004 Datenverarbeitung; Informatik
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Correction to: Knowledge bases and software support for variant interpretation in precision oncology
(2021)
Precision oncology is a rapidly evolving interdisciplinary medical specialty. Comprehensive cancer panels are becoming increasingly available at pathology departments worldwide, creating the urgent need for scalable cancer variant annotation and molecularly informed treatment recommendations. A wealth of mainly academia-driven knowledge bases calls for software tools supporting the multi-step diagnostic process. We derive a comprehensive list of knowledge bases relevant for variant interpretation by a review of existing literature followed by a survey among medical experts from university hospitals in Germany. In addition, we review cancer variant interpretation tools, which integrate multiple knowledge bases. We categorize the knowledge bases along the diagnostic process in precision oncology and analyze programmatic access options as well as the integration of knowledge bases into software tools. The most commonly used knowledge bases provide good programmatic access options and have been integrated into a range of software tools. For the wider set of knowledge bases, access options vary across different parts of the diagnostic process. Programmatic access is limited for information regarding clinical classifications of variants and for therapy recommendations. The main issue for databases used for biological classification of pathogenic variants and pathway context information is the lack of standardized interfaces. There is no single cancer variant interpretation tool that integrates all identified knowledge bases. Specialized tools are available and need to be further developed for different steps in the diagnostic process.
COMMIT
(2022)
Composition and functions of microbial communities affect important traits in diverse hosts, from crops to humans. Yet, mechanistic understanding of how metabolism of individual microbes is affected by the community composition and metabolite leakage is lacking. Here, we first show that the consensus of automatically generated metabolic reconstructions improves the quality of the draft reconstructions, measured by comparison to reference models. We then devise an approach for gap filling, termed COMMIT, that considers metabolites for secretion based on their permeability and the composition of the community. By applying COMMIT with two soil communities from the Arabidopsis thaliana culture collection, we could significantly reduce the gap-filling solution in comparison to filling gaps in individual reconstructions without affecting the genomic support. Inspection of the metabolic interactions in the soil communities allows us to identify microbes with community roles of helpers and beneficiaries. Therefore, COMMIT offers a versatile fully automated solution for large-scale modelling of microbial communities for diverse biotechnological applications. <br /> Author summaryMicrobial communities are important in ecology, human health, and crop productivity. However, detailed information on the interactions within natural microbial communities is hampered by the community size, lack of detailed information on the biochemistry of single organisms, and the complexity of interactions between community members. Metabolic models are comprised of biochemical reaction networks based on the genome annotation, and can provide mechanistic insights into community functions. Previous analyses of microbial community models have been performed with high-quality reference models or models generated using a single reconstruction pipeline. However, these models do not contain information on the composition of the community that determines the metabolites exchanged between the community members. In addition, the quality of metabolic models is affected by the reconstruction approach used, with direct consequences on the inferred interactions between community members. Here, we use fully automated consensus reconstructions from four approaches to arrive at functional models with improved genomic support while considering the community composition. We applied our pipeline to two soil communities from the Arabidopsis thaliana culture collection, providing only genome sequences. Finally, we show that the obtained models have 90% genomic support and demonstrate that the derived interactions are corroborated by independent computational predictions.
Phe2vec
(2021)
Robust phenotyping of patients from electronic health records (EHRs) at scale is a challenge in clinical informatics. Here, we introduce Phe2vec, an automated framework for disease phenotyping from EHRs based on unsupervised learning and assess its effectiveness against standard rule-based algorithms from Phenotype KnowledgeBase (PheKB). Phe2vec is based on pre-computing embeddings of medical concepts and patients' clinical history. Disease phenotypes are then derived from a seed concept and its neighbors in the embedding space. Patients are linked to a disease if their embedded representation is close to the disease phenotype. Comparing Phe2vec and PheKB cohorts head-to-head using chart review, Phe2vec performed on par or better in nine out of ten diseases. Differently from other approaches, it can scale to any condition and was validated against widely adopted expert-based standards. Phe2vec aims to optimize clinical informatics research by augmenting current frameworks to characterize patients by condition and derive reliable disease cohorts.
Working conditions of knowledge workers have been subject to rapid change recently. Digital nomadism is no longer a phenomenon that relates only to entrepreneurs, freelancers, and gig workers. Corporate employees, too, have begun to uncouple their work from stationary (home) offices and 9-to-5 schedules. However, pursuing a permanent job in a corporate environment is still subject to fundamentally different values than postulated by the original notion of digital nomadism. Therefore, this paper explores the work identity of what is referred to as ‘corporate nomads’. By drawing on identity theory and the results of semi-structured interviews, the paper proposes a conceptualization of the corporate nomad archetype and presents nine salient identity issues of corporate nomads (e.g., holding multiple contradictory identities, the flexibility paradox, or collaboration constraints). By introducing the ‘corporate nomad’ archetype to the Information Systems literature, this article helps to rethink established conceptions of “home office” and socio-spatial configurations of knowledge work.
