Time series analysis is a field of data science which is interested in analyzing sequences of numerical values ordered in time. Time series are particularly interesting because they allow us to visualize and understand the evolution of a process over time. Their analysis can reveal trends, relationships and similarities across the data. There exists numerous fields containing data in the form of time series: health care (electrocardiogram, blood sugar, etc.), activity recognition, remote sensing, finance (stock market price), industry (sensors), etc. Time series classification consists of constructing algorithms dedicated to automatically label time series data. The sequential aspect of time series data requires the development of algorithms that are able to harness this temporal property, thus making the existing off-the-shelf machine learning models for traditional tabular data suboptimal for solving the underlying task. In this context, deep learning has emerged in recent years as one of the most effective methods for tackling the supervised classification task, particularly in the field of computer vision. The main objective of this thesis was to study and develop deep neural networks specifically constructed for the classification of time series data. We thus carried out the first large scale experimental study allowing us to compare the existing deep methods and to position them compared other non-deep learning based state-of-the-art methods. Subsequently, we made numerous contributions in this area, notably in the context of transfer learning, data augmentation, ensembling and adversarial attacks. Finally, we have also proposed a novel architecture, based on the famous Inception network (Google), which ranks among the most efficient to date.
We describe NatCat, a large-scale resource for text classification constructed from three data sources: Wikipedia, Stack Exchange, and Reddit. NatCat consists of document-category pairs derived from manual curation that occurs naturally within online communities. To demonstrate its usefulness, we build general purpose text classifiers by training on NatCat and evaluate them on a suite of 11 text classification tasks (CatEval), reporting large improvements compared to prior work. We benchmark different modeling choices and resource combinations and show how tasks benefit from particular NatCat data sources.
We propose average Localisation-Recall-Precision (aLRP), a unified, bounded, balanced and ranking-based loss function for both classification and localisation tasks in object detection. aLRP extends the Localisation-Recall-Precision (LRP) performance metric (Oksuz et al., 2018) inspired from how Average Precision (AP) Loss extends precision to a ranking-based loss function for classification (Chen et al., 2020). aLRP has the following distinct advantages: (i) aLRP is the first ranking-based loss function for both classification and localisation tasks. (ii) Thanks to using ranking for both tasks, aLRP naturally enforces high-quality localisation for high-precision classification. (iii) aLRP provides provable balance between positives and negatives. (iv) Compared to on average $\sim$6 hyperparameters in the loss functions of state-of-the-art detectors, aLRP Loss has only one hyperparameter, which we did not tune in practice. On the COCO dataset, aLRP Loss improves its ranking-based predecessor, AP Loss, up to around $5$ AP points, achieves $48.9$ AP without test time augmentation and outperforms all one-stage detectors. Code available at: https://github.com/kemaloksuz/aLRPLoss .
In frequency division duplex (FDD) multiple-input multiple-output (MIMO) wireless communications, limited channel state information (CSI) feedback is a central tool to support advanced single- and multi-user MIMO beamforming/precoding. To achieve a given CSI quality, the CSI quantization codebook size has to grow exponentially with the number of antennas, leading to quantization complexity, as well as, feedback overhead issues for larger MIMO systems. We have recently proposed a multi-stage recursive Grassmannian quantizer that enables a significant complexity reduction of CSI quantization. In this paper, we show that this recursive quantizer can effectively be combined with deep learning classification to further reduce the complexity, and that it can exploit temporal channel correlations to reduce the CSI feedback overhead.
The nodes of a graph existing in a cluster are more likely to connect to each other than with other nodes in the graph. Then revealing some information about some nodes, the structure of the graph (graph edges) provides this opportunity to know more information about other nodes. From this perspective, this paper revisits the node classification task in a semi-supervised scenario by graph convolutional networks (GCNs). The goal is to benefit from the flow of information that circulates around the revealed node labels. The contribution of this paper is twofold. First, this paper provides a method for extracting side information from a graph realization. Then a new GCN architecture is presented that combines the output of traditional GCN and the extracted side information. Another contribution of this paper is relevant to non-graph observations (independent side information) that exists beside a graph realization in many applications. Indeed, the extracted side information can be replaced by a sequence of side information that is independent of the graph structure. For both cases, the experiments on synthetic and real-world datasets demonstrate that the proposed model achieves a higher prediction accuracy in comparison to the existing state-of-the-art methods for the node classification task.
