As experimental efforts are costly and time consuming, computational characterization of enzyme capabilities is an attractive alternative. We present and evaluate several machine-learning models to predict which of 983 distinct enzymes, as defined via the Enzyme Commission, EC, numbers, are likely to interact with a given query molecule. Our data consists of enzyme-substrate interactions from the BRENDA database. Some interactions are attributed to natural selection and involve the enzyme's natural substrates. The majority of the interactions however involve non-natural substrates, thus reflecting promiscuous enzymatic activities. We frame this enzyme promiscuity prediction problem as a multi-label classification task. We maximally utilize inhibitor and unlabelled data to train prediction models that can take advantage of known hierarchical relationships between enzyme classes. We report that a hierarchical multi-label neural network, EPP-HMCNF, is the best model for solving this problem, outperforming k-nearest neighbors similarity-based and other machine learning models. We show that inhibitor information during training consistently improves predictive power, particularly for EPP-HMCNF. We also show that all promiscuity prediction models perform worse under a realistic data split when compared to a random data split, and when evaluating performance on non-natural substrates compared to natural substrates. We provide Python code for EPP-HMCNF and other models in a repository termed EPP (Enzyme Promiscuity Prediction) at https://github.com/hassounlab/EPP.
In clinical conversational applications, extracted entities tend to capture the main subject of a patient's complaint, namely symptoms or diseases. However, they mostly fail to recognize the characterizations of a complaint such as the time, the onset, and the severity. For example, if the input is "I have a headache and it is extreme", state-of-the-art models only recognize the main symptom entity - headache, but ignore the severity factor of "extreme", that characterizes headache. In this paper, we design a two-stage approach to detect the characterizations of entities like symptoms presented by general users in contexts where they would describe their symptoms to a clinician. We use Word2Vec and BERT to encode clinical text given by the patients. We transform the output and re-frame the task as multi-label classification problem. Finally, we combine the processed encodings with the Linear Discriminant Analysis (LDA) algorithm to classify the characterizations of the main entity. Experimental results demonstrate that our method achieves 40-50% improvement on the accuracy over the state-of-the-art models.
The task of text classification is usually divided into two stages: {\it text feature extraction} and {\it classification}. In this standard formalization categories are merely represented as indexes in the label vocabulary, and the model lacks for explicit instructions on what to classify. Inspired by the current trend of formalizing NLP problems as question answering tasks, we propose a new framework for text classification, in which each category label is associated with a category description. Descriptions are generated by hand-crafted templates or using abstractive/extractive models from reinforcement learning. The concatenation of the description and the text is fed to the classifier to decide whether or not the current label should be assigned to the text. The proposed strategy forces the model to attend to the most salient texts with respect to the label, which can be regarded as a hard version of attention, leading to better performances. We observe significant performance boosts over strong baselines on a wide range of text classification tasks including single-label classification, multi-label classification and multi-aspect sentiment analysis.
Recently, several studies proposed methods to utilize some classes of optimization problems in designing deep neural networks to encode constraints that conventional layers cannot capture. However, these methods are still in their infancy and require special treatments, such as analyzing the KKT condition, for deriving the backpropagation formula. In this paper, we propose a new layer formulation called the fixed-point iteration (FPI) layer that facilitates the use of more complicated operations in deep networks. The backward FPI layer is also proposed for backpropagation, which is motivated by the recurrent back-propagation (RBP) algorithm. But in contrast to RBP, the backward FPI layer yields the gradient by a small network module without an explicit calculation of the Jacobian. In actual applications, both the forward and backward FPI layers can be treated as nodes in the computational graphs. All components in the proposed method are implemented at a high level of abstraction, which allows efficient higher-order differentiations on the nodes. In addition, we present two practical methods of the FPI layer, FPI_NN and FPI_GD, where the update operations of FPI are a small neural network module and a single gradient descent step based on a learnable cost function, respectively. FPI\_NN is intuitive, simple, and fast to train, while FPI_GD can be used for efficient training of energy networks that have been recently studied. While RBP and its related studies have not been applied to practical examples, our experiments show the FPI layer can be successfully applied to real-world problems such as image denoising, optical flow, and multi-label classification.
