Automatically Detecting Self-Reported Birth Defect Outcomes on Twitter for Large-scale Epidemiological Research

In recent work, we identified and studied a small cohort of Twitter users whose pregnancies with birth defect outcomes could be observed via their publicly available tweets. Exploiting social media's large-scale potential to complement the limited methods for studying birth defects, the leading cause of infant mortality, depends on the further development of automatic methods. The primary objective of this study was to take the first step towards scaling the use of social media for observing pregnancies with birth defect outcomes, namely, developing methods for automatically detecting tweets by users reporting their birth defect outcomes. We annotated and pre-processed approximately 23,000 tweets that mention birth defects in order to train and evaluate supervised machine learning algorithms, including feature-engineered and deep learning-based classifiers. We also experimented with various under-sampling and over-sampling approaches to address the class imbalance. A Support Vector Machine (SVM) classifier trained on the original, imbalanced data set, with n-grams, word clusters, and structural features, achieved the best baseline performance for the positive classes: an F1-score of 0.65 for the "defect" class and 0.51 for the "possible defect" class. Our contributions include (i) natural language processing (NLP) and supervised machine learning methods for automatically detecting tweets by users reporting their birth defect outcomes, (ii) a comparison of feature-engineered and deep learning-based classifiers trained on imbalanced, under-sampled, and over-sampled data, and (iii) an error analysis that could inform classification improvements using our publicly available corpus. Future work will focus on automating user-level analyses for cohort inclusion

Anatomical Pattern Analysis for decoding visual stimuli in human brains

Background: A universal unanswered question in neuroscience and machine learning is whether computers can decode the patterns of the human brain. Multi-Voxels Pattern Analysis (MVPA) is a critical tool for addressing this question. However, there are two challenges in the previous MVPA methods, which include decreasing sparsity and noise in the extracted features and increasing the performance of prediction. Methods: In overcoming mentioned challenges, this paper proposes Anatomical Pattern Analysis (APA) for decoding visual stimuli in the human brain. This framework develops a novel anatomical feature extraction method and a new imbalance AdaBoost algorithm for binary classification. Further, it utilizes an Error-Correcting Output Codes (ECOC) method for multiclass prediction. APA can automatically detect active regions for each category of the visual stimuli. Moreover, it enables us to combine homogeneous datasets for applying advanced classification. Results and Conclusions: Experimental studies on 4 visual categories (words, consonants, objects and scrambled photos) demonstrate that the proposed approach achieves superior performance to state-of-the-art methods.Comment: Published in Cognitive Computatio

Machine Learning for Forecasting Mid Price Movement using Limit Order Book Data

Forecasting the movements of stock prices is one the most challenging problems in financial markets analysis. In this paper, we use Machine Learning (ML) algorithms for the prediction of future price movements using limit order book data. Two different sets of features are combined and evaluated: handcrafted features based on the raw order book data and features extracted by ML algorithms, resulting in feature vectors with highly variant dimensionalities. Three classifiers are evaluated using combinations of these sets of features on two different evaluation setups and three prediction scenarios. Even though the large scale and high frequency nature of the limit order book poses several challenges, the scope of the conducted experiments and the significance of the experimental results indicate that Machine Learning highly befits this task carving the path towards future research in this field

Multi-level Feature Fusion-based CNN for Local Climate Zone Classification from Sentinel-2 Images: Benchmark Results on the So2Sat LCZ42 Dataset