In a typical multi-label setting, a picture contains on average few positive labels, and many negative ones. This positive-negative imbalance dominates the optimization process, and can lead to under-emphasizing gradients from positive labels during training, resulting in poor accuracy. In this paper, we introduce a novel asymmetric loss ("ASL"), which operates differently on positive and negative samples. The loss enables to dynamically down-weights and hard-thresholds easy negative samples, while also discarding possibly mislabeled samples. We demonstrate how ASL can balance the probabilities of different samples, and how this balancing is translated to better mAP scores. With ASL, we reach state-of-the-art results on multiple popular multi-label datasets: MS-COCO, Pascal-VOC, NUS-WIDE and Open Images. We also demonstrate ASL applicability for other tasks, such as single-label classification and object detection. ASL is effective, easy to implement, and does not increase the training time or complexity. Implementation is available at: https://github.com/Alibaba-MIIL/ASL.
Recent developments in machine learning have introduced models that approach human performance at the cost of increased architectural complexity. Efforts to make the rationales behind the models' predictions transparent have inspired an abundance of new explainability techniques. Provided with an already trained model, they compute saliency scores for the words of an input instance. However, there exists no definitive guide on (i) how to choose such a technique given a particular application task and model architecture, and (ii) the benefits and drawbacks of using each such technique. In this paper, we develop a comprehensive list of diagnostic properties for evaluating existing explainability techniques. We then employ the proposed list to compare a set of diverse explainability techniques on downstream text classification tasks and neural network architectures. We also compare the saliency scores assigned by the explainability techniques with human annotations of salient input regions to find relations between a model's performance and the agreement of its rationales with human ones. Overall, we find that the gradient-based explanations perform best across tasks and model architectures, and we present further insights into the properties of the reviewed explainability techniques.
Climate change has been a common interest and the forefront of crucial political discussion and decision-making for many years. Shallow clouds play a significant role in understanding the Earth's climate, but they are challenging to interpret and represent in a climate model. By classifying these cloud structures, there is a better possibility of understanding the physical structures of the clouds, which would improve the climate model generation, resulting in a better prediction of climate change or forecasting weather update. Clouds organise in many forms, which makes it challenging to build traditional rule-based algorithms to separate cloud features. In this paper, classification of cloud organization patterns was performed using a new scaled-up version of Convolutional Neural Network (CNN) named as EfficientNet as the encoder and UNet as decoder where they worked as feature extractor and reconstructor of fine grained feature map and was used as a classifier, which will help experts to understand how clouds will shape the future climate. By using a segmentation model in a classification task, it was shown that with a good encoder alongside UNet, it is possible to obtain good performance from this dataset. Dice coefficient has been used for the final evaluation metric, which gave the score of 66.26\% and 66.02\% for public and private (test set) leaderboard on Kaggle competition respectively.
Recently, we have witnessed great progress in the field of medical imaging classification by adopting deep neural networks. However, the recent advanced models still require accessing sufficiently large and representative datasets for training, which is often unfeasible in clinically realistic environments. When trained on limited datasets, the deep neural network is lack of generalization capability, as the trained deep neural network on data within a certain distribution (e.g. the data captured by a certain device vendor or patient population) may not be able to generalize to the data with another distribution. In this paper, we introduce a simple but effective approach to improve the generalization capability of deep neural networks in the field of medical imaging classification. Motivated by the observation that the domain variability of the medical images is to some extent compact, we propose to learn a representative feature space through variational encoding with a novel linear-dependency regularization term to capture the shareable information among medical data collected from different domains. As a result, the trained neural network is expected to equip with better generalization capability to the "unseen" medical data. Experimental results on two challenging medical imaging classification tasks indicate that our method can achieve better cross-domain generalization capability compared with state-of-the-art baselines.
Motivation: With the development of third-generation sequencing technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow protein domain annotation without assembly, thus can produce important insights into the biological functions of the underlying data. However, the high error rate in third-generation sequencing data raises a new challenge to established domain analysis pipelines. The state-of-the-art methods are not optimized for noisy reads and have shown unsatisfactory accuracy of domain classification in third-generation sequencing data. New computational methods are still needed to improve the performance of domain prediction in long noisy reads. Results: In this work, we introduce ProDOMA, a deep learning model that conducts domain classification for third-generation sequencing reads. It uses deep neural networks with 3-frame translation encoding to learn conserved features from partially correct translations. In addition, we formulate our problem as an open-set problem and thus our model can reject unrelated DNA reads such as those from noncoding regions. In the experiments on simulated reads of protein coding sequences and real reads from the human genome, our model outperforms HMMER and DeepFam on protein domain classification. In summary, ProDOMA is a useful end-to-end protein domain analysis tool for long noisy reads without relying on error correction. Availability: The source code and the trained model are freely available at https://github.com/strideradu/ProDOMA. Contact: [email omitted]
In recent years, there has been a rapidly expanding focus on explaining the predictions made by black-box AI systems that handle image and tabular data. However, considerably less attention has been paid to explaining the predictions of opaque AI systems handling time series data. In this paper, we advance a novel model-agnostic, case-based technique -- Native Guide -- that generates counterfactual explanations for time series classifiers. Given a query time series, $T_{q}$, for which a black-box classification system predicts class, $c$, a counterfactual time series explanation shows how $T_{q}$ could change, such that the system predicts an alternative class, $c'$. The proposed instance-based technique adapts existing counterfactual instances in the case-base by highlighting and modifying discriminative areas of the time series that underlie the classification. Quantitative and qualitative results from two comparative experiments indicate that Native Guide generates plausible, proximal, sparse and diverse explanations that are better than those produced by key benchmark counterfactual methods.
