Background: Stratifying cancer patients according to risk of relapse can personalize their care. In this work, we provide an answer to the following research question: How to utilize machine learning to estimate probability of relapse in early-stage non-small-cell lung cancer patients? Methods: For predicting relapse in 1,387 early-stage (I-II), non-small-cell lung cancer (NSCLC) patients from the Spanish Lung Cancer Group data (65.7 average age, 24.8% females, 75.2% males) we train tabular and graph machine learning models. We generate automatic explanations for the predictions of such models. For models trained on tabular data, we adopt SHAP local explanations to gauge how each patient feature contributes to the predicted outcome. We explain graph machine learning predictions with an example-based method that highlights influential past patients. Results: Machine learning models trained on tabular data exhibit a 76% accuracy for the Random Forest model at predicting relapse evaluated with a 10-fold cross-validation (model was trained 10 times with different independent sets of patients in test, train and validation sets, the reported metrics are averaged over these 10 test sets). Graph machine learning reaches 68% accuracy over a 200-patient, held-out test set, calibrated on a held-out set of 100 patients. Conclusions: Our results show that machine learning models trained on tabular and graph data can enable objective, personalised and reproducible prediction of relapse and therefore, disease outcome in patients with early-stage NSCLC. With further prospective and multisite validation, and additional radiological and molecular data, this prognostic model could potentially serve as a predictive decision support tool for deciding the use of adjuvant treatments in early-stage lung cancer. Keywords: Non-Small-Cell Lung Cancer, Tumor Recurrence Prediction, Machine Learning

Through ML we can address SE problems that cannot be completely algorithmically modeled, or for which existing solutions do not provide satisfactory results yet (e.g., defect/fault detection [16, 165, 180]). In addition, ML finds application in SE tasks where data cannot be easily analyzed with other algorithms (e.g., software requirements, code comments, code reviews, issues [9, 91, 174]). Another important aspect of ML is that it can significantly reduce manual effort in common SE tasks (e.g., automatic program repair [157], code suggestion [61], defect prediction [19], malware detection [147], feature location [40]) with great accuracy results [146, 164]. In fields such as health informatics ML and SE are considered complementary disciplines, since the growing scale and complexity of healthcare datasets have posed a challenge for clinical practice and medical research, requiring new engineering approaches from both fields [38]. In the early nineties, Huff and Selfridge [68] recognized the need for creating software systems that partially take some responsibility for their own evolution, offering the ability to implement, measure, and assess changes easily. These changes should also contribute to the overall improvement of the corresponding systems [142].

Deep learning has emerged as a promising paradigm to give access to highly accurate predictions of molecular and materials properties. A common short-coming shared by current approaches, however, is that neural networks only give point estimates of their predictions and do not come with predictive uncertainties associated with these estimates. Existing uncertainty quantification efforts have primarily leveraged the standard deviation of predictions across an ensemble of independently trained neural networks. This incurs a large computational overhead in both training and prediction that often results in order-of-magnitude more expensive predictions. Here, we propose a method to estimate the predictive uncertainty based on a single neural network without the need for an ensemble. This allows us to obtain uncertainty estimates with virtually no additional computational overhead over standard training and inference. We demonstrate that the quality of the uncertainty estimates matches those obtained from deep ensembles. We further examine the uncertainty estimates of our methods and deep ensembles across the configuration space of our test system and compare the uncertainties to the potential energy surface. Finally, we study the efficacy of the method in an active learning setting and find the results to match an ensemble-based strategy at order-of-magnitude reduced computational cost.

Exoplanets in protoplanetary disks cause localized deviations from Keplerian velocity in channel maps of molecular line emission. Current methods of characterizing these deviations are time consuming, and there is no unified standard approach. We demonstrate that machine learning can quickly and accurately detect the presence of planets. We train our model on synthetic images generated from simulations and apply it to real observations to identify forming planets in real systems. Machine learning methods, based on computer vision, are not only capable of correctly identifying the presence of one or more planets, but they can also correctly constrain the location of those planets.

Objective For the UK Biobank standardized phenotype codes are associated with patients who have been hospitalized but are missing for many patients who have been treated exclusively in an outpatient setting. We describe a method for phenotype recognition that imputes phenotype codes for all UK Biobank participants. Materials and Methods POPDx (Population-based Objective Phenotyping by Deep Extrapolation) is a bilinear machine learning framework for simultaneously estimating the probabilities of 1,538 phenotype codes. We extracted phenotypic and health-related information of 392,246 individuals from the UK Biobank for POPDx development and evaluation. A total of 12,803 ICD-10 diagnosis codes of the patients were converted to 1,538 Phecodes as gold standard labels. The POPDx framework was evaluated and compared to other available methods on automated multi-phenotype recognition. Results POPDx can predict phenotypes that are rare or even unobserved in training. We demonstrate substantial improvement of automated multi-phenotype recognition across 22 disease categories, and its application in identifying key epidemiological features associated with each phenotype. Conclusions POPDx helps provide well-defined cohorts for downstream studies. It is a general purpose method that can be applied to other biobanks with diverse but incomplete data.

