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To provide a reliable wireless uplink for users in a given ground area, one can deploy Unmanned Aerial Vehicles (UAVs) as base stations (BSs). In another application, one can use UAVs to collect data from sensors on the ground. For a power-efficient and scalable deployment of such flying BSs, directional antennas can be utilized to efficiently cover arbitrary 2-D ground areas. We consider a large-scale wireless path-loss model with a realistic angle-dependent radiation pattern for the directional antennas. Based on such a model, we determine the optimal 3-D deployment of N UAVs to minimize the average transmit-power consumption of the users in a given target area. The users are assumed to have identical transmitters with ideal omnidirectional antennas and the UAVs have identical directional antennas with given half-power beamwidth (HPBW) and symmetric radiation pattern along the vertical axis. For uniformly distributed ground users, we show that the UAVs have to share a common flight height in an optimal power-efficient deployment, by simulations. We also derive in closed-form the asymptotic optimal common flight height of N UAVs in terms of the area size, data-rate, bandwidth, HPBW, and path-loss exponent.

In many cases, Zoom is now a lifeline that the world has suddenly come to depend on to be able to function in an environment of physical isolation. Zoom’s security-related processes and major safety flaws will be rectified, and its privacy practices will be addressed, now that the company has been put in the spotlight. Zoom’s shortcomings are only one part of the story. The other part concerns the huge and rapid adoption of a software service and the nature of that application’s new user base. Zoom’s traditional market has consisted of business customers, which often have IT departments and security teams. In contrast, given the COVID-19 situation, tens of millions of very inexperienced people have begun to use Zoom for online classes and corporate meetings, and even some very large public assemblies, and they administer and utilize the service without sufficient expertise or the training typically required for such an application. The consequences of inexperienced users adopting key software are something that all developers should keep in mind.

We introduce an approach for the interactive visual analysis of weighted, dynamic networks. These networks arise in areas such as computational neuroscience, sociology, and biology. Network analysis remains challenging due to complex time-varying network behavior. For example, edges disappear/reappear, communities grow/vanish, or overall network topology changes. Our technique, TimeSum, detects the important topological changes in graph data to abstract the dynamic network and visualize one summary representation for each temporal phase, a state. We define a network state as a graph with similar topology over a specific time interval. To enable a holistic comparison of networks, we use a difference network to depict edge and community changes. We present case studies to demonstrate that our methods are effective and useful for extracting and exploring complex dynamic behavior of networks.

In this paper, we investigate secure communication over sparse millimeter-wave (mm-Wave) massive multiple-input multiple-output (MIMO) channels by exploiting the spatial sparsity of legitimate user's channel. We propose a secure communication scheme in which information data is precoded onto dominant angle components of the sparse channel through a limited number of radio-frequency (RF) chains, while artificial noise (AN) is broadcast over the remaining nondominant angles interfering only with the eavesdropper with a high probability. It is shown that the channel sparsity plays a fundamental role analogous to secret keys in achieving secure communication. Hence, by defining two statistical measures of the channel sparsity, we analytically characterize its impact on secrecy rate. In particular, a substantial improvement on secrecy rate can be obtained by the proposed scheme due to the uncertainty, i.e., 'entropy', introduced by the channel sparsity which is unknown to the eavesdropper. It is revealed that sparsity in the power domain can always contribute to the secrecy rate. In contrast, in the angle domain, there exists an optimal level of sparsity that maximizes the secrecy rate. The effectiveness of the proposed scheme and derived results are verified by numerical simulations.

This paper investigates unmanned aerial vehicle (UAV)-aided backscatter communication (BackCom) networks, where the UAV is leveraged to help the backscatter device (BD) forward signals to the receiver. Based on the presence or absence of a direct link between BD and receiver, two protocols, namely transmit-backscatter (TB) protocol and transmit-backscatter-relay (TBR) protocol, are proposed to utilize the UAV to assist the BD. In particular, we formulate the system throughput maximization problems for the two protocols by jointly optimizing the time allocation, reflection coefficient and UAV trajectory. Different static/dynamic circuit power consumption models for the two protocols are analyzed. The resulting optimization problems are shown to be non-convex, which are challenging to solve. We first consider the dynamic circuit power consumption model, and decompose the original problems into three sub-problems, namely time allocation optimization with fixed UAV trajectory and reflection coefficient, reflection coefficient optimization with fixed UAV trajectory and time allocation, and UAV trajectory optimization with fixed reflection coefficient and time allocation. Then, an efficient iterative algorithm is proposed for both protocols by leveraging the block coordinate descent method and successive convex approximation (SCA) techniques. In addition, for the static circuit power consumption model, we obtain the optimal time allocation with a given reflection coefficient and UAV trajectory and the optimal reflection coefficient with low computational complexity by using the Lagrangian dual method. Simulation results show that the proposed protocols are able to achieve significant throughput gains over the compared benchmarks.

