these studies only considered the sequence characteristics of the protein, ignoring the secondary structure of the protein. The number of known GPCR for affinity prediction is only a few thousand, which is insufficient for deep learning training. Therefore, this study aimed to propose a deep transfer learning method called TrGPCR, which used dynamic transfer learning to solve the problem of insufficient GPCR data. We used the Binding Database (BindingDB) as the source domain and the GLASS (GPCR-Ligand Association) database as the target domain. We also introduced protein secondary structures, called pockets, as features to predict binding affinities. Compared with DeepDTA, our model improved by 5.2% on RMSE (root mean square error) and 4.5% on MAE (mean squared error).

The accurate prediction of drug-target affinity (DTA) is a crucial step in drug discovery and design. Traditional experiments are very expensive and time-consuming. Recently, deep learning methods have achieved notable performance improvements in DTA prediction. However, one challenge for deep learning-based models is appropriate and accurate representations of drugs and targets, especially the lack of effective exploration of target representations. Another challenge is how to comprehensively capture the interaction information between different instances, which is also important for predicting DTA. In this study, we propose AttentionMGT-DTA, a multi-modal attention-based model for DTA prediction. AttentionMGT-DTA represents drugs and targets by a molecular graph and binding pocket graph, respectively. Two attention mechanisms are adopted to integrate and interact information between different protein modalities and drug-target pairs. The experimental results showed that our proposed model outperformed state-of-the-art baselines on two benchmark datasets. In addition, AttentionMGT-DTA also had high interpretability by modeling the interaction strength between drug atoms and protein residues. Our code is available at https://github.com/JK-Liu7/AttentionMGT-DTA.

The sequential recommendation, which models sequential behavioral patterns among users for the recommendation, plays a critical role in recommender systems. However, the state-of-the-art Recurrent Neural Networks (RNN) solutions rarely consider the non-linear feature interactions and non-monotone short-term sequential patterns, which are essential for user behavior modeling in sparse sequence data. In this paper, we propose a novel Recurrent Convolutional Neural Network model (RCNN). It not only utilizes the recurrent architecture of RNN to capture complex long-term dependencies, but also leverages the convolutional operation of Convolutional Neural Network (CNN) model to extract short-term sequential patterns among recurrent hidden states. Specifically, we first generate a hidden state at each time step with the recurrent layer. Then the recent hidden states are regarded as an “image”, and RCNN searches non-linear feature interactions and non-monotone local patterns via intra-step horizontal and inter-step vertical convolutional filters, respectively. Moreover, the output of convolutional filters and the hidden state are concatenated and fed into a fully-connected layer to generate the recommendation. Finally, we evaluate the proposed model using four real-world datasets from various application scenarios. The experimental results show that our model RCNN significantly outperforms the state-of-the-art approaches on sequential recommendation.

Multi-label active learning for image classification has been a popular research topic. It faces several challenges, even though related work has made great progress. Existing studies on multi-label active learning do not pay attention to the cleanness of sample data. In reality, data are easily polluted by external influences that are likely to disturb the exploration of data space and have a negative effect on model training. Previous methods of label correlation mining, which are purely based on observed label distribution, are defective. Apart from neglecting noise influence, they also cannot acquire sufficient relevant information. In fact, they neglect inner relation mapping from example space to label space, which is an implicit way of modeling label relationships. To solve these issues, we develop a novel multi-label active learning with low-rank application (ENMAL) algorithm in this paper. A low-rank model is constructed to quantize noise level, and the example-label pairs that contain less noise are emphasized when sampling. A low-rank mapping matrix is learned to signify the mapping relation of a multi-label domain to capture a more comprehensive and reasonable label correlation. Integrating label correlation with uncertainty and considering sample noise, an efficient sampling strategy is developed. We extend ENMAL with automatic labeling (denoted as AL-ENMAL) to further reduce the annotation workload of active learning. Empirical research demonstrates the efficacy of our approaches.