As the class size grows, maintaining a balanced dataset across many classes is challenging because the data are long-tailed in nature; it is even impossible when the sample-of-interest co-exists with each other in one collectable unit, e.g., multiple visual instances in one image. Therefore, long-tailed classification is the key to deep learning at scale. However, existing methods are mainly based on re-weighting/re-sampling heuristics that lack a fundamental theory. In this paper, we establish a causal inference framework, which not only unravels the whys of previous methods, but also derives a new principled solution. Specifically, our theory shows that the SGD momentum is essentially a confounder in long-tailed classification. On one hand, it has a harmful causal effect that misleads the tail prediction biased towards the head. On the other hand, its induced mediation also benefits the representation learning and head prediction. Our framework elegantly disentangles the paradoxical effects of the momentum, by pursuing the direct causal effect caused by an input sample. In particular, we use causal intervention in training, and counterfactual reasoning in inference, to remove the "bad" while keep the "good". We achieve new state-of-the-arts on three long-tailed visual recognition benchmarks: Long-tailed CIFAR-10/-100, ImageNet-LT for image classification and LVIS for instance segmentation.
Detection of some types of toxic language is hampered by extreme scarcity of labeled training data. Data augmentation - generating new synthetic data from a labeled seed dataset - can help. The efficacy of data augmentation on toxic language classification has not been fully explored. We present the first systematic study on how data augmentation techniques impact performance across toxic language classifiers, ranging from shallow logistic regression architectures to BERT - a state-of-the-art pre-trained Transformer network. We compare the performance of eight techniques on very scarce seed datasets. We show that while BERT performed the best, shallow classifiers performed comparably when trained on data augmented with a combination of three techniques, including GPT-2-generated sentences. We discuss the interplay of performance and computational overhead, which can inform the choice of techniques under different constraints.
In the text classification problem, the imbalance of labels in datasets affect the performance of the text-classification models. Practically, the data about user comments on social networking sites not altogether appeared - the administrators often only allow positive comments and hide negative comments. Thus, when collecting the data about user comments on the social network, the data is usually skewed about one label, which leads the dataset to become imbalanced and deteriorate the model's ability. The data augmentation techniques are applied to solve the imbalance problem between classes of the dataset, increasing the prediction model's accuracy. In this paper, we performed augmentation techniques on the VLSP2019 Hate Speech Detection on Vietnamese social texts and the UIT - VSFC: Vietnamese Students' Feedback Corpus for Sentiment Analysis. The result of augmentation increases by about 1.5% in the F1-macro score on both corpora.
The ability to automatically determine the age audience of a novel provides many opportunities for the development of information retrieval tools. Firstly, developers of book recommendation systems and electronic libraries may be interested in filtering texts by the age of the most likely readers. Further, parents may want to select literature for children. Finally, it will be useful for writers and publishers to determine which features influence whether the texts are suitable for children. In this article, we compare the empirical effectiveness of various types of linguistic features for the task of age-based classification of fiction texts. For this purpose, we collected a text corpus of book previews labeled with one of two categories -- children's or adult. We evaluated the following types of features: readability indices, sentiment, lexical, grammatical and general features, and publishing attributes. The results obtained show that the features describing the text at the document level can significantly increase the quality of machine learning models.
Graph embedding is a powerful method to represent graph neurological data (e.g., brain connectomes) in a low dimensional space for brain connectivity mapping, prediction and classification. However, existing embedding algorithms have two major limitations. First, they primarily focus on preserving one-to-one topological relationships between nodes (i.e., regions of interest (ROIs) in a connectome), but they have mostly ignored many-to-many relationships (i.e., set to set), which can be captured using a hyperconnectome structure. Second, existing graph embedding techniques cannot be easily adapted to multi-view graph data with heterogeneous distributions. In this paper, while cross-pollinating adversarial deep learning with hypergraph theory, we aim to jointly learn deep latent embeddings of subject0specific multi-view brain graphs to eventually disentangle different brain states. First, we propose a new simple strategy to build a hyperconnectome for each brain view based on nearest neighbour algorithm to preserve the connectivities across pairs of ROIs. Second, we design a hyperconnectome autoencoder (HCAE) framework which operates directly on the multi-view hyperconnectomes based on hypergraph convolutional layers to better capture the many-to-many relationships between brain regions (i.e., nodes). For each subject, we further regularize the hypergraph autoencoding by adversarial regularization to align the distribution of the learned hyperconnectome embeddings with that of the input hyperconnectomes. We formalize our hyperconnectome embedding within a geometric deep learning framework to optimize for a given subject, thereby designing an individual-based learning framework. Our experiments showed that the learned embeddings by HCAE yield to better results for brain state classification compared with other deep graph embedding methods methods.
