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Prostate cancer patients who undergo prostatectomy are closely monitored for recurrence and metastasis using routine prostate-specific antigen (PSA) measurements. When PSA levels rise, salvage therapies are recommended to decrease the risk of metastasis. However, due to the side effects of these therapies and to avoid over-treatment, it is important to understand which patients and when to initiate these salvage therapies. In this work, we use the University of Michigan Prostatectomy registry Data to tackle this question. Due to the observational nature of this data, we face the challenge that PSA is simultaneously a time-varying confounder and an intermediate variable for salvage therapy. We define different causal salvage therapy effects defined conditionally on different specifications of the longitudinal PSA history. We then illustrate how these effects can be estimated using the framework of joint models for longitudinal and time-to-event data. All proposed methodology is implemented in the freely-available R package JMbayes2.

Pharmaceutical researchers are continually searching for techniques to improve both drug development processes and patient outcomes. An area of recent interest is the potential for machine learning (ML) applications within pharmacology. One such application not yet given close study is the unsupervised clustering of plasma concentration-time curves, hereafter, pharmacokinetic (PK) curves. In this paper, we present our findings on how to cluster PK curves by their similarity. Specifically, we find clustering to be effective at identifying similar-shaped PK curves and informative for understanding patterns within each cluster of PK curves. Because PK curves are time series data objects, our approach utilizes the extensive body of research related to the clustering of time series data as a starting point. As such, we examine many dissimilarity measures between time series data objects to find those most suitable for PK curves. We identify Euclidean distance as generally most appropriate for clustering PK curves, and we further show that dynamic time warping, Fr\'{e}chet, and structure-based measures of dissimilarity like correlation may produce unexpected results. As an illustration, we apply these methods in a case study with 250 PK curves used in a previous pharmacogenomic study. Our case study finds that an unsupervised ML clustering with Euclidean distance, without any subject genetic information, is able to independently validate the same conclusions as the reference pharmacogenomic results. To our knowledge, this is the first such demonstration. Further, the case study demonstrates how the clustering of PK curves may generate insights that could be difficult to perceive solely with population level summary statistics of PK metrics.

Thyroid disorders are most commonly diagnosed using high-resolution Ultrasound (US). Longitudinal nodule tracking is a pivotal diagnostic protocol for monitoring changes in pathological thyroid morphology. This task, however, imposes a substantial cognitive load on clinicians due to the inherent challenge of maintaining a mental 3D reconstruction of the organ. We thus present a framework for automated US image slice localization within a 3D shape representation to ease how such sonographic diagnoses are carried out. Our proposed method learns a common latent embedding space between US image patches and the 3D surface of an individual's thyroid shape, or a statistical aggregation in the form of a statistical shape model (SSM), via contrastive metric learning. Using cross-modality registration and Procrustes analysis, we leverage features from our model to register US slices to a 3D mesh representation of the thyroid shape. We demonstrate that our multi-modal registration framework can localize images on the 3D surface topology of a patient-specific organ and the mean shape of an SSM. Experimental results indicate slice positions can be predicted within an average of 1.2 mm of the ground-truth slice location on the patient-specific 3D anatomy and 4.6 mm on the SSM, exemplifying its usefulness for slice localization during sonographic acquisitions. Code is publically available: \href{//github.com/vuenc/slice-to-shape}{//github.com/vuenc/slice-to-shape}

The dynamics of affective decision making is considered for an intelligent network composed of agents with different types of memory: long-term and short-term memory. The consideration is based on probabilistic affective decision theory, which takes into account the rational utility of alternatives as well as the emotional alternative attractiveness. The objective of this paper is the comparison of two multistep operational algorithms of the intelligent network: one based on discrete dynamics and the other on continuous dynamics. By means of numerical analysis, it is shown that, depending on the network parameters, the characteristic probabilities for continuous and discrete operations can exhibit either close or drastically different behavior. Thus, depending on which algorithm is employed, either discrete or continuous, theoretical predictions can be rather different, which does not allow for a uniquely defined description of practical problems. This finding is important for understanding which of the algorithms is more appropriate for the correct analysis of decision-making tasks. A discussion is given, revealing that the discrete operation seems to be more realistic for describing intelligent networks as well as affective artificial intelligence.

Diagnostic investigation has an important role in risk stratification and clinical decision making of patients with suspected and documented Coronary Artery Disease (CAD). However, the majority of existing tools are primarily focused on the selection of gatekeeper tests, whereas only a handful of systems contain information regarding the downstream testing or treatment. We propose a multi-task deep learning model to support risk stratification and down-stream test selection for patients undergoing Coronary Computed Tomography Angiography (CCTA). The analysis included 14,021 patients who underwent CCTA between 2006 and 2017. Our novel multitask deep learning framework extends the state-of-the art Perceiver model to deal with real-world CCTA report data. Our model achieved an Area Under the receiver operating characteristic Curve (AUC) of 0.76 in CAD risk stratification, and 0.72 AUC in predicting downstream tests. Our proposed deep learning model can accurately estimate the likelihood of CAD and provide recommended downstream tests based on prior CCTA data. In clinical practice, the utilization of such an approach could bring a paradigm shift in risk stratification and downstream management. Despite significant progress using deep learning models for tabular data, they do not outperform gradient boosting decision trees, and further research is required in this area. However, neural networks appear to benefit more readily from multi-task learning than tree-based models. This could offset the shortcomings of using single task learning approach when working with tabular data.

