BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.

The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Here we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility (P. aureginosa only). We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. We conclude that, while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. We finally report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bioontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens. 157 project. Predicting GO terms for a protein (protein-centric) and predicting which proteins are associated 158 with a given function (term-centric) are related but different computational problems: the former is a 159 multi-label classification problem with a structured output, while the latter is a binary classification task. 160Predicting the results of a genome-wide screen for a single or a small number of functions fits the term-centric 161 formulation. To see how well all participating CAFA methods perform term-centric predictions, we mapped 162 results from the protein-centric CAFA3 methods onto these terms. In addition we held a separate CAFA 163 challenge, CAFA-π whose purpose was to attract additional submissions from algorithms that specialize in 164 term-centric tasks. 165 We performed screens for three functions in three species, which we then used to assess protein function 166 prediction. In the bacterium Pseudomonas aeruginosa and the fungus Candida albicans we performed 167 genome-wide screens capable of uncovering genes with two functions, biofilm formation (GO:0042710) and 168 motility (for P. aeruginosa only) (GO:0001539), as described in Methods. In Drosophila melanogaster we 169 performed targeted assays, guided by previous CAFA submissions, of a ...

Our research work describes a team of human Digital Twins (DTs), each tracking fitness-related measurements describing an athlete's behavior in consecutive days (e.g. food income, activity, sleep). After collecting enough measurements, the DT firstly predicts the physical twin performance during training and, in case of non-optimal result, it suggests modifications in the athlete's behavior. The athlete's team is integrated into SmartFit, a software framework for supporting trainers and coaches in monitoring and manage athletes' fitness activity and results. Through IoT sensors embedded in wearable devices and applications for manual logging (e.g. mood, food income), SmartFit continuously captures measurements, initially treated as the dynamic data describing the current physical twins' status. Dynamic data allows adapting each DT's status and triggering the DT's predictions and suggestions. The analyzed measurements are stored as the historical data, further processed by the DT to update (increase) its knowledge and ability to provide reliable predictions. Results show that, thanks to the team of DTs, SmartFit computes trustable predictions of the physical twins' conditions and produces understandable suggestions which can be used by trainers to trigger optimization actions in the athletes' behavior. Though applied in the sport context, SmartFit can be easily adapted to other monitoring tasks. INDEX TERMS Counterfactual explanations, digital twins, Internet of Things, machine learning, smart health, sociotechnical design, wearables.

Network Functions Virtualization is focused on\ud migrating traditional hardware-based network functions to\ud software-based appliances running on standard high volume\ud severs. There are a variety of challenges facing early adopters of\ud Network Function Virtualizations; key among them are resource\ud and service mapping, to support virtual network function orchestration.\ud Service providers need efficient and effective mapping\ud capabilities to optimally deploy network services. This paper\ud describes TeNOR, a micro-service based network function virtualisation\ud orchestrator capable of effectively addressing resource\ud and network service mapping. The functional architecture and\ud data models of TeNOR are described, as well as two proposed\ud approaches to address the resource mapping problem. Key\ud evaluation results are discussed and an assessment of the mapping\ud approaches is performed in terms of the service acceptance ratio\ud and scalability of the proposed approaches

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND 4.0). Created by The Institute of Electrical and Electronics Engineers (IEEE) for the benefit of humanity.

Along‐tract statistics analysis enables the extraction of quantitative diffusion metrics along specific white matter fiber tracts. Besides quantitative metrics derived from classical diffusion tensor imaging (DTI), such as fractional anisotropy and diffusivities, new parameters reflecting the relative contribution of different diffusion compartments in the tissue can be estimated through advanced diffusion MRI methods as neurite orientation dispersion and density imaging (NODDI), leading to a more specific microstructural characterization. In this study, we extracted both DTI‐ and NODDI‐derived quantitative microstructural diffusion metrics along the most eloquent fiber tracts in 15 healthy subjects and in 22 patients with brain tumors. We obtained a robust intraprotocol reference database of normative along‐tract microstructural metrics, and their corresponding plots, from healthy fiber tracts. Each diffusion metric of individual patient's fiber tract was then plotted and statistically compared to the normative profile of the corresponding metric from the healthy fiber tracts. NODDI‐derived metrics appeared to account for the pathological microstructural changes of the peritumoral tissue more accurately than DTI‐derived ones. This approach may be useful for future studies that may compare healthy subjects to patients diagnosed with other pathological conditions.