This paper describes an approach to the facial action units detections. The involved action units (AU) include AU1 (Inner Brow Raiser), AU2 (Outer Brow Raiser), AU4 (Brow Lowerer), AU6 (Cheek Raise), AU12 (Lip Corner Puller), AU15 (Lip Corner Depressor), AU20 (Lip Stretcher), and AU25 (Lip Part). Our work relies on the dataset released by the FG-2020 Competition: Affective Behavior Analysis In-the-Wild (ABAW). The proposed method consists of the data preprocessing, the feature extraction and the AU classification. The data preprocessing includes the detection of face texture and landmarks. The texture static and landmark dynamic features are extracted through neural networks and then fused as the feature latent representation. Finally, the fused feature is taken as the initial hidden state of a recurrent neural network with a trainable lookup AU table. The output of the RNN is the results of AU classification. The detected accuracy is evaluated with 0.5$\times$accuracy + 0.5$\times$F1. Our method achieve 0.56 with the validation data that is specified by the organization committee.
Existing simulations designed for cultural and interpersonal skill training rely on pre-defined responses with a menu option selection interface. Using a multiple-choice interface and restricting trainees' responses may limit the trainees' ability to apply the lessons in real life situations. This systems also uses a simplistic evaluation model, where trainees' selected options are marked as either correct or incorrect. This model may not capture sufficient information that could drive an adaptive feedback mechanism to improve trainees' cultural awareness. This paper describes the design of a dialogue-based simulation for cultural awareness training. The simulation, built around a disaster management scenario involving a joint coalition between the US and the Chinese armies. Trainees were able to engage in realistic dialogue with the Chinese agent. Their responses, at different points, get evaluated by different multi-label classification models. Based on training on our dataset, the models score the trainees' responses for cultural awareness in the Chinese culture. Trainees also get feedback that informs the cultural appropriateness of their responses. The result of this work showed the following; i) A feature-based evaluation model improves the design, modeling and computation of dialogue-based training simulation systems; ii) Output from current automatic speech recognition (ASR) systems gave comparable end results compared with the output from manual transcription; iii) A multi-label classification model trained as a cultural expert gave results which were comparable with scores assigned by human annotators.
A collaborative network is a social network that is comprised of experts who cooperate with each other to fulfill a special goal. Analyzing this network yields meaningful information about the expertise of these experts and their subject areas. To perform the analysis, graph embedding techniques have emerged as an effective and promising tool. Graph embedding attempts to represent graph nodes as low-dimensional vectors. In this paper, we propose a graph embedding method, called ExEm, that uses dominating-set theory and deep learning approaches to capture node representations. ExEm finds dominating nodes of the collaborative network and constructs intelligent random walks that comprise of at least two dominating nodes. One dominating node should appear at the beginning of each path sampled to characterize the local neighborhoods. Moreover, the second dominating node reflects the global structure information. To learn the node embeddings, ExEm exploits three embedding methods including Word2vec, fastText and the concatenation of these two. The final result is the low-dimensional vectors of experts, called expert embeddings. The extracted expert embeddings can be applied to many applications. In order to extend these embeddings into the expert recommendation system, we introduce a novel strategy that uses expert vectors to calculate experts' scores and recommend experts. At the end, we conduct extensive experiments to validate the effectiveness of ExEm through assessing its performance over the multi-label classification, link prediction, and recommendation tasks on common datasets and our collected data formed by crawling the vast author Scopus profiles. The experiments show that ExEm outperforms the baselines especially in dense networks.
This paper presents BigEarthNet that is a large-scale Sentinel-2 multispectral image dataset with a new class nomenclature to advance deep learning (DL) studies in remote sensing (RS). BigEarthNet is made up of 590,326 image patches annotated with multi-labels provided by the CORINE Land Cover (CLC) map of 2018 based on its most thematic detailed Level-3 class nomenclature. Initial research demonstrates that some CLC classes are challenging to be accurately described by considering only Sentinel-2 images. To increase the effectiveness of BigEarthNet, in this paper we introduce an alternative class-nomenclature to allow DL models for better learning and describing the complex spatial and spectral information content of the Sentinel-2 images. This is achieved by interpreting and arranging the CLC Level-3 nomenclature based on the properties of Sentinel-2 images in a new nomenclature of 19 classes. Then, the new class-nomenclature of BigEarthNet is used within state-of-the-art DL models in the context of multi-label classification. Results show that the models trained from scratch on BigEarthNet outperform those pre-trained on ImageNet, especially in relation to some complex classes including agriculture, other vegetated and natural environments. All DL models are made publicly available at http://bigearth.net/#downloads, offering an important resource to guide future progress on RS image analysis.