We consider the problem of optimal unsignalized intersection management for continual streams of randomly arriving robots. This problem involves repeatedly solving different instances of a mixed integer program, for which the computation time using a naive optimization algorithm scales exponentially with the number of robots and lanes. Hence, such an approach is not suitable for real-time implementation. In this paper, we propose a solution framework that combines learning and sequential optimization. In particular, we propose an algorithm for learning a shared policy that given the traffic state information, determines the crossing order of the robots. Then, we optimize the trajectories of the robots sequentially according to that crossing order. This approach inherently guarantees safety at all times. We validate the performance of this approach using extensive simulations. Our approach, on average, significantly outperforms the heuristics from the literature. We also show through simulations that the computation time for our approach scales linearly with the number of robots. We further implement the learnt policies on physical robots with a few modifications to the solution framework to address real-world challenges and establish its real-time implementability.

Rule learning approaches for knowledge graph completion are efficient, interpretable and competitive to purely neural models. The rule aggregation problem is concerned with finding one plausibility score for a candidate fact which was simultaneously predicted by multiple rules. Although the problem is ubiquitous, as data-driven rule learning can result in noisy and large rulesets, it is underrepresented in the literature and its theoretical foundations have not been studied before in this context. In this work, we demonstrate that existing aggregation approaches can be expressed as marginal inference operations over the predicting rules. In particular, we show that the common Max-aggregation strategy, which scores candidates based on the rule with the highest confidence, has a probabilistic interpretation. Finally, we propose an efficient and overlooked baseline which combines the previous strategies and is competitive to computationally more expensive approaches.

Understanding causality helps to structure interventions to achieve specific goals and enables predictions under interventions. With the growing importance of learning causal relationships, causal discovery tasks have transitioned from using traditional methods to infer potential causal structures from observational data to the field of pattern recognition involved in deep learning. The rapid accumulation of massive data promotes the emergence of causal search methods with brilliant scalability. Existing summaries of causal discovery methods mainly focus on traditional methods based on constraints, scores and FCMs, there is a lack of perfect sorting and elaboration for deep learning-based methods, also lacking some considers and exploration of causal discovery methods from the perspective of variable paradigms. Therefore, we divide the possible causal discovery tasks into three types according to the variable paradigm and give the definitions of the three tasks respectively, define and instantiate the relevant datasets for each task and the final causal model constructed at the same time, then reviews the main existing causal discovery methods for different tasks. Finally, we propose some roadmaps from different perspectives for the current research gaps in the field of causal discovery and point out future research directions.

What is learned by sophisticated neural network agents such as AlphaZero? This question is of both scientific and practical interest. If the representations of strong neural networks bear no resemblance to human concepts, our ability to understand faithful explanations of their decisions will be restricted, ultimately limiting what we can achieve with neural network interpretability. In this work we provide evidence that human knowledge is acquired by the AlphaZero neural network as it trains on the game of chess. By probing for a broad range of human chess concepts we show when and where these concepts are represented in the AlphaZero network. We also provide a behavioural analysis focusing on opening play, including qualitative analysis from chess Grandmaster Vladimir Kramnik. Finally, we carry out a preliminary investigation looking at the low-level details of AlphaZero's representations, and make the resulting behavioural and representational analyses available online.

Due to their increasing spread, confidence in neural network predictions became more and more important. However, basic neural networks do not deliver certainty estimates or suffer from over or under confidence. Many researchers have been working on understanding and quantifying uncertainty in a neural network's prediction. As a result, different types and sources of uncertainty have been identified and a variety of approaches to measure and quantify uncertainty in neural networks have been proposed. This work gives a comprehensive overview of uncertainty estimation in neural networks, reviews recent advances in the field, highlights current challenges, and identifies potential research opportunities. It is intended to give anyone interested in uncertainty estimation in neural networks a broad overview and introduction, without presupposing prior knowledge in this field. A comprehensive introduction to the most crucial sources of uncertainty is given and their separation into reducible model uncertainty and not reducible data uncertainty is presented. The modeling of these uncertainties based on deterministic neural networks, Bayesian neural networks, ensemble of neural networks, and test-time data augmentation approaches is introduced and different branches of these fields as well as the latest developments are discussed. For a practical application, we discuss different measures of uncertainty, approaches for the calibration of neural networks and give an overview of existing baselines and implementations. Different examples from the wide spectrum of challenges in different fields give an idea of the needs and challenges regarding uncertainties in practical applications. Additionally, the practical limitations of current methods for mission- and safety-critical real world applications are discussed and an outlook on the next steps towards a broader usage of such methods is given.