The ever accelerating pace of biomedical research results in corresponding acceleration in the volume of biomedical literature created. Since new research builds upon existing knowledge, the rate of increase in the available knowledge encoded in biomedical literature makes the easy access to that implicit knowledge more vital over time. Toward the goal of making implicit knowledge in the biomedical literature easily accessible to biomedical researchers, we introduce a question answering system called Bio-AnswerFinder. Bio-AnswerFinder uses a weighted-relaxed word mover's distance based similarity on word/phrase embeddings learned from PubMed abstracts to rank answers after question focus entity type filtering. Our approach retrieves relevant documents iteratively via enhanced keyword queries from a traditional search engine. To improve document retrieval performance, we introduced a supervised long short term memory neural network to select keywords from the question to facilitate iterative keyword search. Our unsupervised baseline system achieves a mean reciprocal rank score of 0.46 and Precision@1 of 0.32 on 936 questions from BioASQ. The answer sentences are further ranked by a fine-tuned bidirectional encoder representation from transformers (BERT) classifier trained using 100 answer candidate sentences per question for 492 BioASQ questions. To test ranking performance, we report a blind test on 100 questions that three independent annotators scored. These experts preferred BERT based reranking with 7% improvement on MRR and 13% improvement on Precision@1 scores on average.

Efficient intrusion detection and analysis of the security landscape in big data environments present challenge for today’s users. Intrusion behavior can be described by provenance graphs that record the dependency relationships between intrusion processes and the infected files. Existing intrusion detection methods typically analyze and identify the anomaly either in a single provenance path or the whole provenance graph, neither of which can achieve the benefit on both detection accuracy and detection time. We propose Pagoda, a hybrid approach that takes into account the anomaly degree of both a single provenance path and the whole provenance graph. It can identify intrusion quickly if a serious compromise has been found on one path, and can further improve the detection rate by considering the behavior representation in the whole provenance graph. Pagoda uses a persistent memory database to store provenance and aggregates multiple similar items into one provenance record to maximumly reduce unnecessary I/O during the detection analysis. In addition, it encodes duplicate items in the rule database and filters noise that does not contain intrusion information. The experimental results on a wide variety of real-world applications demonstrate its performance and efficiency.

Animal models are widely employed in basic research to test mechanistic hypotheses in a complex biological environment as well as to evaluate the therapeutic potential of candidate compounds in preclinical settings. Rodents, and in particular mice, represent the most common in vivo models for their small size, short lifespan and possibility to manipulate their genome. Over time, a typical laboratory will develop a substantial number of inbred strains and transgenic mouse lines, requiring a substantial effort, in both logistic and economic terms, to maintain an animal colony for research purposes and to safeguard the integrity of results. To meet this need, here we present TopoDB, a robust and extensible web-based platform for the rational management of laboratory animals. TopoDB allows an easy tracking of individual animals within the colony and breeding protocols as well as the convenient storage of both genetic and phenotypic data generated in the different experiments. Altogether, these features facilitate and enhance the design of in vivo research, thus reducing the number of necessary animals and the housing costs. In summary, TopoDB represents a novel valuable tool in modern biomedical research. Database URL: https://github.com/UCSF-MS-DCC/TopoDB.

Respiratory rate measurement is important under different types of health issues. The need for technological developments for measuring respiratory rate has become imperative for healthcare professionals. The paper presents an approach to respiratory monitoring, with the aim to improve the accuracy and efficacy of the data monitored. We use multiple types of sensors on various locations on the body to continuously transmit real-time data, which is processed to calculate the respiration rate. Variations in the respiration rate will help us identify the current health condition of the patient also for diagnosis and further medical treatment. The software tools such as Keil μVision IDE, Mbed Studio IDE, Energia IDE are used to compile and build the system architecture and display information. EasyEDA is used to provide pin map details and complete architecture information.