Accurate identification and localization of the vertebrae in CT scans is a critical and standard preprocessing step for clinical spinal diagnosis and treatment. Existing methods are mainly based on the integration of multiple neural networks, and most of them use the Gaussian heat map to locate the vertebrae's centroid. However, the process of obtaining the vertebrae's centroid coordinates using heat maps is non-differentiable, so it is impossible to train the network to label the vertebrae directly. Therefore, for end-to-end differential training of vertebra coordinates on CT scans, a robust and accurate automatic vertebral labeling algorithm is proposed in this study. Firstly, a novel residual-based multi-label classification and localization network is developed, which can capture multi-scale features, but also utilize the residual module and skip connection to fuse the multi-level features. Secondly, to solve the problem that the process of finding coordinates is non-differentiable and the spatial structure is not destructible, integral regression module is used in the localization network. It combines the advantages of heat map representation and direct regression coordinates to achieve end-to-end training, and can be compatible with any key point detection methods of medical image based on heat map. Finally, multi-label classification of vertebrae is carried out, which use bidirectional long short term memory (Bi-LSTM) to enhance the learning of long contextual information to improve the classification performance. The proposed method is evaluated on a challenging dataset and the results are significantly better than the state-of-the-art methods (mean localization error <3mm).
Tweet classification has attracted considerable attention recently. Most of the existing work on tweet classification focuses on topic classification, which classifies tweets into several predefined categories, and sentiment classification, which classifies tweets into positive, negative and neutral. Since tweets are different from conventional text in that they generally are of limited length and contain informal, irregular or new words, so it is difficult to determine user intention to publish a tweet and user attitude towards certain topic. In this paper, we aim to simultaneously classify tweet purpose, i.e., the intention for user to publish a tweet, and position, i.e., supporting, opposing or being neutral to a given topic. By transforming this problem to a multi-label classification problem, a multi-label classification method with post-processing is proposed. Experiments on real-world data sets demonstrate the effectiveness of this method and the results outperform the individual classification methods.
The family of methods collectively known as classifier chains has become a popular approach to multi-label learning problems. This approach involves linking together off-the-shelf binary classifiers in a chain structure, such that class label predictions become features for other classifiers. Such methods have proved flexible and effective and have obtained state-of-the-art empirical performance across many datasets and multi-label evaluation metrics. This performance led to further studies of how exactly it works, and how it could be improved, and in the recent decade numerous studies have explored classifier chains mechanisms on a theoretical level, and many improvements have been made to the training and inference procedures, such that this method remains among the state-of-the-art options for multi-label learning. Given this past and ongoing interest, which covers a broad range of applications and research themes, the goal of this work is to provide a review of classifier chains, a survey of the techniques and extensions provided in the literature, as well as perspectives for this approach in the domain of multi-label classification in the future. We conclude positively, with a number of recommendations for researchers and practitioners, as well as outlining a number of areas for future research.
Shortage of labeled data has been holding the surge of deep learning in healthcare back, as sample sizes are often small, patient information cannot be shared openly, and multi-center collaborative studies are a burden to set up. Distributed machine learning methods promise to mitigate these problems. We argue for a split learning based approach and apply this distributed learning method for the first time in the medical field to compare performance against (1) centrally hosted and (2) non collaborative configurations for a range of participants. Two medical deep learning tasks are used to compare split learning to conventional single and multi center approaches: a binary classification problem of a data set of 9000 fundus photos, and multi-label classification problem of a data set of 156,535 chest X-rays. The several distributed learning setups are compared for a range of 1-50 distributed participants. Performance of the split learning configuration remained constant for any number of clients compared to a single center study, showing a marked difference compared to the non collaborative configuration after 2 clients (p < 0.001) for both sets. Our results affirm the benefits of collaborative training of deep neural networks in health care. Our work proves the significant benefit of distributed learning in healthcare, and paves the way for future real-world implementations.
Knowledge representation of graph-based systems is fundamental across many disciplines. To date, most existing methods for representation learning primarily focus on networks with simplex labels, yet real-world objects (nodes) are inherently complex in nature and often contain rich semantics or labels, e.g., a user may belong to diverse interest groups of a social network, resulting in multi-label networks for many applications. The multi-label network nodes not only have multiple labels for each node, such labels are often highly correlated making existing methods ineffective or fail to handle such correlation for node representation learning. In this paper, we propose a novel multi-label graph convolutional network (ML-GCN) for learning node representation for multi-label networks. To fully explore label-label correlation and network topology structures, we propose to model a multi-label network as two Siamese GCNs: a node-node-label graph and a label-label-node graph. The two GCNs each handle one aspect of representation learning for nodes and labels, respectively, and they are seamlessly integrated under one objective function. The learned label representations can effectively preserve the inner-label interaction and node label properties, and are then aggregated to enhance the node representation learning under a unified training framework. Experiments and comparisons on multi-label node classification validate the effectiveness of our proposed approach.
