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Artificial Intelligence in Drug Discovery: Applications and Techniques

arXiv.org Artificial Intelligence

Artificial intelligence (AI) has been transforming the practice of drug discovery in the past decade. Various AI techniques have been used in a wide range of applications, such as virtual screening and drug design. In this perspective, we first give an overview on drug discovery and discuss related applications, which can be reduced to two major tasks, i.e., molecular property prediction and molecule generation. We then discuss common data resources, molecule representations and benchmark platforms. Furthermore, to summarize the progress in AI-driven drug discovery, we present the relevant AI techniques including model architectures and learning paradigms in the surveyed papers. We expect that the perspective will serve as a guide for researchers who are interested in working at this intersected area of artificial intelligence and drug discovery. We also provide a GitHub repository\footnote{\url{https://github.com/dengjianyuan/Survey_AI_Drug_Discovery}} with the collection of papers and codes, if applicable, as a learning resource, which will be regularly updated.


Artificial Intelligence: Research Impact on Key Industries; the Upper-Rhine Artificial Intelligence Symposium (UR-AI 2020)

arXiv.org Artificial Intelligence

The TriRhenaTech alliance presents a collection of accepted papers of the cancelled tri-national 'Upper-Rhine Artificial Inteeligence Symposium' planned for 13th May 2020 in Karlsruhe. The TriRhenaTech alliance is a network of universities in the Upper-Rhine Trinational Metropolitan Region comprising of the German universities of applied sciences in Furtwangen, Kaiserslautern, Karlsruhe, and Offenburg, the Baden-Wuerttemberg Cooperative State University Loerrach, the French university network Alsace Tech (comprised of 14 'grandes \'ecoles' in the fields of engineering, architecture and management) and the University of Applied Sciences and Arts Northwestern Switzerland. The alliance's common goal is to reinforce the transfer of knowledge, research, and technology, as well as the cross-border mobility of students.


Rapidly Personalizing Mobile Health Treatment Policies with Limited Data

arXiv.org Machine Learning

Mobile health (mHealth) interventions deliver treatments to users to support healthy behaviors. These interventions offer an opportunity for social impact in a diverse range of domains from substance abuse (Rabbi et al., 2017), to disease management (Hamine et al., 2015) to physical inactivity (Consolvo et al., 2008). For example, to help users increase their physical activity, an mHealth application might send a walking suggestions at times and in locations when a user is likely to be able to pursue the suggestions. The promise of mHealth hinges on the ability to provide interventions at times when users need the support and are receptive to it (Nahum-Shani et al., 2017). Consequently, in developing reinforcement learning (RL) algorithms for mHealth our goal is to be able to learn an optimal policy of when and how to intervene for a given user and context.


The Big Three: A Methodology to Increase Data Science ROI by Answering the Questions Companies Care About

arXiv.org Machine Learning

Companies may be achieving only a third of the value they could be getting from data science in industry applications. In this paper, we propose a methodology for categorizing and answering 'The Big Three' questions (what is going on, what is causing it, and what actions can I take that will optimize what I care about) using data science. The applications of data science seem to be nearly endless in today's modern landscape, with each company jockeying for position in the new data and insights economy. Yet, data scientists seem to be solely focused on using classification, regression, and clustering methods to answer the question 'what is going on'. Answering questions about why things are happening or how to take optimal actions to improve metrics are relegated to niche fields of research and generally neglected in industry data science analysis. We survey technical methods to answer these other important questions, describe areas in which some of these methods are being applied, and provide a practical example of how to apply our methodology and selected methods to a real business use case.