As neurotechnologies have gotten better, a lot of neuroscientific research has been done using these new technologies. Even though labs all over the world produce a lot of neuro-data, most of this data has not been shared to help people from different fields understand neuroscience. The neuro-data sharing is essential because it accelerates the pace of discovery in neuroscience. Effective data sharing will depend on the standardized use of file or data formats, highly reusable data analytics tools, and data storage formats. In this review paper, we review the four domains (data format, data model, data repository, and data analytics) that are currently in use in the neuroscience community. In the end, we are discussing several challenges associated with data sharing.

We studied the security practices of a diverse set of Internet of Things (IoT) devices with different architectures. We found vulnerabilities that can be exploited to launch novel attacks. The real-world implications of IoT attacks show the risks associated with these new technologies, and can help us articulate the need for better security practices.

Slow fading broadcast channels can model a wide range of applications in wireless networks. Due to delay requirements and the unavailability of the channel state information at the transmitter (CSIT), these channels for many applications are non-ergodic. The appropriate measure for designing signals in non-ergodic channels is the outage probability. In this paper, we provide a method to optimize space-time block codes (STBCs) based on the outage probability at moderate SNRs. Multilevel polar coded-modulation is a new class of coded-modulation techniques that benefits from low-complexity decoders and simple rate matching. In this paper, we derive the outage optimality condition for multistage decoding and propose a rule for determining component code rates. We also derive an upper bound on the outage probability of STBCs for designing the set-partitioning-based labeling. Finally, due to the optimality of the outage-minimized STBCs for long codes, we introduce a novel method for the joint optimization of short-to-moderate length polar codes and STBCs.

In this paper, we investigate secure transmission in a massive multiple-input multiple-output system adopting low-resolution digital-to-analog converters (DACs). Artificial noise (AN) is deliberately transmitted simultaneously with the confidential signals to degrade the eavesdropper's channel quality. By applying the Bussgang theorem, a DAC quantization model is developed which facilitates the analysis of the asymptotic achievable secrecy rate. Interestingly, for a fixed power allocation factor φ , low-resolution DACs typically result in a secrecy rate loss, but in certain cases, they provide superior performance, e.g., at low signal-to-noise ratio (SNR). Specifically, we derive a closed-form SNR threshold which determines whether low-resolution or high-resolution DACs are preferable for improving the secrecy rate. Furthermore, a closed-form expression for the optimal φ is derived. With AN generated in the null-space of the user channel and the optimal φ , low-resolution DACs inevitably cause secrecy rate loss. On the other hand, for random AN with the optimal φ , the secrecy rate is hardly affected by the DAC resolution because the negative impact of the quantization noise can be compensated by reducing the AN power. All the derived analytical results are verified by numerical simulations.

We consider the ad-hoc networks consisting of n wireless nodes that are located on the plane. Any two given nodes are called neighbors if they are located within a certain distance (communication range) from one another. A given node can be directly connected to any one of its neighbors, and picks its connections according to a unique topology control algorithm that is available at every node. Given that each node knows only the indices (unique identification numbers) of its one and two-hop neighbors, we identify an algorithm that preserves connectivity and can operate without the need of any synchronization among nodes. Moreover, the algorithm results in a sparse graph with at most 5n edges and a maximum node degree of 10. Existing algorithms with the same promises further require neighbor distance and/or direction information at each node. We also evaluate the performance of our algorithm for random networks. In this case, our algorithm provides an asymptotically connected network with n(1+o(1)) edges with a degree less than or equal to 6 for 1-o(1) fraction of the nodes. We also introduce another asynchronous connectivity-preserving algorithm that can provide an upper bound as well as a lower bound on node degrees.

Herein we present major updates to the National NeuroAIDS Tissue Consortium (NNTC) database. The NNTC's ongoing multisite clinical research study was established to facilitate access to ante-mortem and post-mortem data, tissues and biofluids for the neurohuman immunodeficiency virus (HIV) research community. Recently, the NNTC has expanded to include data from the central nervous system HIV Antiretroviral Therapy Effects Research (CHARTER) study. The data and biospecimens from CHARTER and NNTC cohorts are available to qualified researchers upon request. Data generated by requestors using NNTC biospecimens and tissues are returned to the NNTC upon the conclusion of requestors' work, and this external, experimental data are annotated and curated in the publically accessible NNTC database, thereby extending the utility of each case. A flexible and extensible database ontology allows the integration of disparate data sets, including external experimental data, clinical neuropsychological and neuromedical testing data, tissue pathology and neuroimaging data.

