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"Recommendation": models, code, and papers

Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs

Dec 22, 2021
Lauren M. Sanders, Jason H. Yang, Ryan T. Scott, Amina Ann Qutub, Hector Garcia Martin, Daniel C. Berrios, Jaden J. A. Hastings, Jon Rask, Graham Mackintosh, Adrienne L. Hoarfrost, Stuart Chalk, John Kalantari, Kia Khezeli, Erik L. Antonsen, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Guillermo M. Delgado-Aparicio, Benjamin S. Glicksberg, Casey S. Greene, Melissa Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Christopher E. Mason, Mona Matar, George I. Mias, Jack Miller, Jerry G. Myers Jr., Charlotte Nelson, Jonathan Oribello, Seung-min Park, Patricia Parsons-Wingerter, R. K. Prabhu, Robert J. Reynolds, Amanda Saravia-Butler, Suchi Saria, Aenor Sawyer, Nitin Kumar Singh, Frank Soboczenski, Michael Snyder, Karthik Soman, Corey A. Theriot, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Marinka Zitnik, Sylvain V. Costes

Space biology research aims to understand fundamental effects of spaceflight on organisms, develop foundational knowledge to support deep space exploration, and ultimately bioengineer spacecraft and habitats to stabilize the ecosystem of plants, crops, microbes, animals, and humans for sustained multi-planetary life. To advance these aims, the field leverages experiments, platforms, data, and model organisms from both spaceborne and ground-analog studies. As research is extended beyond low Earth orbit, experiments and platforms must be maximally autonomous, light, agile, and intelligent to expedite knowledge discovery. Here we present a summary of recommendations from a workshop organized by the National Aeronautics and Space Administration on artificial intelligence, machine learning, and modeling applications which offer key solutions toward these space biology challenges. In the next decade, the synthesis of artificial intelligence into the field of space biology will deepen the biological understanding of spaceflight effects, facilitate predictive modeling and analytics, support maximally autonomous and reproducible experiments, and efficiently manage spaceborne data and metadata, all with the goal to enable life to thrive in deep space.

* 28 pages, 4 figures 

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NarrationBot and InfoBot: A Hybrid System for Automated Video Description

Nov 07, 2021
Shasta Ihorn, Yue-Ting Siu, Aditya Bodi, Lothar Narins, Jose M. Castanon, Yash Kant, Abhishek Das, Ilmi Yoon, Pooyan Fazli

Video accessibility is crucial for blind and low vision users for equitable engagements in education, employment, and entertainment. Despite the availability of professional and amateur services and tools, most human-generated descriptions are expensive and time consuming. Moreover, the rate of human-generated descriptions cannot match the speed of video production. To overcome the increasing gaps in video accessibility, we developed a hybrid system of two tools to 1) automatically generate descriptions for videos and 2) provide answers or additional descriptions in response to user queries on a video. Results from a mixed-methods study with 26 blind and low vision individuals show that our system significantly improved user comprehension and enjoyment of selected videos when both tools were used in tandem. In addition, participants reported no significant difference in their ability to understand videos when presented with autogenerated descriptions versus human-revised autogenerated descriptions. Our results demonstrate user enthusiasm about the developed system and its promise for providing customized access to videos. We discuss the limitations of the current work and provide recommendations for the future development of automated video description tools.

* 14 pages 

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MUSBO: Model-based Uncertainty Regularized and Sample Efficient Batch Optimization for Deployment Constrained Reinforcement Learning

Feb 23, 2021
DiJia Su, Jason D. Lee, John M. Mulvey, H. Vincent Poor

In many contemporary applications such as healthcare, finance, robotics, and recommendation systems, continuous deployment of new policies for data collection and online learning is either cost ineffective or impractical. We consider a setting that lies between pure offline reinforcement learning (RL) and pure online RL called deployment constrained RL in which the number of policy deployments for data sampling is limited. To solve this challenging task, we propose a new algorithmic learning framework called Model-based Uncertainty regularized and Sample Efficient Batch Optimization (MUSBO). Our framework discovers novel and high quality samples for each deployment to enable efficient data collection. During each offline training session, we bootstrap the policy update by quantifying the amount of uncertainty within our collected data. In the high support region (low uncertainty), we encourage our policy by taking an aggressive update. In the low support region (high uncertainty) when the policy bootstraps into the out-of-distribution region, we downweight it by our estimated uncertainty quantification. Experimental results show that MUSBO achieves state-of-the-art performance in the deployment constrained RL setting.


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Few-shot link prediction via graph neural networks for Covid-19 drug-repurposing

Jul 20, 2020
Vassilis N. Ioannidis, Da Zheng, George Karypis

Predicting interactions among heterogenous graph structured data has numerous applications such as knowledge graph completion, recommendation systems and drug discovery. Often times, the links to be predicted belong to rare types such as the case in repurposing drugs for novel diseases. This motivates the task of few-shot link prediction. Typically, GCNs are ill-equipped in learning such rare link types since the relation embedding is not learned in an inductive fashion. This paper proposes an inductive RGCN for learning informative relation embeddings even in the few-shot learning regime. The proposed inductive model significantly outperforms the RGCN and state-of-the-art KGE models in few-shot learning tasks. Furthermore, we apply our method on the drug-repurposing knowledge graph (DRKG) for discovering drugs for Covid-19. We pose the drug discovery task as link prediction and learn embeddings for the biological entities that partake in the DRKG. Our initial results corroborate that several drugs used in clinical trials were identified as possible drug candidates. The method in this paper are implemented using the efficient deep graph learning (DGL)


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AI Failures: A Review of Underlying Issues

