At present, the vast majority of human subjects with neurological disease are still diagnosed through in-person assessments and qualitative analysis of patient data. In this paper, we propose to use Topological Data Analysis (TDA) together with machine learning tools to automate the process of Parkinson's disease classification and severity assessment. An automated, stable, and accurate method to evaluate Parkinson's would be significant in streamlining diagnoses of patients and providing families more time for corrective measures. We propose a methodology which incorporates TDA into analyzing Parkinson's disease postural shifts data through the representation of persistence images. Studying the topology of a system has proven to be invariant to small changes in data and has been shown to perform well in discrimination tasks. The contributions of the paper are twofold. We propose a method to 1) classify healthy patients from those afflicted by disease and 2) diagnose the severity of disease. We explore the use of the proposed method in an application involving a Parkinson's disease dataset comprised of healthy-elderly, healthy-young and Parkinson's disease patients. Our code is available at https://github.com/itsmeafra/Sublevel-Set-TDA.
Accurate and fine-grained information about the extent of damage to buildings is essential for directing Humanitarian Aid and Disaster Response (HADR) operations in the immediate aftermath of any natural calamity. In recent years, satellite and UAV (drone) imagery has been used for this purpose, sometimes aided by computer vision algorithms. Existing Computer Vision approaches for building damage assessment typically rely on a two stage approach, consisting of building detection using an object detection model, followed by damage assessment through classification of the detected building tiles. These multi-stage methods are not end-to-end trainable, and suffer from poor overall results. We propose RescueNet, a unified model that can simultaneously segment buildings and assess the damage levels to individual buildings and can be trained end-toend. In order to to model the composite nature of this problem, we propose a novel localization aware loss function, which consists of a Binary Cross Entropy loss for building segmentation, and a foreground only selective Categorical Cross-Entropy loss for damage classification, and show significant improvement over the widely used Cross-Entropy loss. RescueNet is tested on the large scale and diverse xBD dataset and achieves significantly better building segmentation and damage classification performance than previous methods and achieves generalization across varied geographical regions and disaster types.
Environmental Sound Classification (ESC) is an active research area in the audio domain and has seen a lot of progress in the past years. However, many of the existing approaches achieve high accuracy by relying on domain-specific features and architectures, making it harder to benefit from advances in other fields (e.g., the image domain). Additionally, some of the past successes have been attributed to a discrepancy of how results are evaluated (i.e., on unofficial splits of the UrbanSound8K (US8K) dataset), distorting the overall progression of the field. The contribution of this paper is twofold. First, we present a model that is inherently compatible with mono and stereo sound inputs. Our model is based on simple log-power Short-Time Fourier Transform (STFT) spectrograms and combines them with several well-known approaches from the image domain (i.e., ResNet, Siamese-like networks and attention). We investigate the influence of cross-domain pre-training, architectural changes, and evaluate our model on standard datasets. We find that our model out-performs all previously known approaches in a fair comparison by achieving accuracies of 97.0 % (ESC-10), 91.5 % (ESC-50) and 84.2 % / 85.4 % (US8K mono / stereo). Second, we provide a comprehensive overview of the actual state of the field, by differentiating several previously reported results on the US8K dataset between official or unofficial splits. For better reproducibility, our code (including any re-implementations) is made available.
Many large-scale knowledge graphs are now available and ready to provide semantically structured information that is regarded as an important resource for question answering and decision support tasks. However, they are built on rigid symbolic frameworks which makes them hard to be used in other intelligent systems. We present a learning method using generative adversarial architecture designed to embed the entities and relations of the knowledge graphs into a continuous vector space. A generative network (GN) takes two elements of a (subject, predicate, object) triple as input and generates the vector representation of the missing element. A discriminative network (DN) scores a triple to distinguish a positive triple from those generated by GN. The training goal for GN is to deceive DN to make wrong classification. When arriving at a convergence, GN recovers the training data and can be used for knowledge graph completion, while DN is trained to be a good triple classifier. Unlike few previous studies based on generative adversarial architectures, our GN is able to generate unseen instances while they just use GN to better choose negative samples (already existed) for DN. Experiments demonstrate our method can improve classical relational learning models (e.g.TransE) with a significant margin on both the link prediction and triple classification tasks.
