Meta-learning for fake news detection surrounding the Syrian war.

In this article, we pursue the automatic detection of fake news reporting on the Syrian war using machine learning and meta-learning. The proposed approach is based on a suite of features that include a given article's linguistic style; its level of subjectivity, sensationalism, and sectarianism; the strength of its attribution; and its consistency with other news articles from the same "media camp". To train our models, we use FA-KES, a fake news dataset about the Syrian war. A suite of basic machine learning models is explored, as well as the model-agnostic meta-learning algorithm (MAML) suitable for few-shot learning, using datasets of a modest size. Feature-importance analysis confirms that the collected features specific to the Syrian war are indeed very important predictors for the output label. The meta-learning model achieves the best performance, improving upon the baseline approaches that are trained exclusively on text features in FA-KES.

Exploring energy grid resilience: The impact of data, prosumer awareness, and action.

The transition of energy grids toward future smart grids is challenging in every way: politically, economically, legally, and technically. While many aspects progress at a velocity unthinkable a generation ago, one aspect remained mostly dormant: human electricity consumers. The involvement of consumers thus far can be summarized by two questions: "Should I buy the eco-friendly appliance? Will solar pay off for me?" However, social and psychological aspects of consumers can profoundly contribute to resilient smart grids. This vision paper explores the role of active consumer-producers (prosumers) in the resilient operation of smart energy grids. We investigate how data can empower people to become more involved in energy grid operations, the potential of heightened awareness, mechanisms for incentives, and other tools for enhancing prosumer actions toward resilience. We further explore the potential benefits to people and system when people are active, aware participants in the goals and operation of the system.

A community effort to identify and correct mislabeled samples in proteogenomic studies.

Sample mislabeling or misannotation has been a long-standing problem in scientific research, particularly prevalent in large-scale, multi-omic studies due to the complexity of multi-omic workflows. There exists an urgent need for implementing quality controls to automatically screen for and correct sample mislabels or misannotations in multi-omic studies. Here, we describe a crowdsourced precisionFDA NCI-CPTAC Multi-omics Enabled Sample Mislabeling Correction Challenge, which provides a framework for systematic benchmarking and evaluation of mislabel identification and correction methods for integrative proteogenomic studies. The challenge received a large number of submissions from domestic and international data scientists, with highly variable performance observed across the submitted methods. Post-challenge collaboration between the top-performing teams and the challenge organizers has created an open-source software, COSMO, with demonstrated high accuracy and robustness in mislabeling identification and correction in simulated and real multi-omic datasets.

FaNDOM: Fast nested distance-based seeding of optical maps.

Optical mapping (OM) provides single-molecule readouts of fluorescently labeled sequence motifs on long fragments of DNA, resolved to nucleotide-level coordinates. With the advent of microfluidic technologies for analysis of DNA molecules, it is possible to inexpensively generate long OM data ( > 150 kbp) at high coverage. In addition to scaffolding for de novo assembly, OM data can be aligned to a reference genome for identification of genomic structural variants. We introduce FaNDOM (Fast Nested Distance Seeding of Optical Maps)-an optical map alignment tool that greatly reduces the search space of the alignment process. On four benchmark human datasets, FaNDOM was significantly (4-14×) faster than competing tools while maintaining comparable sensitivity and specificity. We used FaNDOM to map variants in three cancer cell lines and identified many biologically interesting structural variants, including deletions, duplications, gene fusions and gene-disrupting rearrangements. FaNDOM is publicly available at https://github.com/jluebeck/FaNDOM.

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response.

Integrated, up-to-date data about SARS-CoV-2 and COVID-19 is crucial for the ongoing response to the COVID-19 pandemic by the biomedical research community. While rich biological knowledge exists for SARS-CoV-2 and related viruses (SARS-CoV, MERS-CoV), integrating this knowledge is difficult and time-consuming, since much of it is in siloed databases or in textual format. Furthermore, the data required by the research community vary drastically for different tasks; the optimal data for a machine learning task, for example, is much different from the data used to populate a browsable user interface for clinicians. To address these challenges, we created KG-COVID-19, a flexible framework that ingests and integrates heterogeneous biomedical data to produce knowledge graphs (KGs), and applied it to create a KG for COVID-19 response. This KG framework also can be applied to other problems in which siloed biomedical data must be quickly integrated for different research applications, including future pandemics.

The COVID-19 Drug and Gene Set Library.

In a short period, many research publications that report sets of experimentally validated drugs as potential COVID-19 therapies have emerged. To organize this accumulating knowledge, we developed the COVID-19 Drug and Gene Set Library (https://amp.pharm.mssm.edu/covid19/), a collection of drug and gene sets related to COVID-19 research from multiple sources. The platform enables users to view, download, analyze, visualize, and contribute drug and gene sets related to COVID-19 research. To evaluate the content of the library, we compared the results from six in vitro drug screens for COVID-19 repurposing candidates. Surprisingly, we observe low overlap across screens while highlighting overlapping candidates that should receive more attention as potential therapeutics for COVID-19. Overall, the COVID-19 Drug and Gene Set Library can be used to identify community consensus, make researchers and clinicians aware of new potential therapies, enable machine-learning applications, and facilitate the research community to work together toward a cure.