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Indolent cancers are characterized by long overall survival (OS) times. Therefore, powering a clinical trial to provide definitive assessment of the effects of an experimental intervention on OS in a reasonable timeframe is generally infeasible. Instead, the primary outcome in many pivotal trials is an intermediate clinical response such as progression-free survival (PFS). In several recently reported pivotal trials of interventions for indolent cancers that yielded promising results on an intermediate outcome, however, more mature data or post-approval trials showed concerning OS trends. These problematic results have prompted a keen interest in quantitative approaches for monitoring OS that can support regulatory decision-making related to the risk of an unacceptably large detrimental effect on OS. For example, the US Food and Drug Administration, the American Association for Cancer Research, and the American Statistical Association recently organized a one-day multi-stakeholder workshop entitled 'Overall Survival in Oncology Clinical Trials'. In this paper, we propose OS monitoring guidelines tailored for the setting of indolent cancers. Our pragmatic approach is modeled, in part, on the monitoring guidelines the FDA has used in cardiovascular safety trials conducted in Type 2 Diabetes Mellitus. We illustrate proposals through application to several examples informed by actual case studies.

Most of the recent work in psychedelic neuroscience has been done using non-invasive neuroimaging, with data recorded from the brains of adult volunteers under the influence of a variety of drugs. While this data provides holistic insights into the effects of psychedelics on whole-brain dynamics, the effects of psychedelics on the meso-scale dynamics of cortical circuits remains much less explored. Here, we report the effects of the serotonergic psychedelic N,N-diproptyltryptamine (DPT) on information-processing dynamics in a sample of in vitro organotypic cultures made from rat cortical tissue. Three hours of spontaneous activity were recorded: an hour of pre-drug control, and hour of exposure to 10$\mu$M DPT solution, and a final hour of washout, once again under control conditions. We found that DPT reversibly alters information dynamics in multiple ways: first, the DPT condition was associated with higher entropy of spontaneous firing activity and reduced the amount of time information was stored in individual neurons. Second, DPT also reduced the reversibility of neural activity, increasing the entropy produced and suggesting a drive away from equilibrium. Third, DPT altered the structure of neuronal circuits, decreasing the overall information flow coming into each neuron, but increasing the number of weak connections, creating a dynamic that combines elements of integration and disintegration. Finally, DPT decreased the higher-order statistical synergy present in sets of three neurons. Collectively, these results paint a complex picture of how psychedelics regulate information processing in meso-scale cortical tissue. Implications for existing hypotheses of psychedelic action, such as the Entropic Brain Hypothesis, are discussed.

In the emerging field of mechanical metamaterials, using periodic lattice structures as a primary ingredient is relatively frequent. However, the choice of aperiodic lattices in these structures presents unique advantages regarding failure, e.g., buckling or fracture, because avoiding repeated patterns prevents global failures, with local failures occurring in turn that can beneficially delay structural collapse. Therefore, it is expedient to develop models for computing efficiently the effective mechanical properties in lattices from different general features while addressing the challenge of presenting topologies (or graphs) of different sizes. In this paper, we develop a deep learning model to predict energetically-equivalent mechanical properties of linear elastic lattices effectively. Considering the lattice as a graph and defining material and geometrical features on such, we show that Graph Neural Networks provide more accurate predictions than a dense, fully connected strategy, thanks to the geometrically induced bias through graph representation, closer to the underlying equilibrium laws from mechanics solved in the direct problem. Leveraging the efficient forward-evaluation of a vast number of lattices using this surrogate enables the inverse problem, i.e., to obtain a structure having prescribed specific behavior, which is ultimately suitable for multiscale structural optimization problems.

In survival contexts, substantial literature exists on estimating optimal treatment regimes, where treatments are assigned based on personal characteristics for the purpose of maximizing the survival probability. These methods assume that a set of covariates is sufficient to deconfound the treatment-outcome relationship. Nevertheless, the assumption can be limited in observational studies or randomized trials in which non-adherence occurs. Thus, we propose a novel approach for estimating the optimal treatment regime when certain confounders are not observable and a binary instrumental variable is available. Specifically, via a binary instrumental variable, we propose two semiparametric estimators for the optimal treatment regime by maximizing Kaplan-Meier-like estimators within a pre-defined class of regimes, one of which possesses the desirable property of double robustness. Because the Kaplan-Meier-like estimators are jagged, we incorporate kernel smoothing methods to enhance their performance. Under appropriate regularity conditions, the asymptotic properties are rigorously established. Furthermore, the finite sample performance is assessed through simulation studies. Finally, we exemplify our method using data from the National Cancer Institute's (NCI) prostate, lung, colorectal, and ovarian cancer screening trial.

The rising popularity of deep learning (DL) methods and techniques has invigorated interest in the topic of SE4DL, the application of software engineering (SE) practices on deep learning software. Despite the novel engineering challenges brought on by the data-driven and non-deterministic paradigm of DL software, little work has been invested into developing AI-targeted SE tools. On the other hand, tools tackling more general engineering issues in DL are actively used and referred to under the umbrella term of ``MLOps tools''. Furthermore, the available literature supports the utility of conventional SE tooling in DL software development. Building upon previous MSR research on tool usage in open-source software works, we identify conventional and MLOps tools adopted in popular applied DL projects that use Python as the main programming language. About 70% of the GitHub repositories mined contained at least one conventional SE tool. Software configuration management tools are the most adopted, while the opposite applies to maintenance tools. Substantially fewer MLOps tools were in use, with only 9 tools out of a sample of 80 used in at least one repository. The majority of them were open-source rather than proprietary. One of these tools, TensorBoard, was found to be adopted in about half of the repositories in our study. Consequently, the use of conventional SE tooling demonstrates its relevance to DL software. Further research is recommended on the adoption of MLOps tooling by open-source projects, focusing on the relevance of particular tool types, the development of required tools, as well as ways to promote the use of already available tools.