Network Function Virtualization (NFV) has become a widely acclaimed approach to facilitate the management and orchestration of network services. However, after rapidly achieving a widespread success, NFV is now challenged by the overwhelming demand of computing power originated by the never-ending growth of innovative applications coming from the Internet world. To overcome this problem, the use of h/w acceleration combined with NFV has been proposed. This way, the computing performance of commodity servers can be greatly enhanced, without losing the advantages offered by NFV in service management. In this paper, to demonstrate the potentialities of NFV and h/w acceleration, a Virtual Network Function for video coding (video Transcoding Unit-vTU) is presented. The vTU is accelerated by a General Purpose GPU, and is based on Open Source software packages for media processing. The vTU architecture is firstly described in details. A thorough characterization of its computing performance is then reported, and the obtained results are compared to those achieved with non-accelerated and/or non-virtualized versions of the vTU itself. Also, the performance provided by an original, GPU accelerated version of the VP8 encoder is presented. The activities described in this paper have been carried out within the EU FP7 T-NOVA project.

Methods for phenotype and outcome prediction are largely based on inductive supervised models that use selected biomarkers to make predictions, without explicitly considering the functional relationships between individuals. We introduce a novel network-based approach named Patient-Net (P-Net) in which biomolecular profiles of patients are modeled in a graph-structured space that represents gene expression relationships between patients. Then a kernel-based semi-supervised transductive algorithm is applied to the graph to explore the overall topology of the graph and to predict the phenotype/clinical outcome of patients. Experimental tests involving several publicly available datasets of patients afflicted with pancreatic, breast, colon and colorectal cancer show that our proposed method is competitive with state-of-the-art supervised and semi-supervised predictive systems. Importantly, P-Net also provides interpretable models that can be easily visualized to gain clues about the relationships between patients, and to formulate hypotheses about their stratification. Phenotype and outcome prediction using sets of selected biomarkers are well-established prediction tasks in the context of computational biology, including different prediction problems ranging from the response to a specific drug 1,2 , diagnosis and prognosis 3-5 , classification of cancer subtypes 6 , outcome and recurrence prediction 7-9 and other related prediction problems 10. State-of-the-art methods for these problems are largely based on inductive supervised models that use sets of selected biomarkers, usually represented as vectors, to predict the phenotype or outcome of interest (see, e.g. 11-13), without taking into account the relationships between individuals. Several works proposed "network-based" methods by constructing graphs of patients, in order to discover the underlying structure of the data (e.g. discovery of subtypes of diseases, clinical stratification of patients) 14-17. These methods mainly used unsupervised approaches and hence have been not specifically designed and are not appropriate for phenotype/outcome prediction problems. Recently a few works proposed semi-supervised "network-based" approaches for the prediction of the phenotype/outcome of patients, on the basis of their bio-molecular profiles (e.g. gene expression of genotypic profiles) 18,19 , including also methods able to integrate multiple sources of omics data 20 , and methods based on Supervised Random Walks 21 , specifically modified for the classification of tumors 22. In this work, we introduce a novel network-based method for modeling in the "patient space". In this context the nodes of the network represent patients through an n-dimensional set of biomarker values (e.g. a set of gene expression values), and edges represent similarities between the biomarkers of a pair of patients. Hence, this "patient-space" differs from the classical "biomarker-space", where nodes represent biomarkers and edges similarities between biomarkers and not between patients 23,24...