The complexity of state-of-the-art modeling techniques for image classification impedes the ability to explain model predictions in an interpretable way. Existing explanation methods generally create importance rankings in terms of pixels or pixel groups. However, the resulting explanations lack an optimal size, do not consider feature dependence and are only related to one class. Counterfactual explanation methods are considered promising to explain complex model decisions, since they are associated with a high degree of human interpretability. In this paper, SEDC is introduced as a model-agnostic instance-level explanation method for image classification to obtain visual counterfactual explanations. For a given image, SEDC searches a small set of segments that, in case of removal, alters the classification. As image classification tasks are typically multiclass problems, SEDC-T is proposed as an alternative method that allows specifying a target counterfactual class. We compare SEDC(-T) with popular feature importance methods such as LRP, LIME and SHAP, and we describe how the mentioned importance ranking issues are addressed. Moreover, concrete examples and experiments illustrate the potential of our approach (1) to obtain trust and insight, and (2) to obtain input for model improvement by explaining misclassifications.
Recently, the coronavirus disease 2019 (COVID-19) has caused a pandemic disease in over 200 countries, influencing billions of humans. To control the infection, identifying and separating the infected people is the most crucial step. The main diagnostic tool is the Reverse Transcription Polymerase Chain Reaction (RT-PCR) test. Still, the sensitivity of the RT-PCR test is not high enough to effectively prevent the pandemic. The chest CT scan test provides a valuable complementary tool to the RT-PCR test, and it can identify the patients in the early-stage with high sensitivity. However, the chest CT scan test is usually time-consuming, requiring about 21.5 minutes per case. This paper develops a novel Joint Classification and Segmentation (JCS) system to perform real-time and explainable COVID-19 chest CT diagnosis. To train our JCS system, we construct a large scale COVID-19 Classification and Segmentation (COVID-CS) dataset, with 144,167 chest CT images of 400 COVID-19 patients and 350 uninfected cases. 3,855 chest CT images of 200 patients are annotated with fine-grained pixel-level labels of opacifications, which are increased attenuation of the lung parenchyma. We also have annotated lesion counts, opacification areas, and locations and thus benefit various diagnosis aspects. Extensive experiments demonstrate that the proposed JCS diagnosis system is very efficient for COVID-19 classification and segmentation. It obtains an average sensitivity of 95.0% and a specificity of 93.0% on the classification test set, and 78.5% Dice score on the segmentation test set of our COVID-CS dataset. The COVID-CS dataset and code are available at https://github.com/yuhuan-wu/JCS.
How to utilize deep learning methods for graph classification tasks has attracted considerable research attention in the past few years. Regarding graph classification tasks, the graphs to be classified may have various graph sizes (i.e., different number of nodes and edges) and have various graph properties (e.g., average node degree, diameter, and clustering coefficient). The diverse property of graphs has imposed significant challenges on existing graph learning techniques since diverse graphs have different best-fit hyperparameters. It is difficult to learn graph features from a set of diverse graphs by a unified graph neural network. This motivates us to use a multiplex structure in a diverse way and utilize a priori properties of graphs to guide the learning. In this paper, we propose MxPool, which concurrently uses multiple graph convolution/pooling networks to build a hierarchical learning structure for graph representation learning tasks. Our experiments on numerous graph classification benchmarks show that our MxPool has superiority over other state-of-the-art graph representation learning methods.
