Chronic obstructive pulmonary disease (COPD) is one of the most common chronic illnesses in the world and the third leading cause of mortality worldwide. It is often underdiagnosed or not diagnosed until later in the disease course. Spirometry tests are the gold standard for diagnosing COPD but can be difficult to obtain, especially in resource-poor countries. Chest X-rays (CXRs), however, are readily available and may serve as a screening tool to identify patients with COPD who should undergo further testing. Currently, no research applies deep learning (DL) algorithms that use large multi-site and multi-modal data to detect COPD patients and evaluate fairness across demographic groups. We use three CXR datasets in our study, CheXpert to pre-train models, MIMIC-CXR to develop, and Emory-CXR to validate our models. The CXRs from patients in the early stage of COPD and not on mechanical ventilation are selected for model training and validation. We visualize the Grad-CAM heatmaps of the true positive cases on the base model for both MIMIC-CXR and Emory-CXR test datasets. We further propose two fusion schemes, (1) model-level fusion, including bagging and stacking methods using MIMIC-CXR, and (2) data-level fusion, including multi-site data using MIMIC-CXR and Emory-CXR, and multi-modal using MIMIC-CXRs and MIMIC-IV EHR, to improve the overall model performance. Fairness analysis is performed to evaluate if the fusion schemes have a discrepancy in the performance among different demographic groups. The results demonstrate that DL models can detect COPD using CXRs, which can facilitate early screening, especially in low-resource regions where CXRs are more accessible than spirometry. The multi-site data fusion scheme could improve the model generalizability on the Emory-CXR test data. Further studies on using CXR or other modalities to predict COPD ought to be in future work.

Automated planetary transit detection has become vital to prioritize candidates for expert analysis given the scale of modern telescopic surveys. While current methods for short-period exoplanet detection work effectively due to periodicity in the light curves, there lacks a robust approach for detecting single-transit events. However, volunteer-labelled transits recently collected by the Planet Hunters TESS (PHT) project now provide an unprecedented opportunity to investigate a data-driven approach to long-period exoplanet detection. In this work, we train a 1-D convolutional neural network to classify planetary transits using PHT volunteer scores as training data. We find using volunteer scores significantly improves performance over synthetic data, and enables the recovery of known planets at a precision and rate matching that of the volunteers. Importantly, the model also recovers transits found by volunteers but missed by current automated methods.

Characterizing the differential excision of mRNA is critical for understanding the functional complexity of a cell or tissue, from normal developmental processes to disease pathogenesis. Most transcript reconstruction methods infer full-length transcripts from high-throughput sequencing data. However, this is a challenging task due to incomplete annotations and the differential expression of transcripts across cell-types, tissues, and experimental conditions. Several recent methods circumvent these difficulties by considering local splicing events, but these methods lose transcript-level splicing information and may conflate transcripts. We develop the first probabilistic model that reconciles the transcript and local splicing perspectives. First, we formalize the sequence of mRNA excisions (SME) reconstruction problem, which aims to assemble variable-length sequences of mRNA excisions from RNA-sequencing data. We then present a novel hierarchical Bayesian admixture model for the Reconstruction of Excised mRNA (BREM). BREM interpolates between local splicing events and full-length transcripts and thus focuses only on SMEs that have high posterior probability. We develop posterior inference algorithms based on Gibbs sampling and local search of independent sets and characterize differential SME usage using generalized linear models based on converged BREM model parameters. We show that BREM achieves higher F1 score for reconstruction tasks and improved accuracy and sensitivity in differential splicing when compared with four state-of-the-art transcript and local splicing methods on simulated data. Lastly, we evaluate BREM on both bulk and scRNA sequencing data based on transcript reconstruction, novelty of transcripts produced, model sensitivity to hyperparameters, and a functional analysis of differentially expressed SMEs, demonstrating that BREM captures relevant biological signal.

Ransomware has appeared as one of the major global threats in recent days. The alarming increasing rate of ransomware attacks and new ransomware variants intrigue the researchers to constantly examine the distinguishing traits of ransomware and refine their detection strategies. Application Programming Interface (API) is a way for one program to collaborate with another; API calls are the medium by which they communicate. Ransomware uses this strategy to interact with the OS and makes a significantly higher number of calls in different sequences to ask for taking action. This research work utilizes the frequencies of different API calls to detect and classify ransomware families. First, a Web-Crawler is developed to automate collecting the Windows Portable Executable (PE) files of 15 different ransomware families. By extracting different frequencies of 68 API calls, we develop our dataset in the first phase of the two-phase feature engineering process. After selecting the most significant features in the second phase of the feature engineering process, we deploy six Supervised Machine Learning models: Na"ive Bayes, Logistic Regression, Random Forest, Stochastic Gradient Descent, K-Nearest Neighbor, and Support Vector Machine. Then, the performances of all the classifiers are compared to select the best model. The results reveal that Logistic Regression can efficiently classify ransomware into their corresponding families securing 99.15% overall accuracy. Finally, instead of relying on the 'Black box' characteristic of the Machine Learning models, we present the post-hoc analysis of our best-performing model using 'SHapley Additive exPlanations' or SHAP values to ascertain the transparency and trustworthiness of the model's prediction.