Transcription factors (TFs) are an important class of regulatory molecules. Despite their importance, only a small number of genes encoding TFs have been characterized in Oryza sativa (rice), often because gene duplication and functional redundancy complicate their analysis. To address this challenge, we developed a web-based tool called the Rice Transcription Factor Phylogenomics Database (RTFDB) and demonstrate its application for predicting TF function. The RTFDB hosts transcriptome and co-expression analyses. Sources include high-throughput data from oligonucleotide microarray (Affymetrix and Agilent) as well as RNA-Seq-based expression profiles. We used the RTFDB to identify tissue-specific and stress-related gene expression. Subsequently, 273 genes preferentially expressed in specific tissues or organs, 455 genes showing a differential expression pattern in response to 4 abiotic stresses, 179 genes responsive to infection of various pathogens and 512 genes showing differential accumulation in response to various hormone treatments were identified through the meta-expression analysis. Pairwise Pearson correlation coefficient analysis between paralogous genes in a phylogenetic tree was used to assess their expression collinearity and thereby provides a hint on their genetic redundancy. Integrating transcriptome with the gene evolutionary information reveals the possible functional redundancy or dominance played by paralog genes in a highly duplicated genome such as rice. With this method, we estimated a predominant role for 83.3% (65/78) of the TF or transcriptional regulator genes that had been characterized via loss-of-function studies. In this regard, the proposed method is applicable for functional studies of other plant species with annotated genome.

GrainGenes (https://wheat.pw.usda.gov or https://graingenes.org) is an international centralized repository for curated, peer-reviewed datasets useful to researchers working on wheat, barley, rye and oat. GrainGenes manages genomic, genetic, germplasm and phenotypic datasets through a dynamically generated web interface for facilitated data discovery. Since 1992, GrainGenes has served geneticists and breeders in both the public and private sectors on six continents. Recently, several new datasets were curated into the database along with new tools for analysis. The GrainGenes homepage was enhanced by making it more visually intuitive and by adding links to commonly used pages. Several genome assemblies and genomic tracks are displayed through the genome browsers at GrainGenes, including the Triticum aestivum (bread wheat) cv. 'Chinese Spring' IWGSC RefSeq v1.0 genome assembly, the Aegilops tauschii (D genome progenitor) Aet v4.0 genome assembly, the Triticum turgidum ssp. dicoccoides (wild emmer wheat) cv. 'Zavitan' WEWSeq v.1.0 genome assembly, a T. aestivum (bread wheat) pangenome, the Hordeum vulgare (barley) cv. 'Morex' IBSC genome assembly, the Secale cereale (rye) select 'Lo7' assembly, a partial hexaploid Avena sativa (oat) assembly and the Triticum durum cv. 'Svevo' (durum wheat) RefSeq Release 1.0 assembly. New genetic maps and markers were added and can be displayed through CMAP. Quantitative trait loci, genetic maps and genes from the Wheat Gene Catalogue are indexed and linked through the Wheat Information System (WheatIS) portal. Training videos were created to help users query and reach the data they need. GSP (Genome Specific Primers) and PIECE2 (Plant Intron Exon Comparison and Evolution) tools were implemented and are available to use. As more small grains reference sequences become available, GrainGenes will play an increasingly vital role in helping researchers improve crops.

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.

Respiratory rate measurement is important under different types of health issues. The need for technological developments for measuring respiratory rate has become imperative for healthcare professionals. The paper presents an approach to respiratory monitoring, with the aim to improve the accuracy and efficacy of the data monitored. We use multiple types of sensors on various locations on the body to continuously transmit real-time data, which is processed to calculate the respiration rate. Variations in the respiration rate will help us identify the current health condition of the patient also for diagnosis and further medical treatment. The software tools such as Keil µVision IDE, Mbed Studio IDE, Energia IDE are used to compile and build the system architecture and display information. EasyEDA is used to provide pin map details and complete architecture information. [ABSTRACT FROM AUTHOR]