We propose a simple yet effective image captioning framework that can determine the quality of an image and notify the user of the reasons for any flaws in the image. Our framework first determines the quality of images and then generates captions using only those images that are determined to be of high quality. The user is notified by the flaws feature to retake if image quality is low, and this cycle is repeated until the input image is deemed to be of high quality. As a component of the framework, we trained and evaluated a low-quality image detection model that simultaneously learns difficulty in recognizing images and individual flaws, and we demonstrated that our proposal can explain the reasons for flaws with a sufficient score. We also evaluated a dataset with low-quality images removed by our framework and found improved values for all four common metrics (e.g., BLEU-4, METEOR, ROUGE-L, CIDEr), confirming an improvement in general-purpose image captioning capability. Our framework would assist the visually impaired, who have difficulty judging image quality.

Speech is the fundamental means of communication between humans. The advent of AI and sophisticated speech technologies have led to the rapid proliferation of human-to-computer-based interactions, fueled primarily by Automatic Speech Recognition (ASR) systems. ASR systems normally take human speech in the form of audio and convert it into words, but for some users, it cannot decode the speech, and any output text is filled with errors that are incomprehensible to the human reader. These systems do not work equally for everyone and actually hinder the productivity of some users. In this paper, we present research that addresses ASR biases against gender, race, and the sick and disabled, while exploring studies that propose ASR debiasing techniques for mitigating these discriminations. We also discuss techniques for designing a more accessible and inclusive ASR technology. For each approach surveyed, we also provide a summary of the investigation and methods applied, the ASR systems and corpora used, and the research findings, and highlight their strengths and/or weaknesses. Finally, we propose future opportunities for Natural Language Processing researchers to explore in the next level creation of ASR technologies.

In this paper, we study multi-block min-max bilevel optimization problems, where the upper level is non-convex strongly-concave minimax objective and the lower level is a strongly convex objective, and there are multiple blocks of dual variables and lower level problems. Due to the intertwined multi-block min-max bilevel structure, the computational cost at each iteration could be prohibitively high, especially with a large number of blocks. To tackle this challenge, we present a single-loop randomized stochastic algorithm, which requires updates for only a constant number of blocks at each iteration. Under some mild assumptions on the problem, we establish its sample complexity of $O(1/\epsilon^4)$ for finding an $\epsilon$-stationary point. This matches the optimal complexity for solving stochastic nonconvex optimization under a general unbiased stochastic oracle model. Moreover, we provide two applications of the proposed method in multi-task deep AUC (area under ROC curve) maximization and multi-task deep partial AUC maximization. Experimental results validate our theory and demonstrate the effectiveness of our method on problems with hundreds of tasks.

While physical phenomena are stated in terms of physical laws that are homogeneous in all dimensions, the mechanisms and patterns of the physical phenomena are independent of the form of the units describing the physical process. Accordingly, across different conditions, the similarity of a process may be captured through a dimensionless reformulation of the physical problem with Buckingham $\Pi$ theorem. Here, we apply Buckingham $\Pi$ theorem for creating dimensionless indices for capturing the similarity of the flood process, and in turn, these indices allow machine learning to map the likelihood of pluvial (flash) flooding over a landscape. In particular, we use these dimensionless predictors with a logistic regression machine learning (ML) model for a probabilistic determination of flood risk. The logistic regression derived flood maps compare well to 2D hydraulic model results that are the basis of the Federal Emergency Management Agency (FEMA) maps. As a result, the indices and logistic regression also provide the potential to expand existing FEMA maps to new (unmapped) areas and a wider spectrum of flood flows and precipitation events. Our results demonstrate that the new dimensionless indices capture the similarity of the flood process across different topographies and climate regions. Consequently, these dimensionless indices may expand observations of flooding (e.g., satellite) to the risk of flooding in new areas, as well as provide a basis for the rapid, real-time estimation of flood risk on a worldwide scale.

Auditing machine learning-based (ML) healthcare tools for bias is critical to preventing patient harm, especially in communities that disproportionately face health inequities. General frameworks are becoming increasingly available to measure ML fairness gaps between groups. However, ML for health (ML4H) auditing principles call for a contextual, patient-centered approach to model assessment. Therefore, ML auditing tools must be (1) better aligned with ML4H auditing principles and (2) able to illuminate and characterize communities vulnerable to the most harm. To address this gap, we propose supplementing ML4H auditing frameworks with SLOGAN (patient Severity-based LOcal Group biAs detectioN), an automatic tool for capturing local biases in a clinical prediction task. SLOGAN adapts an existing tool, LOGAN (LOcal Group biAs detectioN), by contextualizing group bias detection in patient illness severity and past medical history. We investigate and compare SLOGAN's bias detection capabilities to LOGAN and other clustering techniques across patient subgroups in the MIMIC-III dataset. On average, SLOGAN identifies larger fairness disparities in over 75% of patient groups than LOGAN while maintaining clustering quality. Furthermore, in a diabetes case study, health disparity literature corroborates the characterizations of the most biased clusters identified by SLOGAN. Our results contribute to the broader discussion of how machine learning biases may perpetuate existing healthcare disparities.