The relationship between acute kidney injury (AKI) prediction and nephrotoxic drugs, or drugs that adversely affect kidney function, is one that has yet to be explored in the critical care setting. One contributing factor to this gap in research is the limited investigation of drug modalities in the intensive care unit (ICU) context, due to the challenges of processing prescription data into the corresponding drug representations and a lack in the comprehensive understanding of these drug representations. This study addresses this gap by proposing a novel approach that leverages patient prescription data as a modality to improve existing models for AKI prediction. We base our research on Electronic Health Record (EHR) data, extracting the relevant patient prescription information and converting it into the selected drug representation for our research, the extended-connectivity fingerprint (ECFP). Furthermore, we adopt a unique multimodal approach, developing machine learning models and 1D Convolutional Neural Networks (CNN) applied to clinical drug representations, establishing a procedure which has not been used by any previous studies predicting AKI. The findings showcase a notable improvement in AKI prediction through the integration of drug embeddings and other patient cohort features. By using drug features represented as ECFP molecular fingerprints along with common cohort features such as demographics and lab test values, we achieved a considerable improvement in model performance for the AKI prediction task over the baseline model which does not include the drug representations as features, indicating that our distinct approach enhances existing baseline techniques and highlights the relevance of drug data in predicting AKI in the ICU setting
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Integration：Integration, the VLSI Journal。
Explanation：集成，VLSI雜志。
Publisher：Elsevier。
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Cellular reprogramming can be used for both the prevention and cure of different diseases. However, the efficiency of discovering reprogramming strategies with classical wet-lab experiments is hindered by lengthy time commitments and high costs. In this study, we develop a novel computational framework based on deep reinforcement learning that facilitates the identification of reprogramming strategies. For this aim, we formulate a control problem in the context of cellular reprogramming for the frameworks of BNs and PBNs under the asynchronous update mode. Furthermore, we introduce the notion of a pseudo-attractor and a procedure for identification of pseudo-attractor state during training. Finally, we devise a computational framework for solving the control problem, which we test on a number of different models.
Chemical synthesis, which is crucial for advancing material synthesis and drug discovery, impacts various sectors including environmental science and healthcare. The rise of technology in chemistry has generated extensive chemical data, challenging researchers to discern patterns and refine synthesis processes. Artificial intelligence (AI) helps by analyzing data to optimize synthesis and increase yields. However, AI faces challenges in processing literature data due to the unstructured format and diverse writing style of chemical literature. To overcome these difficulties, we introduce an end-to-end AI agent framework capable of high-fidelity extraction from extensive chemical literature. This AI agent employs large language models (LLMs) for prompt generation and iterative optimization. It functions as a chemistry assistant, automating data collection and analysis, thereby saving manpower and enhancing performance. Our framework's efficacy is evaluated using accuracy, recall, and F1 score of reaction condition data, and we compared our method with human experts in terms of content correctness and time efficiency. The proposed approach marks a significant advancement in automating chemical literature extraction and demonstrates the potential for AI to revolutionize data management and utilization in chemistry.
Due to its optimal complexity, the multigrid (MG) method is one of the most popular approaches for solving large-scale linear systems arising from the discretization of partial differential equations. However, the parallel implementation of standard MG methods, which are inherently multiplicative, suffers from increasing communication complexity. In such cases, the additive variants of MG methods provide a good alternative due to their inherently parallel nature, although they exhibit slower convergence. This work combines the additive multigrid method with the multipreconditioned conjugate gradient (MPCG) method. In the proposed approach, the MPCG method employs the corrections from the different levels of the MG hierarchy as separate preconditioned search directions. In this approach, the MPCG method updates the current iterate by using the linear combination of the preconditioned search directions, where the optimal coefficients for the linear combination are computed by exploiting the energy norm minimization of the CG method. The idea behind our approach is to combine the $A$-conjugacy of the search directions of the MPCG method and the quasi $H_1$-orthogonality of the corrections from the MG hierarchy. In the numerical section, we study the performance of the proposed method compared to the standard additive and multiplicative MG methods used as preconditioners for the CG method.
Accurate frictional contact is critical in simulating the assembly of rod-like structures in the practical world, such as knots, hairs, flagella, and more. Due to their high geometric nonlinearity and elasticity, rod-on-rod contact remains a challenging problem tackled by researchers in both computational mechanics and computer graphics. Typically, frictional contact is regarded as constraints for the equations of motions of a system. Such constraints are often computed independently at every time step in a dynamic simulation, thus slowing down the simulation and possibly introducing numerical convergence issues. This paper proposes a fully implicit penalty-based frictional contact method, Implicit Contact Model (IMC), that efficiently and robustly captures accurate frictional contact responses. We showcase our algorithm's performance in achieving visually realistic results for the challenging and novel contact scenario of flagella bundling in fluid medium, a significant phenomenon in biology that motivates novel engineering applications in soft robotics. In addition to this, we offer a side-by-side comparison with Incremental Potential Contact (IPC), a state-of-the-art contact handling algorithm. We show that IMC possesses comparable performance to IPC while converging at a faster rate.