Monitoring and control systems integrated into agricultural machinery enable the development of agricultural analyses with advanced management tools, but the full use of all available data is often limited by the lack of uniformity among data transmitted from different agricultural machines. This paper presents an agricultural data aggregation and conversion model that allows for the collection and use of data captured from different agricultural machines in the course of work; these data differ in their original file formats and cannot be combined and used in a common analysis system. Programming work was carried out to create the model, and a specialised software interface enabled raster data processing using a Python library together with the open-source Hypertext Preprocessor and JavaScript programming language libraries. A PostGIS extension was utilised to engage field geometry and map-layering tools. Model validation showed that the data aggregation and conversion functions ensure the evaluation of semantic content and the transformation of the aggregated data into a unified format which is suitable for further use in intelligent farming management applications. The developed model will encourage precision agriculture, with the aim of improving work efficiency and the rational use of resources, the economy, and ecology in agriculture.

Abstract The creation of new knowledge from manipulating and analysing existing knowledge is one of the primary objectives of any cognitive system. Most of the effort on Big Data research has been focussed upon Volume and Velocity, while Variety, “the ugly duckling” of Big Data, is often neglected and difficult to solve. A principal challenge with Variety is being able to understand and comprehend the data. This paper proposes and evaluates an automated approach for metadata identification and enrichment in describing Big Data. The paper focuses on the use of self-learning systems that will enable automatic compliance of data against regulatory requirements along with the capability of generating valuable and readily usable metadata towards data classification. Two experiments towards data confidentiality and data identification were conducted in evaluating the feasibility of the approach. The focus of the experiments was to confirm that repetitive manual tasks can be automated, thus reducing the focus of a Data Scientist on data identification and thereby providing more focus towards the extraction and analysis of the data itself. The origin of the datasets used were Private/Business and Public/Governmental and exhibited diverse characteristics in relation to the number of files and size of the files. The experimental work confirmed that: (a) the use of algorithmic techniques attributed to the substantial decrease in false positives regarding the identification of confidential information; (b) evidence that the use of a fraction of a data set along with statistical analysis and supervised learning is sufficient in identifying the structure of information within it. With this approach, the issues of understanding the nature of data can be mitigated, enabling a greater focus on meaningful interpretation of the heterogeneous data.

TFCat (Time-Frequency Catalogue) is a data interchange format based on JSON (JavaScript Object Notation), which has been initially designed for exchanging low frequency radio events and features. It defines several types of JSON objects and how they are combined to represent data related to temporal-spectral features of a time spectrogram (a.k.a., dynamic spectrum), their properties, and their temporal and spectral extents. This implementation is inheriting from the GeoJSON file format. The TFCat python library is implementing this specification and provides a software interface permitting to create, update and validate TFCat objects efficiently.

cnpy++ is an easy-to-use C++17 library to read and write data in the NumPy file format (.npy and .npz files), offering more features than other implementations. Besides writing standard arrays of data, it also supports writing data that are exposed via C++ iterators, allowing to serialize data structures that do not reside in contiguous memory. Furthermore, support for structured arrays is provided, which facilitates reading and writing tabular data with labeled columns conveniently.

The performance of millimeter wave (mmWave) multiple-input multiple-output (MIMO) systems is limited by the sparse nature of propagation channels and the restricted number of radio frequency chains at transceivers. The introduction of reconfigurable antennas offers an additional degree of freedom on designing mmWave MIMO systems. This paper provides a theoretical framework for studying the mmWave MIMO with reconfigurable antennas. Based on the virtual channel model, we present an architecture of reconfigurable mmWave MIMO with beamspace hybrid analog-digital beamformers and reconfigurable antennas at both the transmitter and the receiver. We show that employing reconfigurable antennas can provide throughput gain for the mmWave MIMO. We derive the expression for the average throughput gain of using reconfigurable antennas in the system, and further derive the expression for the outage throughput gain for the scenarios where the channels are (quasi) static. Moreover, we propose a low-complexity algorithm for reconfiguration state selection and beam selection. Our numerical results verify the derived expressions for the throughput gains and demonstrate the near-optimal throughput performance of the proposed low-complexity algorithm.

Debugging data processing logic in data-intensive scalable computing (DISC) systems is a difficult and time-consuming effort. Today's DISC systems offer very little tooling for debugging programs, and as a result, programmers spend countless hours collecting evidence (e.g., from log files) and performing trial-and-error debugging. To aid this effort, we built Titian, a library that enables data provenance-tracking data through transformations-in Apache Spark. Data scientists using the Titian Spark extension will be able to quickly identify the input data at the root cause of a potential bug or outlier result. Titian is built directly into the Spark platform and offers data provenance support at interactive speeds-orders of magnitude faster than alternative solutions-while minimally impacting Spark job performance; observed overheads for capturing data lineage rarely exceed 30% above the baseline job execution time.