In a standard multi-output classification scenario, both features and labels of training data are partially observed. This challenging issue is widely witnessed due to sensor or database failures, crowd-sourcing and noisy communication channels in industrial data analytic services. Classic methods for handling multi-output classification with incomplete supervision information usually decompose the problem into an imputation stage that reconstructs the missing training information, and a learning stage that builds a classifier based on the imputed training set. These methods fail to fully leverage the dependencies between features and labels. In order to take full advantage of these dependencies we consider a purely probabilistic setting in which the features imputation and multi-label classification problems are jointly solved. Indeed, we show that a simple Restricted Boltzmann Machine can be trained with an adapted algorithm based on mean-field equations to efficiently solve problems of inductive and transductive learning in which both features and labels are missing at random. The effectiveness of the approach is demonstrated empirically on various datasets, with particular focus on a real-world Internet-of-Things security dataset.
Paper-reviewer recommendation task is of significant academic importance for conference chairs and journal editors. How to effectively and accurately recommend reviewers for the submitted papers is a meaningful and still tough task. In this paper, we propose a Multi-Label Classification method using a hierarchical and transparent Representation named Hiepar-MLC. Further, we propose a simple multi-label-based reviewer assignment MLBRA strategy to select the appropriate reviewers. It is interesting that we also explore the paper-reviewer recommendation in the coarse-grained granularity.
The goal of eXtreme Multi-label Learning (XML) is to automatically annotate a given data point with the most relevant subset of labels from an extremely large vocabulary of labels (e.g., a million labels). Lately, many attempts have been made to address this problem that achieve reasonable performance on benchmark datasets. In this paper, rather than coming-up with an altogether new method, our objective is to present and validate a simple baseline for this task. Precisely, we investigate an on-the-fly global and structure preserving feature embedding technique using random projections whose learning phase is independent of training samples and label vocabulary. Further, we show how an ensemble of multiple such learners can be used to achieve further boost in prediction accuracy with only linear increase in training and prediction time. Experiments on three public XML benchmarks show that the proposed approach obtains competitive accuracy compared with many existing methods. Additionally, it also provides around 6572x speed-up ratio in terms of training time and around 14.7x reduction in model-size compared to the closest competitors on the largest publicly available dataset.
Multi-label image and video classification are fundamental yet challenging tasks in computer vision. The main challenges lie in capturing spatial or temporal dependencies between labels and discovering the locations of discriminative features for each class. In order to overcome these challenges, we propose to use cross-modality attention with semantic graph embedding for multi label classification. Based on the constructed label graph, we propose an adjacency-based similarity graph embedding method to learn semantic label embeddings, which explicitly exploit label relationships. Then our novel cross-modality attention maps are generated with the guidance of learned label embeddings. Experiments on two multi-label image classification datasets (MS-COCO and NUS-WIDE) show our method outperforms other existing state-of-the-arts. In addition, we validate our method on a large multi-label video classification dataset (YouTube-8M Segments) and the evaluation results demonstrate the generalization capability of our method.
Currently there are several well-known approaches to non-intrusive appliance load monitoring rule based, stochastic finite state machines, neural networks and sparse coding. Recently several studies have proposed a new approach based on multi label classification. Different appliances are treated as separate classes, and the task is to identify the classes given the aggregate smart-meter reading. Prior studies in this area have used off the shelf algorithms like MLKNN and RAKEL to address this problem. In this work, we propose a deep learning based technique. There are hardly any studies in deep learning based multi label classification; two new deep learning techniques to solve the said problem are fundamental contributions of this work. These are deep dictionary learning and deep transform learning. Thorough experimental results on benchmark datasets show marked improvement over existing studies.
This work follows the approach of multi-label classification for non-intrusive load monitoring (NILM). We modify the popular sparse representation based classification (SRC) approach (developed for single label classification) to solve multi-label classification problems. Results on benchmark REDD and Pecan Street dataset shows significant improvement over state-of-the-art techniques with small volume of training data.
Sentiment Analysis of microblog feeds has attracted considerable interest in recent times. Most of the current work focuses on tweet sentiment classification. But not much work has been done to explore how reliable the opinions of the mass (crowd wisdom) in social network microblogs such as twitter are in predicting outcomes of certain events such as election debates. In this work, we investigate whether crowd wisdom is useful in predicting such outcomes and whether their opinions are influenced by the experts in the field. We work in the domain of multi-label classification to perform sentiment classification of tweets and obtain the opinion of the crowd. This learnt sentiment is then used to predict outcomes of events such as: US Presidential Debate winners, Grammy Award winners, Super Bowl Winners. We find that in most of the cases, the wisdom of the crowd does indeed match with that of the experts, and in cases where they don't (particularly in the case of debates), we see that the crowd's opinion is actually influenced by that of the experts.