Precision oncology seeks to predict the best therapeutic option for individual patients based on the molecular characteristics of their tumors. To assess the preclinical feasibility of drug sensitivity prediction, several studies have measured drug responses for cytotoxic and targeted therapies across large collections of genomically and transcriptomically characterized cancer cell lines and trained predictive models using standard methods like elastic net regression. Here we use existing drug response data sets to demonstrate that multitask learning across drugs strongly improves the accuracy and interpretability of drug prediction models. Our method uses trace norm regularization with a highly efficient ADMM (alternating direction method of multipliers) optimization algorithm that readily scales to large data sets. We anticipate that our approach will enhance efforts to exploit growing drug response compendia in order to advance personalized therapy.

The COVID-19 pandemic has created unprecedented challenges worldwide. Strained healthcare providers make difficult decisions on patient triage, treatment and care management on a daily basis. Policy makers have imposed social distancing measures to slow the disease, at a steep economic price. We design analytical tools to support these decisions and combat the pandemic. Specifically, we propose a comprehensive data-driven approach to understand the clinical characteristics of COVID-19, predict its mortality, forecast its evolution, and ultimately alleviate its impact. By leveraging cohort-level clinical data, patient-level hospital data, and census-level epidemiological data, we develop an integrated four-step approach, combining descriptive, predictive and prescriptive analytics. First, we aggregate hundreds of clinical studies into the most comprehensive database on COVID-19 to paint a new macroscopic picture of the disease. Second, we build personalized calculators to predict the risk of infection and mortality as a function of demographics, symptoms, comorbidities, and lab values. Third, we develop a novel epidemiological model to project the pandemic’s spread and inform social distancing policies. Fourth, we propose an optimization model to re-allocate ventilators and alleviate shortages. Our results have been used at the clinical level by several hospitals to triage patients, guide care management, plan ICU capacity, and re-distribute ventilators. At the policy level, they are currently supporting safe back-to-work policies at a major institution and vaccine trial location planning at Janssen Pharmaceuticals, and have been integrated into the US Center for Disease Control’s pandemic forecast. Electronic supplementary material The online version of this article (10.1007/s10729-020-09542-0) contains supplementary material, which is available to authorized users. Supplementary Information The online version contains supplementary material available at (10.1007/s10729-020-09542-0)

The COVID-19 pandemic has created unprecedented challenges worldwide. Strained healthcare providers make difficult decisions on patient triage, treatment and care management on a daily basis. Policy makers have imposed social distancing measures to slow the disease, at a steep economic price. We design analytical tools to support these decisions and combat the pandemic. Specifically, we propose a comprehensive data-driven approach to understand the clinical characteristics of COVID-19, predict its mortality, forecast its evolution, and ultimately alleviate its impact. By leveraging cohort-level clinical data, patient-level hospital data, and census-level epidemiological data, we develop an integrated four-step approach, combining descriptive, predictive and prescriptive analytics. First, we aggregate hundreds of clinical studies into the most comprehensive database on COVID-19 to paint a new macroscopic picture of the disease. Second, we build personalized calculators to predict the risk of infection and mortality as a function of demographics, symptoms, comorbidities, and lab values. Third, we develop a novel epidemiological model to project the pandemic's spread and inform social distancing policies. Fourth, we propose an optimization model to reallocate ventilators and alleviate shortages. Our results have been used at the clinical level by several hospitals to triage patients, guide care management, plan ICU capacity, and re-distribute ventilators. At the policy level, they are currently supporting safe back-to-work policies at a major institution and equitable vaccine distribution planning at a major pharmaceutical company, and have been integrated into the US Center for Disease Control's pandemic forecast.

There has recently been much interest in extending vector-based word representations to multiple languages, such that words can be compared across languages. In this paper, we shift the focus from words to documents and introduce a method for embedding documents written in any language into a single, language-independent vector space. For training, our approach leverages a multilingual corpus where the same concept is covered in multiple languages (but not necessarily via exact translations), such as Wikipedia. Our method, Cr5 (Crosslingual reduced-rank ridge regression), starts by training a ridge-regression-based classifier that uses languagespecific bag-of-word features in order to predict the concept that a given document is about. We show that, when constraining the learned weight matrix to be of low rank, it can be factored to obtain the desired mappings from language-specific bags-of-words to language-independent embeddings. As opposed to most prior methods, which use pretrained monolingual word vectors, postprocess them to make them crosslingual, and finally average word vectors to obtain document vectors, Cr5 is trained end-to-end and is thus natively crosslingual as well as document-level. Moreover, since our algorithm uses the singular value decomposition as its core operation, it is highly scalable. Experiments show that our method achieves state-of-the-art performance on a crosslingual document retrieval task. Finally, although not trained for embedding sentences and words, it also achieves competitive performance on crosslingual sentence and word retrieval tasks.

The COVID-19 pandemic has created unprecedented challenges worldwide. Strained healthcare providers make difficult decisions on patient triage, treatment and care management on a daily basis. Policy makers have imposed social distancing measures to slow the disease, at a steep economic price. We design analytical tools to support these decisions and combat the pandemic. Specifically, we propose a comprehensive data-driven approach to understand the clinical characteristics of COVID-19, predict its mortality, forecast its evolution, and ultimately alleviate its impact. By leveraging cohort-level clinical data, patient-level hospital data, and census-level epidemiological data, we develop an integrated four-step approach, combining descriptive, predictive and prescriptive analytics. First, we aggregate hundreds of clinical studies into the most comprehensive database on COVID-19 to paint a new macroscopic picture of the disease. Second, we build personalized calculators to predict the risk of infection and mortality as a function of demographics, symptoms, comorbidities, and lab values. Third, we develop a novel epidemiological model to project the pandemic's spread and inform social distancing policies. Fourth, we propose an optimization model to reallocate ventilators and alleviate shortages. Our results have been used at the clinical level by several hospitals to triage patients, guide care management, plan ICU capacity, and re-distribute ventilators. At the policy level, they are currently supporting safe back-to-work policies at a major institution and equitable vaccine distribution planning at a major pharmaceutical company, and have been integrated into the US Center for Disease Control's pandemic forecast. COVID-19 | Epidemiological modeling | Machine learning | OptimizationI n just a few weeks, the whole world has been upended by the outbreak of COVID-19, an acute respiratory disease caused by a new coronavirus called SARS-CoV-2. The virus is highly contagious: it is easily transmitted from person to person via respiratory droplet nuclei and can persist on surfaces for days (1, 2). As a result, COVID-19 has spread rapidly-classified by the World Health Organization as a public health emergency on January 30, 2020 and as a pandemic on March 11. As of mid-May, over 4.5 million cases and 300,000 deaths have been reported globally (3).Because no treatment is currently available, healthcare providers and policy makers are wrestling with unprecedented challenges. Hospitals and other care facilities are facing shortages of beds, ventilators and personal protective equipmentraising hard questions on how to treat COVID-19 patients with scarce supplies and how to allocate resources to prevent further shortages. At the policy level, most countries have imposed "social distancing" measures to slow the spread of the pandemic. These measures allow strained healthcare systems to cope with the disease by "flattening the curve" (4) but also come at a steep economic price (5,6). Nearly all governments are now confronted to ...