Student teachers often struggle to keep track of everything that is happening in the classroom, and particularly to notice and respond when students cause disruptions. The complexity of the classroom environment is a potential contributing factor that has not been empirically tested. In this experimental study, we utilized a virtual reality (VR) classroom to examine whether classroom complexity affects the likelihood of student teachers noticing disruptions and how they react after noticing. Classroom complexity was operationalized as the number of disruptions and the existence of overlapping disruptions (multidimensionality) as well as the existence of parallel teaching tasks (simultaneity). Results showed that student teachers (n = 50) were less likely to notice the scripted disruptions, and also less likely to respond to the disruptions in a comprehensive and effortful manner when facing greater complexity. These results may have implications for both teacher training and the design of VR for training or research purpose. This study contributes to the field from two aspects: 1) it revealed how features of the classroom environment can affect student teachers' noticing of and reaction to disruptions; and 2) it extends the functionality of the VR environment-from a teacher training tool to a testbed of fundamental classroom processes that are difficult to manipulate in real-life.
Advancements in computer vision techniques driven by machine learning have facilitated robust and efficient estimation of attributes such as depth, optical flow, albedo, and shading. To encapsulate all such underlying properties associated with images and videos, we evolve the concept of intrinsic images towards intrinsic attributes. Further, rapid hardware growth in the form of high-quality smartphone cameras, readily available depth sensors, mobile GPUs, or dedicated neural processing units have made image and video processing pervasive. In this thesis, we explore the synergies between the above two advancements and propose novel image and video processing techniques and systems based on them. To begin with, we investigate intrinsic image decomposition approaches and analyze how they can be implemented on mobile devices. We propose an approach that considers not only diffuse reflection but also specular reflection; it allows us to decompose an image into specularity, albedo, and shading on a resource constrained system (e.g., smartphones or tablets) using the depth data provided by the built-in depth sensors. In addition, we explore how on-device depth data can further be used to add an immersive dimension to 2D photos, e.g., showcasing parallax effects via 3D photography. In this regard, we develop a novel system for interactive 3D photo generation and stylization on mobile devices. Further, we investigate how adaptive manipulation of baseline-albedo (i.e., chromaticity) can be used for efficient visual enhancement under low-lighting conditions. The proposed technique allows for interactive editing of enhancement settings while achieving improved quality and performance. We analyze the inherent optical flow and temporal noise as intrinsic properties of a video. We further propose two new techniques for applying the above intrinsic attributes for the purpose of consistent video filtering. To this end, we investigate how to remove temporal inconsistencies perceived as flickering artifacts. One of the techniques does not require costly optical flow estimation, while both provide interactive consistency control. Using intrinsic attributes for image and video processing enables new solutions for mobile devices – a pervasive visual computing device – and will facilitate novel applications for Augmented Reality (AR), 3D photography, and video stylization. The proposed low-light enhancement techniques can also improve the accuracy of high-level computer vision tasks (e.g., face detection) under low-light conditions. Finally, our approach for consistent video filtering can extend a wide range of image-based processing for videos.
The use of neural networks is considered as the state of the art in the field of image classification. A large number of different networks are available for this purpose, which, appropriately trained, permit a high level of classification accuracy. Typically, these networks are applied to uncompressed image data, since a corresponding training was also carried out using image data of similar high quality. However, if image data contains image errors, the classification accuracy deteriorates drastically. This applies in particular to coding artifacts which occur due to image and video compression. Typical application scenarios for video compression are narrowband transmission channels for which video coding is required but a subsequent classification is to be carried out on the receiver side. In this paper we present a special H.264/Advanced Video Codec (AVC) based video codec that allows certain regions of a picture to be coded with near constant picture quality in order to allow a reliable classification using neural networks, whereas the remaining image will be coded using constant bit rate. We have combined this feature with the ability to run with lowest latency properties, which is usually also required in remote control applications scenarios. The codec has been implemented as a fully hardwired High Definition video capable hardware architecture which is suitable for Field Programmable Gate Arrays.
We present a general approach to planning with incomplete information in Answer Set Programming (ASP). More precisely, we consider the problems of conformant and conditional planning with sensing actions and assumptions. We represent planning problems using a simple formalism where logic programs describe the transition function between states, the initial states and the goal states. For solving planning problems, we use Quantified Answer Set Programming (QASP), an extension of ASP with existential and universal quantifiers over atoms that is analogous to Quantified Boolean Formulas (QBFs). We define the language of quantified logic programs and use it to represent the solutions different variants of conformant and conditional planning. On the practical side, we present a translation-based QASP solver that converts quantified logic programs into QBFs and then executes a QBF solver, and we evaluate experimentally the approach on conformant and conditional planning benchmarks.
Business processes are often specified in descriptive or normative models. Both types of models should adhere to internal and external regulations, such as company guidelines or laws. Employing compliance checking techniques, it is possible to verify process models against rules. While traditionally compliance checking focuses on well-structured processes, we address case management scenarios. In case management, knowledge workers drive multi-variant and adaptive processes. Our contribution is based on the fragment-based case management approach, which splits a process into a set of fragments. The fragments are synchronized through shared data but can, otherwise, be dynamically instantiated and executed. We formalize case models using Petri nets. We demonstrate the formalization for design-time and run-time compliance checking and present a proof-of-concept implementation. The application of the implemented compliance checking approach to a use case exemplifies its effectiveness while designing a case model. The empirical evaluation on a set of case models for measuring the performance of the approach shows that rules can often be checked in less than a second.