Proxy causal learning (PCL) is a method for estimating the causal effect of treatments on outcomes in the presence of unobserved confounding, using proxies (structured side information) for the confounder. This is achieved via two-stage regression: in the first stage, we model relations among the treatment and proxies; in the second stage, we use this model to learn the effect of treatment on the outcome, given the context provided by the proxies. PCL guarantees recovery of the true causal effect, subject to identifiability conditions. We propose a novel method for PCL, the deep feature proxy variable method (DFPV), to address the case where the proxies, treatments, and outcomes are high-dimensional and have nonlinear complex relationships, as represented by deep neural network features. We show that DFPV outperforms recent state-of-the-art PCL methods on challenging synthetic benchmarks, including settings involving high dimensional image data. Furthermore, we show that PCL can be applied to off-policy evaluation for the confounded bandit problem, in which DFPV also exhibits competitive performance.
Dynamic treatment regimes (DTRs) are sequences of functions that formalize the process of precision medicine. DTRs take as input patient information and output treatment recommendations. A major focus of the DTR literature has been on the estimation of optimal DTRs, the sequences of decision rules that result in the best outcome in expectation, across the complete population were they to be applied. While there is a rich literature on optimal DTR estimation, to date there has been minimal consideration of the impacts of nonadherence on these estimation procedures. Nonadherence refers to any process through that an individual's prescribed treatment does not match their true treatment. We explore the impacts of nonadherence and demonstrate that generally, when nonadherence is ignored, suboptimal regimes will be estimated. In light of these findings we propose a method for estimating optimal DTRs in the presence of nonadherence. The resulting estimators are consistent and asymptotically normal, with a double robustness property. Using simulations we demonstrate the reliability of these results, and illustrate comparable performance between the proposed estimation procedure adjusting for the impacts of nonadherence and estimators that are computed on data without nonadherence.
We explore the use of aggregative crowdsourced forecasting (ACF) as a mechanism to help operationalize ``collective intelligence'' of human-machine teams for coordinated actions. We adopt the definition for Collective Intelligence as: ``A property of groups that emerges from synergies among data-information-knowledge, software-hardware, and individuals (those with new insights as well as recognized authorities) that enables just-in-time knowledge for better decisions than these three elements acting alone.'' Collective Intelligence emerges from new ways of connecting humans and AI to enable decision-advantage, in part by creating and leveraging additional sources of information that might otherwise not be included. Aggregative crowdsourced forecasting (ACF) is a recent key advancement towards Collective Intelligence wherein predictions (X\% probability that Y will happen) and rationales (why I believe it is this probability that X will happen) are elicited independently from a diverse crowd, aggregated, and then used to inform higher-level decision-making. This research asks whether ACF, as a key way to enable Operational Collective Intelligence, could be brought to bear on operational scenarios (i.e., sequences of events with defined agents, components, and interactions) and decision-making, and considers whether such a capability could provide novel operational capabilities to enable new forms of decision-advantage.
Believable proxies of human behavior can empower interactive applications ranging from immersive environments to rehearsal spaces for interpersonal communication to prototyping tools. In this paper, we introduce generative agents--computational software agents that simulate believable human behavior. Generative agents wake up, cook breakfast, and head to work; artists paint, while authors write; they form opinions, notice each other, and initiate conversations; they remember and reflect on days past as they plan the next day. To enable generative agents, we describe an architecture that extends a large language model to store a complete record of the agent's experiences using natural language, synthesize those memories over time into higher-level reflections, and retrieve them dynamically to plan behavior. We instantiate generative agents to populate an interactive sandbox environment inspired by The Sims, where end users can interact with a small town of twenty five agents using natural language. In an evaluation, these generative agents produce believable individual and emergent social behaviors: for example, starting with only a single user-specified notion that one agent wants to throw a Valentine's Day party, the agents autonomously spread invitations to the party over the next two days, make new acquaintances, ask each other out on dates to the party, and coordinate to show up for the party together at the right time. We demonstrate through ablation that the components of our agent architecture--observation, planning, and reflection--each contribute critically to the believability of agent behavior. By fusing large language models with computational, interactive agents, this work introduces architectural and interaction patterns for enabling believable simulations of human behavior.
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.
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.
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