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This paper reports a case study of an application of high-resolution agent-based modeling and simulation to pandemic response planning on a university campus. In the summer of 2020, we were tasked with a COVID-19 pandemic response project to create a detailed behavioral simulation model of the entire campus population at Binghamton University. We conceptualized this problem as an agent migration process on a multilayer transportation network, in which each layer represented a different transportation mode. As no direct data were available about people's behaviors on campus, we collected as much indirect information as possible to inform the agents' behavioral rules. Each agent was assumed to move along the shortest path between two locations within each transportation layer and switch layers at a parking lot or a bus stop, along with several other behavioral assumptions. Using this model, we conducted simulations of the whole campus population behaviors on a typical weekday, involving more than 25,000 agents. We measured the frequency of close social contacts at each spatial location and identified several busy locations and corridors on campus that needed substantial behavioral intervention. Moreover, systematic simulations with varying population density revealed that the effect of population density reduction was nonlinear, and that reducing the population density to 40-45% would be optimal and sufficient to suppress disease spreading on campus. These results were reported to the university administration and utilized in the pandemic response planning, which led to successful outcomes.

We consider the problem of selecting an optimal subset of information sources for a hypothesis testing/classification task where the goal is to identify the true state of the world from a finite set of hypotheses, based on finite observation samples from the sources. In order to characterize the learning performance, we propose a misclassification penalty framework, which enables non-uniform treatment of different misclassification errors. In a centralized Bayesian learning setting, we study two variants of the subset selection problem: (i) selecting a minimum cost information set to ensure that the maximum penalty of misclassifying the true hypothesis remains bounded and (ii) selecting an optimal information set under a limited budget to minimize the maximum penalty of misclassifying the true hypothesis. Under mild assumptions, we prove that the objective (or constraints) of these combinatorial optimization problems are weak (or approximate) submodular, and establish high-probability performance guarantees for greedy algorithms. Further, we propose an alternate metric for information set selection which is based on the total penalty of misclassification. We prove that this metric is submodular and establish near-optimal guarantees for the greedy algorithms for both the information set selection problems. Finally, we present numerical simulations to validate our theoretical results over several randomly generated instances.

Foundation models in computational pathology promise to unlock the development of new clinical decision support systems and models for precision medicine. However, there is a mismatch between most clinical analysis, which is defined at the level of one or more whole slide images, and foundation models to date, which process the thousands of image tiles contained in a whole slide image separately. The requirement to train a network to aggregate information across a large number of tiles in multiple whole slide images limits these models' impact. In this work, we present a slide-level foundation model for H&E-stained histopathology, PRISM, that builds on Virchow tile embeddings and leverages clinical report text for pre-training. Using the tile embeddings, PRISM produces slide-level embeddings with the ability to generate clinical reports, resulting in several modes of use. Using text prompts, PRISM achieves zero-shot cancer detection and sub-typing performance approaching and surpassing that of a supervised aggregator model. Using the slide embeddings with linear classifiers, PRISM surpasses supervised aggregator models. Furthermore, we demonstrate that fine-tuning of the PRISM slide encoder yields label-efficient training for biomarker prediction, a task that typically suffers from low availability of training data; an aggregator initialized with PRISM and trained on as little as 10% of the training data can outperform a supervised baseline that uses all of the data.

We consider a general proportional odds model for survival data under binary treatment, where the functional form of the covariates is left unspecified. We derive the efficient score for the conditional survival odds ratio given the covariates using modern semiparametric theory. The efficient score may be useful in the development of doubly robust estimators, although computational challenges remain.

Addressing the challenge of low-resource information extraction remains an ongoing issue due to the inherent information scarcity within limited training examples. Existing data augmentation methods, considered potential solutions, struggle to strike a balance between weak augmentation (e.g., synonym augmentation) and drastic augmentation (e.g., conditional generation without proper guidance). This paper introduces a novel paradigm that employs targeted augmentation and back validation to produce augmented examples with enhanced diversity, polarity, accuracy, and coherence. Extensive experimental results demonstrate the effectiveness of the proposed paradigm. Furthermore, identified limitations are discussed, shedding light on areas for future improvement.

In volume rendering, transfer functions are used to classify structures of interest, and to assign optical properties such as color and opacity. They are commonly defined as 1D or 2D functions that map simple features to these optical properties. As the process of designing a transfer function is typically tedious and unintuitive, several approaches have been proposed for their interactive specification. In this paper, we present a novel method to define transfer functions for volume rendering by leveraging the feature extraction capabilities of self-supervised pre-trained vision transformers. To design a transfer function, users simply select the structures of interest in a slice viewer, and our method automatically selects similar structures based on the high-level features extracted by the neural network. Contrary to previous learning-based transfer function approaches, our method does not require training of models and allows for quick inference, enabling an interactive exploration of the volume data. Our approach reduces the amount of necessary annotations by interactively informing the user about the current classification, so they can focus on annotating the structures of interest that still require annotation. In practice, this allows users to design transfer functions within seconds, instead of minutes. We compare our method to existing learning-based approaches in terms of annotation and compute time, as well as with respect to segmentation accuracy. Our accompanying video showcases the interactivity and effectiveness of our method.