The ADReSS Challenge at INTERSPEECH 2020 defines a shared task through which different approaches to the automated recognition of Alzheimer's dementia based on spontaneous speech can be compared. ADReSS provides researchers with a benchmark speech dataset which has been acoustically pre-processed and balanced in terms of age and gender, defining two cognitive assessment tasks, namely: the Alzheimer's speech classification task and the neuropsychological score regression task. In the Alzheimer's speech classification task, ADReSS challenge participants create models for classifying speech as dementia or healthy control speech. In the the neuropsychological score regression task, participants create models to predict mini-mental state examination scores. This paper describes the ADReSS Challenge in detail and presents a baseline for both tasks, including feature extraction procedures and results for classification and regression models. ADReSS aims to provide the speech and language Alzheimer's research community with a platform for comprehensive methodological comparisons. This will hopefully contribute to addressing the lack of standardisation that currently affects the field and shed light on avenues for future research and clinical applicability.
Skin lesion datasets consist predominantly of normal samples with only a small percentage of abnormal ones, giving rise to the class imbalance problem. Also, skin lesion images are largely similar in overall appearance owing to the low inter-class variability. In this paper, we propose a two-stage framework for automatic classification of skin lesion images using adversarial training and transfer learning toward melanoma detection. In the first stage, we leverage the inter-class variation of the data distribution for the task of conditional image synthesis by learning the inter-class mapping and synthesizing under-represented class samples from the over-represented ones using unpaired image-to-image translation. In the second stage, we train a deep convolutional neural network for skin lesion classification using the original training set combined with the newly synthesized under-represented class samples. The training of this classifier is carried out by minimizing the focal loss function, which assists the model in learning from hard examples, while down-weighting the easy ones. Experiments conducted on a dermatology image benchmark demonstrate the superiority of our proposed approach over several standard baseline methods, achieving significant performance improvements. Interestingly, we show through feature visualization and analysis that our method leads to context based lesion assessment that can reach an expert dermatologist level.
Time-critical analysis of social media streams is important for humanitarian organizations for planing rapid response during disasters. The \textit{crisis informatics} research community has developed several techniques and systems for processing and classifying big crisis-related data posted on social media. However, due to the dispersed nature of the datasets used in the literature (e.g., for training models), it is not possible to compare the results and measure the progress made towards building better models for crisis informatics tasks. In this work, we attempt to bridge this gap by combining various existing crisis-related datasets. We consolidate eight human-annotated datasets and provide 166.1k and 141.5k tweets for \textit{informativeness} and \textit{humanitarian} classification tasks, respectively. We believe that the consolidated dataset will help train more sophisticated models. Moreover, we provide benchmarks for both binary and multiclass classification tasks using several deep learning architecrures including, CNN, fastText, and transformers. We make the dataset and scripts available at: https://crisisnlp.qcri.org/crisis_datasets_benchmarks.html
A unique member of the power transformation family is known as the Box-Cox transformation. The latter can be seen as a mathematical operation that leads to finding the optimum lambda ({\lambda}) value that maximizes the log-likelihood function to transform a data to a normal distribution and to reduce heteroscedasticity. In data analytics, a normality assumption underlies a variety of statistical test models. This technique, however, is best known in statistical analysis to handle one-dimensional data. Herein, this paper revolves around the utility of such a tool as a pre-processing step to transform two-dimensional data, namely, digital images and to study its effect. Moreover, to reduce time complexity, it suffices to estimate the parameter lambda in real-time for large two-dimensional matrices by merely considering their probability density function as a statistical inference of the underlying data distribution. We compare the effect of this light-weight Box-Cox transformation with well-established state-of-the-art low light image enhancement techniques. We also demonstrate the effectiveness of our approach through several test-bed data sets for generic improvement of visual appearance of images and for ameliorating the performance of a colour pattern classification algorithm as an example application. Results with and without the proposed approach, are compared using the AlexNet (transfer deep learning) pretrained model. To the best of our knowledge, this is the first time that the Box-Cox transformation is extended to digital images by exploiting histogram transformation.