In multi-label image classification, each image is always associated with multiple labels and labels are usually correlated with each other. The intrinsic relation among labels can definitely contribute to classifier training. However, most previous studies on active learning for multi-label image classification purely mine label correlation based on observed label distribution. They ignore the mapping relation between examples and their labels. This mapping relation also implicates label relationship. Ignoring the mapping relation leads to an uncomprehensive label correlation estimation and results in a bad performance for classification. In this paper, we propose a novel multi-label active learning with low-rank mapping for image classification, called LMMAL, to solve this issue. More precisely, we train a low-rank mapping matrix to signify the mapping relation between the feature space and the label space of a certain multi-label dataset. Using this low-rank mapping relation, we exploit a full label correlation. Subsequently, an effective sampling strategy is designed by integrating this potential information with uncertainty to select the most informative example-label pairs. In addition, we extend LMMAL with automatic labeling (denoted as AL-LMMAL) to further reduce the annotation workload of active learning. Empirical results demonstrate the effectiveness of our approaches.

Multi-label active learning for image classification has attracted great attention over recent years and a lot of relevant works are published continuously. However, there still remain some problems that need to be solved, such as existing multi-label active learning algorithms do not reflect on the cleanness of sample data and their ways on label correlation mining are defective. For one thing, sample data is usually contaminated in reality, which disturbs the estimation of data distribution and further hinders the model training. For another, previous approaches for label relationship exploration are purely based on the observed label distribution of an incomplete training set, which cannot provide sufficiently efficient information. To address these issues, we propose a novel adaptive low-rank multi-label active learning algorithm, called LRMAL. Specifically, we first use low-rank matrix recovery to learn an effective low-rank feature representation from the noisy data. In a subsequent sampling phase, we make use of its superiorities to evaluate the general informativeness of each unlabeled example-label pair. Based on an intrinsic mapping relation between the example space and the label space of a certain multi-label dataset, we recover the incomplete labels of a training set for a more comprehensive label correlation mining. Furthermore, to reduce the redundancy among the selected example-label pairs, we use a diversity measurement to diversify the sampled data. Finally, an effective sampling strategy is developed by integrating these two aspects of potential information with uncertainty based on an adaptive integration scheme. Experimental results demonstrate the effectiveness of our approach.

Multi‐label image classification has attracted considerable attention in machine learning recently. Active learning is widely used in multi‐label learning because it can effectively reduce the human annotation workload required to construct high‐performance classifiers. However, annotation by experts is costly, especially when the number of labels in a dataset is large. Inspired by the idea of semi‐supervised learning, in this study, the authors propose a novel, semi‐supervised multi‐label active learning (SSMAL) method that combines automated annotation with human annotation to reduce the annotation workload associated with the active learning process. In SSMAL, they capture three aspects of potentially useful information – classification prediction information, label correlation information, and example spatial information – and they use this information to develop an effective strategy for automated annotation of selected unlabelled example‐label pairs. The experimental results obtained in this study demonstrate the effectiveness of the authors' proposed approach.

Multilabel image classification has been a hot topic in the field of computer vision and image understanding in recent years. To achieve better classification performance with fewer labeled images, multilabel active learning is used for this scenario. Several active learning methods have been proposed for multilabel image classification. However, all of them assume that either all training images have complete labels or label correlations are given at the beginning. These two assumptions are unrealistic. In fact, it is very difficult to obtain complete labels for each example, in particular when the size of labels in a multilabel dataset is very large. Typically, only partial labels are available. This is one type of “weak label” problem. To solve this weak label problem inside multilabel active learning, this paper proposes a novel solution called AE-WLMAL. AE-WLMAL explores conditional label correlations on the weak label problem with the help of input features and then utilizes label correlations to construct a unified sampling strategy and evaluate the informativeness of each example-label pair in a multilabel dataset for active sampling. In addition, a pruning strategy is adopted to further improve its computation efficiency. Moreover, AE-WLAML exploits label correlations to infer labels for unlabeled images, which further reduces human labeling cost. Our experimental results on seven real-world datasets show that AE-WLMAL consistently outperforms existing approaches.