We present the notion of a multilevel, slashable quorum system, where an application can obtain gradual levels of assurance that a certain value is bound to be decided (or "finalized") in a global consensus procedure, unless a large number of Byzantine processes are exposed to slashing (that is, penalty on staked assets). Our construction is a highly parameterized generalization of quorum systems based on finite projective spaces, with asymptotic high availability and optimal slashing properties. In particular, we show that any quorum system whose ground elements are disjoint subsets of nodes (e.g. "commmittees" in committee-based consensus protocols) has asymptotic high availability under very reasonable conditions, a general proof with significance of its own. Under similarly relaxed conditions, we show that our construction has asymptotically optimal slashing properties with respect to message complexity and process load; this illustrates a fundamental trade off between message complexity, load, and slashing. Our multilevel construction allows nodes to decide how many "levels" of finalization assurance they wish to obtain, noting that this functionality, if applied to a proof-of-stake blockchain, can be seen either as (i) a form of an early, slashing-based, probabilistic block finalization; or (ii) a service for reorg tolerance.

We investigate the impact of non-regular path expressions on the decidability of satisfiability checking and querying in description logics extending ALC. Our primary objects of interest are ALCreg and ALCvpl, the extensions of with path expressions employing, respectively, regular and visibly-pushdown languages. The first one, ALCreg, is a notational variant of the well-known Propositional Dynamic Logic of Fischer and Ladner. The second one, ALCvpl, was introduced and investigated by Loding and Serre in 2007. The logic ALCvpl generalises many known decidable non-regular extensions of ALCreg. We provide a series of undecidability results. First, we show that decidability of the concept satisfiability problem for ALCvpl is lost upon adding the seemingly innocent Self operator. Second, we establish undecidability for the concept satisfiability problem for ALCvpl extended with nominals. Interestingly, our undecidability proof relies only on one single non-regular (visibly-pushdown) language, namely on r#s# := { r^n s^n | n in N } for fixed role names r and s. Finally, in contrast to the classical database setting, we establish undecidability of query entailment for queries involving non-regular atoms from r#s#, already in the case of ALC-TBoxes.

We focus on a specific use case in anomaly detection where the distribution of normal samples is supported by a lower-dimensional manifold. Here, regularized autoencoders provide a popular approach by learning the identity mapping on the set of normal examples, while trying to prevent good reconstruction on points outside of the manifold. Typically, this goal is implemented by controlling the capacity of the model, either directly by reducing the size of the bottleneck layer or implicitly by imposing some sparsity (or contraction) constraints on parts of the corresponding network. However, neither of these techniques does explicitly penalize the reconstruction of anomalous signals often resulting in poor detection. We tackle this problem by adapting a self-supervised learning regime that exploits discriminative information during training but focuses on the submanifold of normal examples. Informally, our training objective regularizes the model to produce locally consistent reconstructions, while replacing irregularities by acting as a filter that removes anomalous patterns. To support this intuition, we perform a rigorous formal analysis of the proposed method and provide a number of interesting insights. In particular, we show that the resulting model resembles a non-linear orthogonal projection of partially corrupted images onto the submanifold of uncorrupted samples. On the other hand, we identify the orthogonal projection as an optimal solution for a number of regularized autoencoders including the contractive and denoising variants. We support our theoretical analysis by empirical evaluation of the resulting detection and localization performance of the proposed method. In particular, we achieve a new state-of-the-art result on the MVTec AD dataset -- a challenging benchmark for visual anomaly detection in the manufacturing domain.

Data irregularity in cancer genomics studies has been widely observed in the form of outliers and heavy-tailed distributions in the complex traits. In the past decade, robust variable selection methods have emerged as powerful alternatives to the non-robust ones to identify important genes associated with heterogeneous disease traits and build superior predictive models. In this study, to keep the remarkable features of the quantile LASSO and fully Bayesian regularized quantile regression while overcoming their disadvantage in the analysis of high-dimensional genomics data, we propose the spike-and-slab quantile LASSO through a fully Bayesian spike-and-slab formulation under the robust likelihood by adopting the asymmetric Laplace distribution (ALD). The proposed robust method has inherited the prominent properties of selective shrinkage and self-adaptivity to the sparsity pattern from the spike-and-slab LASSO (Ro\v{c}kov\'a and George, 2018). Furthermore, the spike-and-slab quantile LASSO has a computational advantage to locate the posterior modes via soft-thresholding rule guided Expectation-Maximization (EM) steps in the coordinate descent framework, a phenomenon rarely observed for robust regularization with non-differentiable loss functions. We have conducted comprehensive simulation studies with a variety of heavy-tailed errors in both homogeneous and heterogeneous model settings to demonstrate the superiority of the spike-and-slab quantile LASSO over its competing methods. The advantage of the proposed method has been further demonstrated in case studies of the lung adenocarcinomas (LUAD) and skin cutaneous melanoma (SKCM) data from The Cancer Genome Atlas (TCGA).