As a unique classification scheme for urban forms and functions, the local climate zone (LCZ) system provides essential general information for any studies related to urban environments, especially on a large scale. Remote sensing data-based classification approaches are the key to large-scale mapping and monitoring of LCZs. The potential of deep learning-based approaches is not yet fully explored, even though advanced convolutional neural networks (CNNs) continue to push the frontiers for various computer vision tasks. One reason is that published studies are based on different datasets, usually at a regional scale, which makes it impossible to fairly and consistently compare the potential of different CNNs for real-world scenarios. This study is based on the big So2Sat LCZ42 benchmark dataset dedicated to LCZ classification. Using this dataset, we studied a range of CNNs of varying sizes. In addition, we proposed a CNN to classify LCZs from Sentinel-2 images, Sen2LCZ-Net. Using this base network, we propose fusing multi-level features using the extended Sen2LCZ-Net-MF. With this proposed simple network architecture and the highly competitive benchmark dataset, we obtain results that are better than those obtained by the state-of-the-art CNNs, while requiring less computation with fewer layers and parameters. Large-scale LCZ classification examples of completely unseen areas are presented, demonstrating the potential of our proposed Sen2LCZ-Net-MF as well as the So2Sat LCZ42 dataset. We also intensively investigated the influence of network depth and width and the effectiveness of the design choices made for Sen2LCZ-Net-MF. Our work will provide important baselines for future CNN-based algorithm developments for both LCZ classification and other urban land cover land use classification

Scalable Deep Learning Logo Detection

Existing logo detection methods usually consider a small number of logo classes and limited images per class with a strong assumption of requiring tedious object bounding box annotations, therefore not scalable to real-world dynamic applications. In this work, we tackle these challenges by exploring the webly data learning principle without the need for exhaustive manual labelling. Specifically, we propose a novel incremental learning approach, called Scalable Logo Self-co-Learning (SL^2), capable of automatically self-discovering informative training images from noisy web data for progressively improving model capability in a cross-model co-learning manner. Moreover, we introduce a very large (2,190,757 images of 194 logo classes) logo dataset "WebLogo-2M" by an automatic web data collection and processing method. Extensive comparative evaluations demonstrate the superiority of the proposed SL^2 method over the state-of-the-art strongly and weakly supervised detection models and contemporary webly data learning approaches

Separation of pulsar signals from noise with supervised machine learning algorithms

We evaluate the performance of four different machine learning (ML) algorithms: an Artificial Neural Network Multi-Layer Perceptron (ANN MLP ), Adaboost, Gradient Boosting Classifier (GBC), XGBoost, for the separation of pulsars from radio frequency interference (RFI) and other sources of noise, using a dataset obtained from the post-processing of a pulsar search pi peline. This dataset was previously used for cross-validation of the SPINN-based machine learning engine, used for the reprocessing of HTRU-S survey data arXiv:1406.3627. We have used Synthetic Minority Over-sampling Technique (SMOTE) to deal with high class imbalance in the dataset. We report a variety of quality scores from all four of these algorithms on both the non-SMOTE and SMOTE datasets. For all the above ML methods, we report high accuracy and G-mean in both the non-SMOTE and SMOTE cases. We study the feature importances using Adaboost, GBC, and XGBoost and also from the minimum Redundancy Maximum Relevance approach to report algorithm-agnostic feature ranking. From these methods, we find that the signal to noise of the folded profile to be the best feature. We find that all the ML algorithms report FPRs about an order of magnitude lower than the corresponding FPRs obtained in arXiv:1406.3627, for the same recall value.Comment: 14 pages, 2 figures. Accepted for publication in Astronomy and Computin

LapTool-Net: A Contextual Detector of Surgical Tools in Laparoscopic Videos Based on Recurrent Convolutional Neural Networks

We propose a new multilabel classifier, called LapTool-Net to detect the presence of surgical tools in each frame of a laparoscopic video. The novelty of LapTool-Net is the exploitation of the correlation among the usage of different tools and, the tools and tasks - namely, the context of the tools' usage. Towards this goal, the pattern in the co-occurrence of the tools is utilized for designing a decision policy for a multilabel classifier based on a Recurrent Convolutional Neural Network (RCNN) architecture to simultaneously extract the spatio-temporal features. In contrast to the previous multilabel classification methods, the RCNN and the decision model are trained in an end-to-end manner using a multitask learning scheme. To overcome the high imbalance and avoid overfitting caused by the lack of variety in the training data, a high down-sampling rate is chosen based on the more frequent combinations. Furthermore, at the post-processing step, the prediction for all the frames of a video are corrected by designing a bi-directional RNN to model the long-term task's order. LapTool-net was trained using a publicly available dataset of laparoscopic cholecystectomy. The results show LapTool-Net outperforms existing methods significantly, even while using fewer training samples and a shallower architecture.Comment: 18 pages, 4 figures, Submitted to Medical Image Analysi