Representation learning is a critical ingredient for natural language processing systems. Recent Transformer language models like BERT learn powerful textual representations, but these models are targeted towards token- and sentence-level training objectives and do not leverage information on inter-document relatedness, which limits their document-level representation power. For applications on scientific documents, such as classification and recommendation, the embeddings power strong performance on end tasks. We propose SPECTER, a new method to generate document-level embedding of scientific documents based on pretraining a Transformer language model on a powerful signal of document-level relatedness: the citation graph. Unlike existing pretrained language models, SPECTER can be easily applied to downstream applications without task-specific fine-tuning. Additionally, to encourage further research on document-level models, we introduce SciDocs, a new evaluation benchmark consisting of seven document-level tasks ranging from citation prediction, to document classification and recommendation. We show that SPECTER outperforms a variety of competitive baselines on the benchmark.
Analyzing the ever-increasing volume of posts on social media sites such as Facebook and Twitter requires improved information processing methods for profiling authorship. Document classification is central to this task, but the performance of traditional supervised classifiers has degraded as the volume of social media has increased. This paper addresses this problem in the context of gender detection through ensemble classification that employs multi-model deep learning architectures to generate specialized understanding from different feature spaces.
Diabetic Retinopathy is a global health problem, influences 100 million individuals worldwide, and in the next few decades, these incidences are expected to reach epidemic proportions. Diabetic Retinopathy is a subtle eye disease that can cause sudden, irreversible vision loss. The early-stage Diabetic Retinopathy diagnosis can be challenging for human experts, considering the visual complexity of fundus photography retinal images. However, Early Stage detection of Diabetic Retinopathy can significantly alter the severe vision loss problem. The competence of computer-aided detection systems to accurately detect the Diabetic Retinopathy had popularized them among researchers. In this study, we have utilized a pre-trained DenseNet121 network with several modifications and trained on APTOS 2019 dataset. The proposed method outperformed other state-of-the-art networks in early-stage detection and achieved 96.51% accuracy in severity grading of Diabetic Retinopathy for multi-label classification and achieved 94.44% accuracy for single-class classification method. Moreover, the precision, recall, f1-score, and quadratic weighted kappa for our network was reported as 86%, 87%, 86%, and 91.96%, respectively. Our proposed architecture is simultaneously very simple, accurate, and efficient concerning computational time and space.
We study the problem of learning from aggregate observations where supervision signals are given to sets of instances instead of individual instances, while the goal is still to predict labels of unseen individuals. A well-known example is multiple instance learning (MIL). In this paper, we extend MIL beyond binary classification to other problems such as multiclass classification and regression. We present a general probabilistic framework that accommodates a variety of aggregate observations, e.g., pairwise similarity/triplet comparison for classification and mean/difference/rank observation for regression. Simple maximum likelihood solutions can be applied to various differentiable models such as deep neural networks and gradient boosting machines. Moreover, we develop the concept of consistency up to an equivalence relation to characterize our estimator and show that it has nice convergence properties under mild assumptions. Experiments on three problem settings -- classification via triplet comparison and regression via mean/rank observation indicate the effectiveness of the proposed method.
Recent studies have shown that deep convolutional neural networks (DCNN) are vulnerable to adversarial examples and sensitive to perceptual quality as well as the acquisition condition of images. These findings raise a big concern for the adoption of DCNN-based applications for critical tasks. In the literature, various defense strategies have been introduced to increase the robustness of DCNN, including re-training an entire model with benign noise injection, adversarial examples, or adding extra layers. In this paper, we investigate the connection between adversarial manipulation and image quality, subsequently propose a protective mechanism that doesnt require re-training a DCNN. Our method combines image quality assessment with knowledge distillation to detect input images that would trigger a DCCN to produce egregiously wrong results. Using the ResNet model trained on ImageNet as an example, we demonstrate that the detector can effectively identify poor quality and adversarial images.