For multi-scale problems, the conventional physics-informed neural networks (PINNs) face some challenges in obtaining available predictions. In this paper, based on PINNs, we propose a practical deep learning framework for multi-scale problems by reconstructing the loss function and associating it with special neural network architectures. New PINN methods derived from the improved PINN framework differ from the conventional PINN method mainly in two aspects. First, the new methods use a novel loss function by modifying the standard loss function through a (grouping) regularization strategy. The regularization strategy implements a different power operation on each loss term so that all loss terms composing the loss function are of approximately the same order of magnitude, which makes all loss terms be optimized synchronously during the optimization process. Second, for the multi-frequency or high-frequency problems, in addition to using the modified loss function, new methods upgrade the neural network architecture from the common fully-connected neural network to special network architectures such as the Fourier feature architecture, and the integrated architecture developed by us. The combination of the above two techniques leads to a significant improvement in the computational accuracy of multi-scale problems. Several challenging numerical examples demonstrate the effectiveness of the proposed methods. The proposed methods not only significantly outperform the conventional PINN method in terms of computational efficiency and computational accuracy, but also compare favorably with the state-of-the-art methods in the recent literature. The improved PINN framework facilitates better application of PINNs to multi-scale problems.

Due to cancer's complex nature and variable response to therapy, precision oncology informed by omics sequence analysis has become the current standard of care. However, the amount of data produced for each patients makes it difficult to quickly identify the best treatment regimen. Moreover, limited data availability has hindered computational methods' abilities to learn patterns associated with effective drug-cell line pairs. In this work, we propose the use of contrastive learning to improve learned drug and cell line representations by preserving relationship structures associated with drug mechanism of action and cell line cancer types. In addition to achieving enhanced performance relative to a state-of-the-art method, we find that classifiers using our learned representations exhibit a more balances reliance on drug- and cell line-derived features when making predictions. This facilitates more personalized drug prioritizations that are informed by signals related to drug resistance.

The effects of treatments on continuous outcomes can be estimated by the mean difference (i.e. by measurement units) and the relative effect scales (i.e. by percentages), both of which provide only a single effect size estimate over the study population. Quantile treatment effect (QTE) analysis is more informative as it describes the effect of the treatment across the whole population. A drawback of QTE has been that it is usually presented over the quantiles of the control group distribution, whereas presentation over the measurement units is often more informative. We developed a method to estimate back-transformed QTE (BQTE), that presents QTE as a function of the outcome value in the control group, using piecewise linear interpolation and bootstrapping. We further applied the BQTE function to provide informative bounds on the treatment effect at the upper and lower tails of the population. To illustrate the approach, we used 3 data sets of treatment for the common cold: zinc gluconate lozenges, zinc acetate lozenges, and nasal carrageenan. In all data sets, the relative scale provided a better summary of the BQTE distribution than the mean difference. The BQTE approach is particularly useful for describing the variability of effects on the duration of illnesses, length of hospital stay and other continuous outcomes that can vary greatly in the population. Using this method, it is possible to present the QTE by the measurement units, which provides an informative addition to the standard presentation by quantiles.

Difference-in-differences (DID) is a popular approach to identify the causal effects of treatments and policies in the presence of unmeasured confounding. DID identifies the sample average treatment effect in the treated (SATT). However, a goal of such research is often to inform decision-making in target populations outside the treated sample. Transportability methods have been developed to extend inferences from study samples to external target populations; these methods have primarily been developed and applied in settings where identification is based on conditional independence between the treatment and potential outcomes, such as in a randomized trial. This paper develops identification and estimators for effects in a target population, based on DID conducted in a study sample that differs from the target population. We present a range of assumptions under which one may identify causal effects in the target population and employ causal diagrams to illustrate these assumptions. In most realistic settings, results depend critically on the assumption that any unmeasured confounders are not effect measure modifiers on the scale of the effect of interest. We develop several estimators of transported effects, including a doubly robust estimator based on the efficient influence function. Simulation results support theoretical properties of the proposed estimators. We discuss the potential application of our approach to a study of the effects of a US federal smoke-free housing policy, where the original study was conducted in New York City alone and the goal is extend inferences to other US cities.

Breast cancer remains a global challenge, causing over 1 million deaths globally in 2018. To achieve earlier breast cancer detection, screening x-ray mammography is recommended by health organizations worldwide and has been estimated to decrease breast cancer mortality by 20-40%. Nevertheless, significant false positive and false negative rates, as well as high interpretation costs, leave opportunities for improving quality and access. To address these limitations, there has been much recent interest in applying deep learning to mammography; however, obtaining large amounts of annotated data poses a challenge for training deep learning models for this purpose, as does ensuring generalization beyond the populations represented in the training dataset. Here, we present an annotation-efficient deep learning approach that 1) achieves state-of-the-art performance in mammogram classification, 2) successfully extends to digital breast tomosynthesis (DBT; "3D mammography"), 3) detects cancers in clinically-negative prior mammograms of cancer patients, 4) generalizes well to a population with low screening rates, and 5) outperforms five-out-of-five full-time breast imaging specialists by improving absolute sensitivity by an average of 14%. Our results demonstrate promise towards software that can improve the accuracy of and access to screening mammography worldwide.