Multi-tier networks have many applications in different fields. We define a novel two-tier quantizer that can be applied to different node deployment problems including the energy conservation in two-tier wireless sensor networks consisting of N access points (APs) and M fusion centers (FCs). We aim at finding an optimal deployment of APs and FCs to minimize the average weighted total, or Lagrangian, of sensor and AP powers. For one FC, M=1, we show that the optimal deployment of APs is simply a linear transformation of the optimal N-level quantizer for density f, and the sole FC should be located at the geometric centroid of the sensing field. We also provide the exact expression of the AP-Sensor power function and prove its convexity. For more than one FC, M>1, we provide a necessary condition for the optimal deployment. Furthermore, to numerically optimize the AP and FC deployment, we propose three Lloyd-like algorithms and analyze their convergence. Simulation results show that our algorithms outperform the existing algorithms.

For 38 years, the IEEE Symposium on Security and Privacy has been the premier forum for presenting computer security and electronic privacy developments and for bringing together leading researchers and practitioners. We invited authors to submit revised versions of their symposium papers, recast as articles suitable for publication in IEEE Security & Privacy magazine. Specifically, we asked the original authors to revise their papers to speak to the magazine's audience, which goes beyond the symposium's traditional academically focused audience to also include policymakers and practitioners.

https://www.maizegdb.org/snpversity.

The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices.

The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings. We here examine how the IEDB complies with these principles and identify broad areas of success, but also areas for improvement. We describe short-term improvements to the IEDB that are being implemented now, as well as a long-term vision of true 'machine-actionable interoperability', which we believe will require community agreement on standardization of knowledge representation that can be built on top of the shared use of ontologies.

Natural language descriptions of organismal phenotypes, a principal object of study in biology, are abundant in the biological literature. Expressing these phenotypes as logical statements using ontologies would enable large-scale analysis on phenotypic information from diverse systems. However, considerable human effort is required to make these phenotype descriptions amenable to machine reasoning. Natural language processing tools have been developed to facilitate this task, and the training and evaluation of these tools depend on the availability of high quality, manually annotated gold standard data sets. We describe the development of an expert-curated gold standard data set of annotated phenotypes for evolutionary biology. The gold standard was developed for the curation of complex comparative phenotypes for the Phenoscape project. It was created by consensus among three curators and consists of entity-quality expressions of varying complexity. We use the gold standard to evaluate annotations created by human curators and those generated by the Semantic CharaParser tool. Using four annotation accuracy metrics that can account for any level of relationship between terms from two phenotype annotations, we found that machine-human consistency, or similarity, was significantly lower than inter-curator (human-human) consistency. Surprisingly, allowing curatorsaccess to external information did not significantly increase the similarity of their annotations to the gold standard or have a significant effect on inter-curator consistency. We found that the similarity of machine annotations to the gold standard increased after new relevant ontology terms had been added. Evaluation by the original authors of the character descriptions indicated that the gold standard annotations came closer to representing their intended meaning than did either the curator or machine annotations. These findings point toward ways to better design software to augment human curators and the use of the gold standard corpus will allow training and assessment of new tools to improve phenotype annotation accuracy at scale.

Visualizations themselves have become a data format. Akin to other data formats such as text and images, visualizations are increasingly created, stored, shared, and (re-)used with artificial intelligence (AI) techniques. In this survey, we probe the underlying vision of formalizing visualizations as an emerging data format and review the recent advance in applying AI techniques to visualization data (AI4VIS). We define visualization data as the digital representations of visualizations in computers and focus on data visualization (e.g., charts and infographics). We build our survey upon a corpus spanning ten different fields in computer science with an eye toward identifying important common interests. Our resulting taxonomy is organized around WHAT is visualization data and its representation, WHY and HOW to apply AI to visualization data. We highlight a set of common tasks that researchers apply to the visualization data and present a detailed discussion of AI approaches developed to accomplish those tasks. Drawing upon our literature review, we discuss several important research questions surrounding the management and exploitation of visualization data, as well as the role of AI in support of those processes. We make the list of surveyed papers and related material available online at. [ABSTRACT FROM AUTHOR]