Fully Convolutional Neural Networks to Detect Clinical Dermoscopic Features

The presence of certain clinical dermoscopic features within a skin lesion may indicate melanoma, and automatically detecting these features may lead to more quantitative and reproducible diagnoses. We reformulate the task of classifying clinical dermoscopic features within superpixels as a segmentation problem, and propose a fully convolutional neural network to detect clinical dermoscopic features from dermoscopy skin lesion images. Our neural network architecture uses interpolated feature maps from several intermediate network layers, and addresses imbalanced labels by minimizing a negative multi-label Dice-F$_1$ score, where the score is computed across the mini-batch for each label. Our approach ranked first place in the 2017 ISIC-ISBI Part 2: Dermoscopic Feature Classification Task challenge over both the provided validation and test datasets, achieving a 0.895% area under the receiver operator characteristic curve score. We show how simple baseline models can outrank state-of-the-art approaches when using the official metrics of the challenge, and propose to use a fuzzy Jaccard Index that ignores the empty set (i.e., masks devoid of positive pixels) when ranking models. Our results suggest that (i) the classification of clinical dermoscopic features can be effectively approached as a segmentation problem, and (ii) the current metrics used to rank models may not well capture the efficacy of the model. We plan to make our trained model and code publicly available.Comment: Accepted JBHI versio

Surface Defect Classification in Real-Time Using Convolutional Neural Networks

Surface inspection systems are an important application domain for computer vision, as they are used for defect detection and classification in the manufacturing industry. Existing systems use hand-crafted features which require extensive domain knowledge to create. Even though Convolutional neural networks (CNNs) have proven successful in many large-scale challenges, industrial inspection systems have yet barely realized their potential due to two significant challenges: real-time processing speed requirements and specialized narrow domain-specific datasets which are sometimes limited in size. In this paper, we propose CNN models that are specifically designed to handle capacity and real-time speed requirements of surface inspection systems. To train and evaluate our network models, we created a surface image dataset containing more than 22000 labeled images with many types of surface materials and achieved 98.0% accuracy in binary defect classification. To solve the class imbalance problem in our datasets, we introduce neural data augmentation methods which are also applicable to similar domains that suffer from the same problem. Our results show that deep learning based methods are feasible to be used in surface inspection systems and outperform traditional methods in accuracy and inference time by considerable margins.Comment: Supplementary material will follo

Feature versus Raw Sequence: Deep Learning Comparative Study on Predicting Pre-miRNA

Should we input known genome sequence features or input sequence itself in deep learning framework? As deep learning more popular in various applications, researchers often come to question whether to generate features or use raw sequences for deep learning. To answer this question, we study the prediction accuracy of precursor miRNA prediction of feature-based deep belief network and sequence-based convolution neural network. Tested on a variant of six-layer convolution neural net and three-layer deep belief network, we find the raw sequence input based convolution neural network model performs similar or slightly better than feature based deep belief networks with best accuracy values of 0.995 and 0.990, respectively. Both the models outperform existing benchmarks models. The results shows us that if provided large enough data, well devised raw sequence based deep learning models can replace feature based deep learning models. However, construction of well behaved deep learning model can be very challenging. In cased features can be easily extracted, feature-based deep learning models may be a better alternative.Comment: 12 pages, 2 figures. arXiv admin note: substantial text overlap with arXiv:1704.0383