Jul 18, 2020
Debarag Narayan Banerjee, Sasanka Sekhar Chanda

Instances of Artificial Intelligence (AI) systems failing to deliver consistent, satisfactory performance are legion. We investigate why AI failures occur. We address only a narrow subset of the broader field of AI Safety. We focus on AI failures on account of flaws in conceptualization, design and deployment. Other AI Safety issues like trade-offs between privacy and security or convenience, bad actors hacking into AI systems to create mayhem or bad actors deploying AI for purposes harmful to humanity and are out of scope of our discussion. We find that AI systems fail on account of omission and commission errors in the design of the AI system, as well as upon failure to develop an appropriate interpretation of input information. Moreover, even when there is no significant flaw in the AI software, an AI system may fail because the hardware is incapable of robust performance across environments. Finally an AI system is quite likely to fail in situations where, in effect, it is called upon to deliver moral judgments -- a capability AI does not possess. We observe certain trade-offs in measures to mitigate a subset of AI failures and provide some recommendations.

* 8 pages 

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Learning Individualized Treatment Rules with Estimated Translated Inverse Propensity Score

Jul 02, 2020
Zhiliang Wu, Yinchong Yang, Yunpu Ma, Yushan Liu, Rui Zhao, Michael Moor, Volker Tresp

Randomized controlled trials typically analyze the effectiveness of treatments with the goal of making treatment recommendations for patient subgroups. With the advance of electronic health records, a great variety of data has been collected in clinical practice, enabling the evaluation of treatments and treatment policies based on observational data. In this paper, we focus on learning individualized treatment rules (ITRs) to derive a treatment policy that is expected to generate a better outcome for an individual patient. In our framework, we cast ITRs learning as a contextual bandit problem and minimize the expected risk of the treatment policy. We conduct experiments with the proposed framework both in a simulation study and based on a real-world dataset. In the latter case, we apply our proposed method to learn the optimal ITRs for the administration of intravenous (IV) fluids and vasopressors (VP). Based on various offline evaluation methods, we could show that the policy derived in our framework demonstrates better performance compared to both the physicians and other baselines, including a simple treatment prediction approach. As a long-term goal, our derived policy might eventually lead to better clinical guidelines for the administration of IV and VP.


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A Comprehensive Scoping Review of Bayesian Networks in Healthcare: Past, Present and Future

Feb 28, 2020
Evangelia Kyrimi, Scott McLachlan, Kudakwashe Dube, Mariana R. Neves, Ali Fahmi, Norman Fenton

No comprehensive review of Bayesian networks (BNs) in healthcare has been published in the past, making it difficult to organize the research contributions in the present and identify challenges and neglected areas that need to be addressed in the future. This unique and novel scoping review of BNs in healthcare provides an analytical framework for comprehensively characterizing the domain and its current state. The review shows that: (1) BNs in healthcare are not used to their full potential; (2) a generic BN development process is lacking; (3) limitations exists in the way BNs in healthcare are presented in the literature, which impacts understanding, consensus towards systematic methodologies, practice and adoption of BNs; and (4) a gap exists between having an accurate BN and a useful BN that impacts clinical practice. This review empowers researchers and clinicians with an analytical framework and findings that will enable understanding of the need to address the problems of restricted aims of BNs, ad hoc BN development methods, and the lack of BN adoption in practice. To map the way forward, the paper proposes future research directions and makes recommendations regarding BN development methods and adoption in practice.


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Adversarial Representation Learning on Large-Scale Bipartite Graphs

Jun 27, 2019
Chaoyang He, Tian Xie, Yu Rong, Wenbing Huang, Junzhou Huang, Xiang Ren, Cyrus Shahabi

Graph representation on large-scale bipartite graphs is central for a variety of applications, ranging from social network analysis to recommendation system development. Existing methods exhibit two key drawbacks: 1. unable to characterize the inconsistency of the node features within the bipartite-specific structure; 2. unfriendly to support large-scale bipartite graphs. To this end, we propose ABCGraph, a scalable model for unsupervised learning on large-scale bipartite graphs. At its heart, ABCGraph utilizes the proposed Bipartite Graph Convolutional Network (BGCN) as the encoder and adversarial learning as the training loss to learn representations from nodes in two different domains and bipartite structures, in an unsupervised manner. Moreover, we devise a cascaded architecture to capture the multi-hop relationship in bipartite structure and improves the scalability as well. Extensive experiments on multiple datasets of varying scales verify the effectiveness of ABCGraph compared to state-of-the-arts. For the experiment on a real-world large-scale bipartite graph system, fast training speed and low memory cost demonstrate the scalability of ABCGraph model.

* 15 pages. Submitted to NeurIPS 2019 (Thirty-third Conference on Neural Information Processing Systems) 

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Bayesian Optimization with Directionally Constrained Search

Jun 22, 2019
Yang Li, Yaqiang Yao

Bayesian optimization offers a flexible framework to optimize an objective function that is expensive to be evaluated. A Bayesian optimizer iteratively queries the function values on its carefully selected points. Subsequently, it makes a sensible recommendation about where the optimum locates based on its accumulated knowledge. This procedure usually demands a long execution time. In practice, however, there often exists a computational budget or an evaluation limitation allocated to an optimizer, due to the resource scarcity. This constraint demands an optimizer to be aware of its remaining budget and able to spend it wisely, in order to return as better a point as possible. In this paper, we propose a Bayesian optimization approach in this evaluation-limited scenario. Our approach is based on constraining searching directions so as to dedicate the model capability to the most promising area. It could be viewed as a combination of local and global searching policies, which aims at reducing inefficient exploration in the local searching areas, thus making a searching policy more efficient. Experimental studies are conducted on both synthetic and real-world applications. The results demonstrate the superior performance of our newly proposed approach in searching for the optimum within a prescribed evaluation budget.


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