1,344 research outputs found

    Setting the basis of best practices and standards for curation and annotation of logical models in biology

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    International audienceThe fast accumulation of biological data calls for their integration, analysis and exploitation through more systematic approaches. The generation of novel, relevant hypotheses from this enormous quantity of data remains challenging. Logical models have long been used to answer a variety of questions regarding the dynamical behaviours of regulatory networks. As the number of published logical models increases, there is a pressing need for systematic model annotation, referencing and curation in community-supported and standardised formats. This article summarises the key topics and future directions of a meeting entitled ‘Annotation and curation of computational models in biology’, organised as part of the 2019 [BC]2 conference. The purpose of the meeting was to develop and drive forward a plan towards the standardised annotation of logical models, review and connect various ongoing projects of experts from different communities involved in the modelling and annotation of molecular biological entities, interactions, pathways and models. This article defines a roadmap towards the annotation and curation of logical models, including milestones for best practices and minimum standard requirements

    On efficient temporal subgraph query processing

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    A Systematic Review of Robustness in Deep Learning for Computer Vision: Mind the gap?

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    Deep neural networks for computer vision are deployed in increasingly safety-critical and socially-impactful applications, motivating the need to close the gap in model performance under varied, naturally occurring imaging conditions. Robustness, ambiguously used in multiple contexts including adversarial machine learning, refers here to preserving model performance under naturally-induced image corruptions or alterations. We perform a systematic review to identify, analyze, and summarize current definitions and progress towards non-adversarial robustness in deep learning for computer vision. We find this area of research has received disproportionately less attention relative to adversarial machine learning, yet a significant robustness gap exists that manifests in performance degradation similar in magnitude to adversarial conditions. Toward developing a more transparent definition of robustness, we provide a conceptual framework based on a structural causal model of the data generating process and interpret non-adversarial robustness as pertaining to a model's behavior on corrupted images corresponding to low-probability samples from the unaltered data distribution. We identify key architecture-, data augmentation-, and optimization tactics for improving neural network robustness. This robustness perspective reveals that common practices in the literature correspond to causal concepts. We offer perspectives on how future research may mind this evident and significant non-adversarial robustness gap

    Data science for buildings, a multi-scale approach bridging occupants to smart-city energy planning

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    Data science for buildings, a multi-scale approach bridging occupants to smart-city energy planning

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    In a context of global carbon emission reduction goals, buildings have been identified to detain valuable energy-saving abilities. With the exponential increase of smart, connected building automation systems, massive amounts of data are now accessible for analysis. These coupled with powerful data science methods and machine learning algorithms present a unique opportunity to identify untapped energy-saving potentials from field information, and effectively turn buildings into active assets of the built energy infrastructure.However, the diversity of building occupants, infrastructures, and the disparities in collected information has produced disjointed scales of analytics that make it tedious for approaches to scale and generalize over the building stock.This coupled with the lack of standards in the sector has hindered the broader adoption of data science practices in the field, and engendered the following questioning:How can data science facilitate the scaling of approaches and bridge disconnected spatiotemporal scales of the built environment to deliver enhanced energy-saving strategies?This thesis focuses on addressing this interrogation by investigating data-driven, scalable, interpretable, and multi-scale approaches across varying types of analytical classes. The work particularly explores descriptive, predictive, and prescriptive analytics to connect occupants, buildings, and urban energy planning together for improved energy performances.First, a novel multi-dimensional data-mining framework is developed, producing distinct dimensional outlines supporting systematic methodological approaches and refined knowledge discovery. Second, an automated building heat dynamics identification method is put forward, supporting large-scale thermal performance examination of buildings in a non-intrusive manner. The method produced 64\% of good quality model fits, against 14\% close, and 22\% poor ones out of 225 Dutch residential buildings. %, which were open-sourced in the interest of developing benchmarks. Third, a pioneering hierarchical forecasting method was designed, bridging individual and aggregated building load predictions in a coherent, data-efficient fashion. The approach was evaluated over hierarchies of 37, 140, and 383 nodal elements and showcased improved accuracy and coherency performances against disjointed prediction systems.Finally, building occupants and urban energy planning strategies are investigated under the prism of uncertainty. In a neighborhood of 41 Dutch residential buildings, occupants were determined to significantly impact optimal energy community designs in the context of weather and economic uncertainties.Overall, the thesis demonstrated the added value of multi-scale approaches in all analytical classes while fostering best data-science practices in the sector from benchmarks and open-source implementations

    See It to Believe It? {T}he Role of Visualisation in Systems Research

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    The promises of large language models for protein design and modeling.

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    The recent breakthroughs of Large Language Models (LLMs) in the context of natural language processing have opened the way to significant advances in protein research. Indeed, the relationships between human natural language and the language of proteins invite the application and adaptation of LLMs to protein modelling and design. Considering the impressive results of GPT-4 and other recently developed LLMs in processing, generating and translating human languages, we anticipate analogous results with the language of proteins. Indeed, protein language models have been already trained to accurately predict protein properties, generate novel functionally characterized proteins, achieving state-of-the-art results. In this paper we discuss the promises and the open challenges raised by this novel and exciting research area, and we propose our perspective on how LLMs will affect protein modeling and design
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