We all know a single image may convey a message more effectively than a lot of written words. But what consists of an image? When it comes to image segmentation, a common answer might be "things" and "stuff". The concept of things and stuff is used when describing image segmentation methods such as instance and semantic segmentation. Instance segmentation is the identification of countable objects, while semantic segmentation is the identification of regions of texture.

A confusion matrix is a table used to summarize the performance of a classification model. In case you aren't familiar, classification models are machine learning algorithms used to solve problems that have a categorical outcome, such as predicting whether an email is a spam or not. Accuracy is the most popular metric used to evaluate classification models. However, it isn't always the most reliable, which is why data scientists generate confusion matrices and use metrics like precision and recall instead. Confusion matrices are one of the most frequently tested concepts by data science interviewers. Hiring managers often ask candidates to interpret confusion matrices, or provide them with a use case and ask them to calculate a model's precision and recall by hand.

Considerable research attention has been paid to table detection by developing not only rule-based approaches reliant on hand-crafted heuristics but also deep learning approaches. Although recent studies successfully perform table detection with enhanced results, they often experience performance degradation when they are used for transferred domains whose table layout features might differ from the source domain in which the underlying model has been trained. To overcome this problem, we present DATa, a novel Domain Adaptation-aided deep Table detection method that guarantees satisfactory performance in a specific target domain where few trusted labels are available. To this end, we newly design lexical features and an augmented model used for re-training. More specifically, after pre-training one of state-of-the-art vision-based models as our backbone network, we re-train our augmented model, consisting of the vision-based model and the multilayer perceptron (MLP) architecture. Using new confidence scores acquired based on the trained MLP architecture as well as an initial prediction of bounding boxes and their confidence scores, we calculate each confidence score more accurately. To validate the superiority of DATa, we perform experimental evaluations by adopting a real-world benchmark dataset in a source domain and another dataset in our target domain consisting of materials science articles. Experimental results demonstrate that the proposed DATa method substantially outperforms competing methods that only utilize visual representations in the target domain. Such gains are possible owing to the capability of eliminating high false positives or false negatives according to the setting of a confidence score threshold.

Data valuation, or the valuation of individual datum contributions, has seen growing interest in machine learning due to its demonstrable efficacy for tasks such as noisy label detection. In particular, due to the desirable axiomatic properties, several Shapley value approximation methods have been proposed. In these methods, the value function is typically defined as the predictive accuracy over the entire development set. However, this limits the ability to differentiate between training instances that are helpful or harmful to their own classes. Intuitively, instances that harm their own classes may be noisy or mislabeled and should receive a lower valuation than helpful instances. In this work, we propose CS-Shapley, a Shapley value with a new value function that discriminates between training instances' in-class and out-of-class contributions. Our theoretical analysis shows the proposed value function is (essentially) the unique function that satisfies two desirable properties for evaluating data values in classification. Further, our experiments on two benchmark evaluation tasks (data removal and noisy label detection) and four classifiers demonstrate the effectiveness of CS-Shapley over existing methods. Lastly, we evaluate the "transferability" of data values estimated from one classifier to others, and our results suggest Shapley-based data valuation is transferable for application across different models.

Pain monitoring is essential to the quality of care for patients undergoing a medical procedure with sedation. An automated mechanism for detecting pain could improve sedation dose titration. Previous studies on facial pain detection have shown the viability of computer vision methods in detecting pain in unoccluded faces. However, the faces of patients undergoing procedures are often partially occluded by medical devices and face masks. A previous preliminary study on pain detection on artificially occluded faces has shown a feasible approach to detect pain from a narrow band around the eyes. This study has collected video data from masked faces of 14 patients undergoing procedures in an interventional radiology department and has trained a deep learning model using this dataset. The model was able to detect expressions of pain accurately and, after causal temporal smoothing, achieved an average precision (AP) of 0.72 and an area under the receiver operating characteristic curve (AUC) of 0.82. These results outperform baseline models and show viability of computer vision approaches for pain detection of masked faces during procedural sedation. Cross-dataset performance is also examined when a model is trained on a publicly available dataset and tested on the sedation videos. The ways in which pain expressions differ in the two datasets are qualitatively examined.

The asteroidal main belt is crossed by a web of mean-motion and secular resonances, that occur when there is a commensurability between fundamental frequencies of the asteroids and planets. Traditionally, these objects were identified by visual inspection of the time evolution of their resonant argument, which is a combination of orbital elements of the asteroid and the perturbing planet(s). Since the population of asteroids affected by these resonances is, in some cases, of the order of several thousand, this has become a taxing task for a human observer. Recent works used Convolutional Neural Networks (CNN) models to perform such task automatically. In this work, we compare the outcome of such models with those of some of the most advanced and publicly available CNN architectures, like the VGG, Inception and ResNet. The performance of such models is first tested and optimized for overfitting issues, using validation sets and a series of regularization techniques like data augmentation, dropout, and batch normalization. The three best-performing models were then used to predict the labels of larger testing databases containing thousands of images. The VGG model, with and without regularizations, proved to be the most efficient method to predict labels of large datasets. Since the Vera C. Rubin observatory is likely to discover up to four million new asteroids in the next few years, the use of these models might become quite valuable to identify populations of resonant minor bodies.