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The matched case-control design, up until recently mostly pertinent to epidemiological studies, is becoming customary in biomedical applications as well. For instance, in omics studies, it is quite common to compare cancer and healthy tissue from the same patient. Furthermore, researchers today routinely collect data from various and variable sources that they wish to relate to the case-control status. This highlights the need to develop and implement statistical methods that can take these tendencies into account. We present an R package penalizedclr, that provides an implementation of the penalized conditional logistic regression model for analyzing matched case-control studies. It allows for different penalties for different blocks of covariates, and it is therefore particularly useful in the presence of multi-source omics data. Both L1 and L2 penalties are implemented. Additionally, the package implements stability selection for variable selection in the considered regression model. The proposed method fills a gap in the available software for fitting high-dimensional conditional logistic regression model accounting for the matched design and block structure of predictors/features. The output consists of a set of selected variables that are significantly associated with case-control status. These features can then be investigated in terms of functional interpretation or validation in further, more targeted studies.

Autonomous vehicles rely on accurate trajectory prediction to inform decision-making processes related to navigation and collision avoidance. However, current trajectory prediction models show signs of overfitting, which may lead to unsafe or suboptimal behavior. To address these challenges, this paper presents a comprehensive framework that categorizes and assesses the definitions and strategies used in the literature on evaluating and improving the robustness of trajectory prediction models. This involves a detailed exploration of various approaches, including data slicing methods, perturbation techniques, model architecture changes, and post-training adjustments. In the literature, we see many promising methods for increasing robustness, which are necessary for safe and reliable autonomous driving.

Mediation analysis is a statistical approach that can provide insights regarding the intermediary processes by which an intervention or exposure affects a given outcome. Mediation analyses rose to prominence, particularly in social science research, with the publication of the seminal paper by Baron and Kenny and is now commonly applied in many research disciplines, including health services research. Despite the growth in popularity, applied researchers may still encounter challenges in terms of conducting mediation analyses in practice. In this paper, we provide an overview of conceptual and methodological challenges that researchers face when conducting mediation analyses. Specifically, we discuss the following key challenges: (1) Conceptually differentiating mediators from other third variables, (2) Extending beyond the single mediator context, (3) Identifying appropriate datasets in which measurement and temporal ordering supports the hypothesized mediation model, (4) Selecting mediation effects that reflect the scientific question of interest, (5) Assessing the validity of underlying assumptions of no omitted confounders, (6) Addressing measurement error regarding the mediator, and (7) Clearly reporting results from mediation analyses. We discuss each challenge and highlight ways in which the applied researcher can approach these challenges.

Several recent initiatives have proposed new directions for research practices and their operations in the computer science community, from updated codes of conduct that clarify the use of AI-assisted tools to the inclusion of ethical statements and the organization of working groups on the environmental footprint of digitalization. In this position paper, we focus on the specific case of networking research. We reflect on the technical realization of the community and its incidence beyond techno-centric contributions. In particular, we structure the discussion around two frameworks that were recently developed in different contexts to describe the sense of engagement and responsibilities to which the practitioner of a computing-related area may be confronted.

Effect modification occurs when the impact of the treatment on an outcome varies based on the levels of other covariates known as effect modifiers. Modeling of these effect differences is important for etiological goals and for purposes of optimizing treatment. Structural nested mean models (SNMMs) are useful causal models for estimating the potentially heterogeneous effect of a time-varying exposure on the mean of an outcome in the presence of time-varying confounding. In longitudinal health studies, information on many demographic, behavioural, biological, and clinical covariates may be available, among which some might cause heterogeneous treatment effects. A data-driven approach for selecting the effect modifiers of an exposure may be necessary if these effect modifiers are \textit{a priori} unknown and need to be identified. Although variable selection techniques are available in the context of estimating conditional average treatment effects using marginal structural models, or in the context of estimating optimal dynamic treatment regimens, all of these methods consider an outcome measured at a single point in time. In the context of an SNMM for repeated outcomes, we propose a doubly robust penalized G-estimator for the causal effect of a time-varying exposure with a simultaneous selection of effect modifiers and prove the oracle property of our estimator. We conduct a simulation study to evaluate the performance of the proposed estimator in finite samples and for verification of its double-robustness property. Our work is motivated by a study of hemodiafiltration for treating patients with end-stage renal disease at the Centre Hospitalier de l'Universit\'e de Montr\'eal.