Image classification is a hot topic of pattern recognition in computer vision. In order to achieve high accuracy of classification, a certain amount of high quality pictures are needed. As a matter of fact, high quality pictures are scarce. Active learning can solve such a problem. Label dependences play an important role in multi-label active learning for image classification. The interdependences between different labels are usually different and asymmetrical. This paper first brings the asymmetrical conditional label dependences into a novel active learning method for multi-label image classification based on the asymmetrical conditional label dependence, called ACDAL. Our extensive experimental results on three image and two non-image datasets show that our new approach ACDAL significantly outperforms existing approaches.

Learning from imbalanced multilabel data is a challenging task. It has attracted considerable attention recently. In this paper we propose a MultiLabel Best First Over-sampling (ML-BFO) to improve the performance of multilabel classification algorithms, based on imbalance minimization and Wilson's ENN rule. Our experimental results show that ML-BFO not only duplicates fewer samples but also reduces the imbalance level much more than two state-of-the-art multilabel sampling methods, i.e., an over-sampling method LP-ROS and an under-sampling method MLeNN. Besides, ML-BFO significantly improves the performance of multilabel classification algorithms, and performs much better than LP-ROS and MLeNN.

Label correlation analysis is very important for multi-label classification. And there is no study to measure the label correlation for example-label based active learning. In this paper, from a statistical point of view, we proposed a cosine similarity based multi-label active learning (CosMAL), which uses cosine similarity to accurately evaluate the correlations between all labels. It further uses the average correlation between the potential label and the other unlabeled labels as the label information for each sample-label pair. And then we select the most informativeness example-label pairs. Our empirical results demonstrate that our proposed method CosMAL outperforms the state-of-the-art active learning for multi-label classification. It significantly reduces the labeling workload and improves the performance of a classifier learned.

Active learning is to select the most informative examples to request their labels. Most previous studies in active learning for multi-label classification didn't pay enough attention on label correlations. This leads to a bad performance for classification. In this paper, we proposed a chi-square statistics multi-label active learning (CSMAL) algorithm, which uses chi-square statistics to accurately evaluate correlations between labels. CSMAL considers not only positive relationships but also negative ones. It uses the average correlation between a potential label and its rest unlabeled labels as the label information for each sample-label pair. CSMAL further integrates uncertainty and label information to select example-label pairs to request labels. Our empirical results demonstrate that our proposed method CSMAL outperforms the state-of-the-art active learning methods for multi-label classification. It significantly reduces the labeling workloads and improves the performance of a classifier built.

In order to achieve better classification performance with even fewer labeled images, active learning is suitable for these situations. Several active learning methods have been proposed for multi-label image classification, but all of them assume that all training images with complete labels. However, as a matter of fact, it is very difficult to get complete labels for each example, especially when the size of labels in a multi-label domain is huge. Usually, only partial labels are available. This is one kind of "weak label" problems. This paper proposes an ingeniously solution to this "weak label" problem on multi-label active learning for image classification (called WLMAL). It explores label correlation on the weak label problem with the help of input features, and then utilizes label correlation to evaluate the informativeness of each example-label pair in a multi-label dataset for active sampling. Our experimental results on three real-world datasets show that our proposed approach WLMAL consistently outperforms existing approaches significantly.

Multi-label image data is becoming ubiquitous. Image semantic understanding is typically formulated as a classification problem. This paper focuses on multi-label active learning for image classification. It first extends a traditional example based active learning method for multilabel active learning for image classification. Since the traditional example based active method doesn't work well, we propose a novel example-label based multi-label active learning method. Our experimental results on two image datasets demonstrate that the proposed method significantly reduces the labeling workload and improves the performance of the built classifier. Additionally, we conduct experiments on two other types of multi-label datasets for validating the versatility of our proposed method, and the experimental results show the consistent effect.