This paper presents an analysis and the research results of system couplers in CAx systems that ensure the correct transfer of product data from the “supplier” system to the “recipient” system. This study presents the results of the compatibility tests between the systems based on the verification of geometric models and their attributes after importing/exporting 2D and 3D objects using neutral data exchange formats. The purpose of the research was to identify neutral formats that do not introduce errors after data transversion in certain types of geometry. Tests and analyses were carried out on selected formats depending on the type of object, such as 2D objects (DXF), solid objects (IGES, STEP, SAT, and PARASOLID), and surface objects (IGES, STEP, SAT, and X_T). One of the results of our research and analysis is the need for continuous development of CAD/CAE systems because current neutral formats are not 100% effective.

Mass spectrometry is a widely used technology to identify and quantify biomolecules such as lipids, metabolites and proteins necessary for biomedical research. In this study, we catalogued freely available software tools, libraries, databases, repositories and resources that support lipidomics data analysis and determined the scope of currently used analytical technologies. Because of the tremendous importance of data interoperability, we assessed the support of standardized data formats in mass spectrometric (MS)-based lipidomics workflows. We included tools in our comparison that support targeted as well as untargeted analysis using direct infusion/shotgun (DI-MS), liquid chromatography−mass spectrometry, ion mobility or MS imaging approaches on MS1 and potentially higher MS levels. As a result, we determined that the Human Proteome Organization-Proteomics Standards Initiative standard data formats, mzML and mzTab-M, are already supported by a substantial number of recent software tools. We further discuss how mzTab-M can serve as a bridge between data acquisition and lipid bioinformatics tools for interpretation, capturing their output and transmitting rich annotated data for downstream processing. However, we identified several challenges of currently available tools and standards. Potential areas for improvement were: adaptation of common nomenclature and standardized reporting to enable high throughput lipidomics and improve its data handling. Finally, we suggest specific areas where tools and repositories need to improve to become FAIRer. [ABSTRACT FROM AUTHOR]

Formal synthesis is the process of generating a program satisfying a high-level formal specification. In recent times, effective formal synthesis methods have been proposed based on the use of inductive learning. We refer to this class of methods that learn programs from examples as formal inductive synthesis. In this paper, we present a theoretical framework for formal inductive synthesis. We discuss how formal inductive synthesis differs from traditional machine learning. We then describe oracle-guided inductive synthesis (OGIS), a framework that captures a family of synthesizers that operate by iteratively querying an oracle. An instance of OGIS that has had much practical impact is counterexample-guided inductive synthesis (CEGIS). We present a theoretical characterization of CEGIS for learning any program that computes a recursive language. In particular, we analyze the relative power of CEGIS variants where the types of counterexamples generated by the oracle varies. We also consider the impact of bounded versus unbounded memory available to the learning algorithm. In the special case where the universe of candidate programs is finite, we relate the speed of convergence to the notion of teaching dimension studied in machine learning theory. Altogether, the results of the paper take a first step towards a theoretical foundation for the emerging field of formal inductive synthesis.

Managing dynamic information in large multi-site, multi-species, and multi-discipline consortia is a challenging task for data management applications. Often in academic research studies the goals for informatics teams are to build applications that provide extract-transform-load (ETL) functionality to archive and catalog source data that has been collected by the research teams. In consortia that cross species and methodological or scientific domains, building interfaces which supply data in a usable fashion and make intuitive sense to scientists from dramatically different backgrounds increases the complexity for developers. Further, reusing source data from outside one’s scientific domain is fraught with ambiguities in understanding the data types, analysis methodologies, and how to combine the data with those from other research teams. We report on the design, implementation, and performance of a semantic data management application to support the NIMH funded Conte Center at the University of California, Irvine. The Center is testing a theory of the consequences of “fragmented” (unpredictable, high entropy) early-life experiences on adolescent cognitive and emotional outcomes in both humans and rodents. It employs cross-species neuroimaging, epigenomic, molecular, and neuroanatomical approaches in humans and rodents to assess the potential consequences of fragmented unpredictable experience on brain structure and circuitry. To address this multi-technology, multi-species approach, the system uses semantic web techniques based on the Neuroimaging Data Model (NIDM) to facilitate data ETL functionality. We find this approach enables a low-cost, easy to maintain, and semantically meaningful information management system, enabling the diverse research teams to access and use the data.