Aqueous solubility is a valuable yet challenging property to predict. Computing solubility using first-principles methods requires accounting for the competing effects of entropy and enthalpy, resulting in long computations for relatively poor accuracy. Data-driven approaches, such as deep learning, offer improved accuracy and computational efficiency but typically lack uncertainty quantification. Additionally, ease of use remains a concern for any computational technique, resulting in the sustained popularity of group-based contribution methods. In this work, we addressed these problems with a deep learning model with predictive uncertainty that runs on a static website (without a server). This approach moves computing needs onto the website visitor without requiring installation, removing the need to pay for and maintain servers. Our model achieves satisfactory results in solubility prediction. Furthermore, we demonstrate how to create molecular property prediction models that balance uncertainty and ease of use. The code is available at //github.com/ur-whitelab/mol.dev, and the model is usable at //mol.dev.

In instrumental variable (IV) settings, such as in imperfect randomized trials and observational studies with Mendelian randomization, one may encounter a continuous exposure, the causal effect of which is not of true interest. Instead, scientific interest may lie in a coarsened version of this exposure. Although there is a lengthy literature on the impact of coarsening of an exposure with several works focusing specifically on IV settings, all methods proposed in this literature require parametric assumptions. Instead, just as in the standard IV setting, one can consider partial identification via bounds making no parametric assumptions. This was first pointed out in Alexander Balke's PhD dissertation. We extend and clarify his work and derive novel bounds in several settings, including for a three-level IV, which will most likely be the case in Mendelian randomization. We demonstrate our findings in two real data examples, a randomized trial for peanut allergy in infants and a Mendelian randomization setting investigating the effect of homocysteine on cardiovascular disease.

Predicting and understanding the changes in cognitive performance, especially after a longitudinal intervention, is a fundamental goal in neuroscience. Longitudinal brain stimulation-based interventions like transcranial direct current stimulation (tDCS) induce short-term changes in the resting membrane potential and influence cognitive processes. However, very little research has been conducted on predicting these changes in cognitive performance post-intervention. In this research, we intend to address this gap in the literature by employing different EEG-based functional connectivity analyses and machine learning algorithms to predict changes in cognitive performance in a complex multitasking task. Forty subjects were divided into experimental and active-control conditions. On Day 1, all subjects executed a multitasking task with simultaneous 32-channel EEG being acquired. From Day 2 to Day 7, subjects in the experimental condition undertook 15 minutes of 2mA anodal tDCS stimulation during task training. Subjects in the active-control condition undertook 15 minutes of sham stimulation during task training. On Day 10, all subjects again executed the multitasking task with EEG acquisition. Source-level functional connectivity metrics, namely phase lag index and directed transfer function, were extracted from the EEG data on Day 1 and Day 10. Various machine learning models were employed to predict changes in cognitive performance. Results revealed that the multi-layer perceptron and directed transfer function recorded a cross-validation training RMSE of 5.11% and a test RMSE of 4.97%. We discuss the implications of our results in developing real-time cognitive state assessors for accurately predicting cognitive performance in dynamic and complex tasks post-tDCS intervention

With the development and popularity of sensors installed in manufacturing systems, complex data are collected during manufacturing processes, which brings challenges for traditional process control methods. This paper proposes a novel process control and monitoring method for the complex structure of high-dimensional image-based overlay errors (modeled in tensor form), which are collected in semiconductor manufacturing processes. The proposed method aims to reduce overlay errors using limited control recipes. We first build a high-dimensional process model and propose different tensor-on-vector regression algorithms to estimate parameters in the model to alleviate the curse of dimensionality. Then, based on the estimate of tensor parameters, the exponentially weighted moving average (EWMA) controller for tensor data is designed whose stability is theoretically guaranteed. Considering the fact that low-dimensional control recipes cannot compensate for all high-dimensional disturbances on the image, control residuals are monitored to prevent significant drifts of uncontrollable high-dimensional disturbances. Through extensive simulations and real case studies, the performances of parameter estimation algorithms and the EWMA controller in tensor space are evaluated. Compared with existing image-based feedback controllers, the superiority of our method is verified especially when disturbances are not stable.

Artificial neural networks thrive in solving the classification problem for a particular rigid task, acquiring knowledge through generalized learning behaviour from a distinct training phase. The resulting network resembles a static entity of knowledge, with endeavours to extend this knowledge without targeting the original task resulting in a catastrophic forgetting. Continual learning shifts this paradigm towards networks that can continually accumulate knowledge over different tasks without the need to retrain from scratch. We focus on task incremental classification, where tasks arrive sequentially and are delineated by clear boundaries. Our main contributions concern 1) a taxonomy and extensive overview of the state-of-the-art, 2) a novel framework to continually determine the stability-plasticity trade-off of the continual learner, 3) a comprehensive experimental comparison of 11 state-of-the-art continual learning methods and 4 baselines. We empirically scrutinize method strengths and weaknesses on three benchmarks, considering Tiny Imagenet and large-scale unbalanced iNaturalist and a sequence of recognition datasets. We study the influence of model capacity, weight decay and dropout regularization, and the order in which the tasks are presented, and qualitatively compare methods in terms of required memory, computation time, and storage.