A Survey on Causal Inference

arXiv.org Artificial Intelligence

Causal inference is a critical research topic across many domains, such as statistics, computer science, education, public policy and economics, for decades. Nowadays, estimating causal effect from observational data has become an appealing research direction owing to the large amount of available data and low budget requirement, compared with randomized controlled trials. Embraced with the rapidly developed machine learning area, various causal effect estimation methods for observational data have sprung up. In this survey, we provide a comprehensive review of causal inference methods under the potential outcome framework, one of the well known causal inference framework. The methods are divided into two categories depending on whether they require all three assumptions of the potential outcome framework or not. For each category, both the traditional statistical methods and the recent machine learning enhanced methods are discussed and compared. The plausible applications of these methods are also presented, including the applications in advertising, recommendation, medicine and so on. Moreover, the commonly used benchmark datasets as well as the open-source codes are also summarized, which facilitate researchers and practitioners to explore, evaluate and apply the causal inference methods.


Artificial Intelligence for Social Good: A Survey

arXiv.org Artificial Intelligence

Its impact is drastic and real: Youtube's AIdriven recommendation system would present sports videos for days if one happens to watch a live baseball game on the platform [1]; email writing becomes much faster with machine learning (ML) based auto-completion [2]; many businesses have adopted natural language processing based chatbots as part of their customer services [3]. AI has also greatly advanced human capabilities in complex decision-making processes ranging from determining how to allocate security resources to protect airports [4] to games such as poker [5] and Go [6]. All such tangible and stunning progress suggests that an "AI summer" is happening. As some put it, "AI is the new electricity" [7]. Meanwhile, in the past decade, an emerging theme in the AI research community is the so-called "AI for social good" (AI4SG): researchers aim at developing AI methods and tools to address problems at the societal level and improve the wellbeing of the society.


A 20-Year Community Roadmap for Artificial Intelligence Research in the US

arXiv.org Artificial Intelligence

Decades of research in artificial intelligence (AI) have produced formidable technologies that are providing immense benefit to industry, government, and society. AI systems can now translate across multiple languages, identify objects in images and video, streamline manufacturing processes, and control cars. The deployment of AI systems has not only created a trillion-dollar industry that is projected to quadruple in three years, but has also exposed the need to make AI systems fair, explainable, trustworthy, and secure. Future AI systems will rightfully be expected to reason effectively about the world in which they (and people) operate, handling complex tasks and responsibilities effectively and ethically, engaging in meaningful communication, and improving their awareness through experience. Achieving the full potential of AI technologies poses research challenges that require a radical transformation of the AI research enterprise, facilitated by significant and sustained investment. These are the major recommendations of a recent community effort coordinated by the Computing Community Consortium and the Association for the Advancement of Artificial Intelligence to formulate a Roadmap for AI research and development over the next two decades.


Parameterized Exploration

arXiv.org Artificial Intelligence

We introduce Parameterized Exploration (PE), a simple family of methods for model-based tuning of the exploration schedule in sequential decision problems. Unlike common heuristics for exploration, our method accounts for the time horizon of the decision problem as well as the agent's current state of knowledge of the dynamics of the decision problem. We show our method as applied to several common exploration techniques has superior performance relative to un-tuned counterparts in Bernoulli and Gaussian multi-armed bandits, contextual bandits, and a Markov decision process based on a mobile health (mHealth) study. We also examine the effects of the accuracy of the estimated dynamics model on the performance of PE.


Developing parsimonious ensembles using ensemble diversity within a reinforcement learning framework

arXiv.org Machine Learning

Heterogeneous ensembles built from the predictions of a wide variety and large number of diverse base predictors represent a potent approach to building predictive models for problems where the ideal base/individual predictor may not be obvious. Ensemble selection is an especially promising approach here, not only for improving prediction performance, but also because of its ability to select a collectively predictive subset, often a relatively small one, of the base predictors. In this paper, we present a set of algorithms that explicitly incorporate ensemble diversity, a known factor influencing predictive performance of ensembles, into a reinforcement learning framework for ensemble selection. We rigorously tested these approaches on several challenging problems and associated data sets, yielding that several of them produced more accurate ensembles than those that don't explicitly consider diversity. More importantly, these diversity-incorporating ensembles were much smaller in size, i.e., more parsimonious, than the latter types of ensembles. This can eventually aid the interpretation or reverse engineering of predictive models assimilated into the resultant ensemble(s).