We consider the situation where the observed sample contains some observations whose class of origin is known (that is, they are classified with respect to the g underlying classes of interest), and where the remaining observations in the sample are unclassified (that is, their class labels are unknown). For class-conditional distributions taken to be known up to a vector of unknown parameters, the aim is to estimate the Bayes' rule of allocation for the allocation of subsequent unclassified observations. Estimation on the basis of both the classified and unclassified data can be undertaken in a straightforward manner by fitting a g-component mixture model by maximum likelihood (ML) via the EM algorithm in the situation where the observed data can be assumed to be an observed random sample from the adopted mixture distribution. This assumption applies if the missing-data mechanism is ignorable in the terminology pioneered by Rubin (1976). An initial likelihood approach was to use the so-called classification ML approach whereby the missing labels are taken to be parameters to be estimated along with the parameters of the class-conditional distributions. However, as it can lead to inconsistent estimates, the focus of attention switched to the mixture ML approach after the appearance of the EM algorithm (Dempster et al., 1977). Particular attention is given here to the asymptotic relative efficiency (ARE) of the Bayes' rule estimated from a partially classified sample. Lastly, we consider briefly some recent results in situations where the missing label pattern is non-ignorable for the purposes of ML estimation for the mixture model.
With the rapid growth of research publications, there is a vast amount of scholarly knowledge that needs to be organized in digital libraries. To deal with this challenge, techniques relying on knowledge-graph structures are being advocated. Within such graph-based pipelines, inferring relation types between related scientific concepts is a crucial step. Recently, advanced techniques relying on language models pre-trained on the large corpus have been popularly explored for automatic relation classification. Despite remarkable contributions that have been made, many of these methods were evaluated under different scenarios, which limits their comparability. To this end, we present a thorough empirical evaluation on eight Bert-based classification models by focusing on two key factors: 1) Bert model variants, and 2) classification strategies. Experiments on three corpora show that domain-specific pre-training corpus benefits the Bert-based classification model to identify the type of scientific relations. Although the strategy of predicting a single relation each time achieves a higher classification accuracy than the strategy of identifying multiple relation types simultaneously in general, the latter strategy demonstrates a more consistent performance in the corpus with either a large or small size of annotations. Our study aims to offer recommendations to the stakeholders of digital libraries for selecting the appropriate technique to build knowledge-graph-based systems for enhanced scholarly information organization.
Many important real-world applications involve time-series data with skewed distribution. Compared to conventional imbalance learning problems, the classification of imbalanced time-series data is more challenging due to high dimensionality and high inter-variable correlation. This paper proposes a structure preserving Oversampling method to combat the High-dimensional Imbalanced Time-series classification (OHIT). OHIT first leverages a density-ratio based shared nearest neighbor clustering algorithm to capture the modes of minority class in high-dimensional space. It then for each mode applies the shrinkage technique of large-dimensional covariance matrix to obtain accurate and reliable covariance structure. Finally, OHIT generates the structure-preserving synthetic samples based on multivariate Gaussian distribution by using the estimated covariance matrices. Experimental results on several publicly available time-series datasets (including unimodal and multimodal) demonstrate the superiority of OHIT against the state-of-the-art oversampling algorithms in terms of F1, G-mean, and AUC.
An outbreak of a novel coronavirus disease (i.e., COVID-19) has been recorded in Wuhan, China since late December 2019, which subsequently became pandemic around the world. Although COVID-19 is an acutely treated disease, it can also be fatal with a risk of fatality of 4.03% in China and the highest of 13.04% in Algeria and 12.67% Italy (as of 8th April 2020). The onset of serious illness may result in death as a consequence of substantial alveolar damage and progressive respiratory failure. Although laboratory testing, e.g., using reverse transcription polymerase chain reaction (RT-PCR), is the golden standard for clinical diagnosis, the tests may produce false negatives. Moreover, under the pandemic situation, shortage of RT-PCR testing resources may also delay the following clinical decision and treatment. Under such circumstances, chest CT imaging has become a valuable tool for both diagnosis and prognosis of COVID-19 patients. In this study, we propose a weakly supervised deep learning strategy for detecting and classifying COVID-19 infection from CT images. The proposed method can minimise the requirements of manual labelling of CT images but still be able to obtain accurate infection detection and distinguish COVID-19 from non-COVID-19 cases. Based on the promising results obtained qualitatively and quantitatively, we can envisage a wide deployment of our developed technique in large-scale clinical studies.