Extreme multi-label classification (XMLC) is a learning task of tagging instances with a small subset of relevant labels chosen from an extremely large pool of possible labels. Problems of this scale can be efficiently handled by organizing labels as a tree, like in hierarchical softmax used for multi-class problems. In this paper, we thoroughly investigate probabilistic label trees (PLTs) which can be treated as a generalization of hierarchical softmax for multi-label problems. We first introduce the PLT model and discuss training and inference procedures and their computational costs. Next, we prove the consistency of PLTs for a wide spectrum of performance metrics. To this end, we upperbound their regret by a function of surrogate-loss regrets of node classifiers. Furthermore, we consider a problem of training PLTs in a fully online setting, without any prior knowledge of training instances, their features, or labels. In this case, both node classifiers and the tree structure are trained online. We prove a specific equivalence between the fully online algorithm and an algorithm with a tree structure given in advance. Finally, we discuss several implementations of PLTs and introduce a new one, napkinXC, which we empirically evaluate and compare with state-of-the-art algorithms.
Rovers require knowledge of terrain to plan trajectories that maximize safety and efficiency. Terrain type classification relies on input from human operators or machine learning-based image classification algorithms. However, high level terrain classification is typically not sufficient to prevent incidents such as rovers becoming unexpectedly stuck in a sand trap; in these situations, online rover-terrain interaction data can be leveraged to accurately predict future dynamics and prevent further damage to the rover. This paper presents a meta-learning-based approach to adapt probabilistic predictions of rover dynamics by augmenting a nominal model affine in parameters with a Bayesian regression algorithm (P-ALPaCA). A regularization scheme is introduced to encourage orthogonality of nominal and learned features, leading to interpretable probabilistic estimates of terrain parameters in varying terrain conditions.
Crop type classification using satellite observations is an important tool for providing insights about planted area and enabling estimates of crop condition and yield, especially within the growing season when uncertainties around these quantities are highest. As the climate changes and extreme weather events become more frequent, these methods must be resilient to changes in domain shifts that may occur, for example, due to shifts in planting timelines. In this work, we present an approach for within-season crop type classification using moderate spatial resolution (30 m) satellite data that addresses domain shift related to planting timelines by normalizing inputs by crop growth stage. We use a neural network leveraging both convolutional and recurrent layers to predict if a pixel contains corn, soybeans, or another crop or land cover type. We evaluated this method for the 2019 growing season in the midwestern US, during which planting was delayed by as much as 1-2 months due to extreme weather that caused record flooding. We show that our approach using growth stage-normalized time series outperforms fixed-date time series, and achieves overall classification accuracy of 85.4% prior to harvest (September-November) and 82.8% by mid-season (July-September).
Since December of 2019, novel coronavirus disease COVID-19 has spread around the world infecting millions of people and upending the global economy. One of the driving reasons behind its high rate of infection is due to the unreliability and lack of RT-PCR testing. At times the turnaround results span as long as a couple of days, only to yield a roughly 70% sensitivity rate. As an alternative, recent research has investigated the use of Computer Vision with Convolutional Neural Networks (CNNs) for the classification of COVID-19 from CT scans. Due to an inherent lack of available COVID-19 CT data, these research efforts have been forced to leverage the use of Transfer Learning. This commonly employed Deep Learning technique has shown to improve model performance on tasks with relatively small amounts of data, as long as the Source feature space somewhat resembles the Target feature space. Unfortunately, a lack of similarity is often encountered in the classification of medical images as publicly available Source datasets usually lack the visual features found in medical images. In this study, we propose the use of Multi-Source Transfer Learning (MSTL) to improve upon traditional Transfer Learning for the classification of COVID-19 from CT scans. With our multi-source fine-tuning approach, our models outperformed baseline models fine-tuned with ImageNet. We additionally, propose an unsupervised label creation process, which enhances the performance of our Deep Residual Networks. Our best performing model was able to achieve an accuracy of 0.893 and a Recall score of 0.897, outperforming its baseline Recall score by 9.3%.