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Most VE-frameworks try to support many different input and output devices. They do not concentrate so much on the rendering because this is tradi- tionally done by graphics workstation. In this short paper we present a modern VE framework that has a small kernel and is able to use different renderers. This includes sound renderers, physics renderers and software based graphics renderers. While our VE framework, named basho is still under development we have an alpha version running under Linux and MacOS X.
In this paper, we introduce an optical sensor system, which is integrated into an industrial push-button. The sensor allows to classify the type of material that is in contact with the button when pressed into different material categories on the basis of the material's so called "spectral signature". An approach for a safety sensor system at circular table saws on the same base has been introduced previously on SIAS-2007. This contactless working sensor is able to distinguish reliably between skin, textiles, leather and various other kinds of materials. A typical application for this intelligent push-button is the use at possibly dangerous machines, whose operating instructions include either the prohibition or the obligation to wear gloves during the work at the machine. An exemple of machines at which no gloves are allowed are pillar drilling machines, because of the risk of getting caught in the drill chuck and being turned in by the machine. In many cases this causes very serious hand injuries. Depending on the application needs, the sensor system integrated into the push-button can be configured flexibly by software to prevent the operator from accidentally starting a machine with or without gloves, which can decrease the risk of severe accidents significantly. Especially two-hand controls are incentive to manipulation for easier handling. By equipping both push-buttons of a two-hand control with material classification properties, the user is forced to operate the controls with his bare fingers. That limitation disallows the manipulation of a two-hand control by a simple rodding device.
Die Forschung zur kontrovers diskutierten Robotik in der Pflege und Begleitung von Personen mit Demenz steht noch am Anfang, wenngleich bereits erste Systeme auf dem Markt sind. Der Beitrag gibt entlang beispielhafter, fallbezogener Auszüge Einblicke in das laufende multidisziplinäre Projekt EmoRobot, das sich explorativ und interpretativ mit der Erkundung des Einsatzes von Robotik in der emotionsorientierten Pflege und Versorgung von Personen mit Demenz befasst. Fokussiert werden dabei die je eigenen Relevanzen der Personen mit Demenz.
Noncooperative Game Theory
(2016)
Kleinere, günstigere und effizientere Sensoren und Aktoren sowie Funkprotokolle haben dazu geführt, dass Smart Home Produkte in zunehmend auch für den privaten Massenmarkt erschwinglich werden. Damit stehen Hersteller und Anbieter vor der Herausforderung, komplexe cyber-physische Systeme für Jedermann handhabbar zu gestalten. Es fehlen allerdings empirische Erkenntnisse über die Rolle von Smart Home im Alltag. Wir präsentieren Ergebnisse aus einer Living Lab Studie, in der 14 Haushalte mit einer am Markt erhältlichen Smart Home Nachrüstlösung ausgestattet und über neun Monate empirisch begleitet wurden. Anhand der Analyse von Interviews, Beobachtungen und Co-Design Workshops in den Phasen der Produktauswahl, Installation, Konfiguration und längerfristigen Nutzung zeigen wir Herausforderungen und Potentiale von Smart Home Systemen auf. Unsere Erkenntnisse deuten darauf hin, dass das Smart Home immer noch von technischen Details dominiert wird. Zugleich fehlen Nutzern angemessene Steuerungs- und Kontrollmöglichkeiten, um weiterhin die Entscheidungshoheit im eigenen Zuhause zu behalten.
„Industrie 4.0“ und weitere Schlagwörter wie „Big Data“, „Internet der Dinge“ oder „Cyber-physical Systems“ werden gegenwärtig in der Wirtschaft häufig aufgegriffen. Ausgangspunkt hierfür ist die Vernetzung von IT-Technologien sowie die durchgängige Digitalisierung. Nicht nur die Geschäftsfelder und Business-Modelle der Unternehmen selbst unterliegen dabei ei-nem entsprechend radikalen Wandel, dieser bezieht sich auch auf die Arbeitsumgebungen der Mitarbeiter, sowie den privaten und den öffentlichen Raum (Botthof, 2015; Hartmann, 2015).
Informations- und Kommunikationstechnologie (IKT) in den Bereichen Smart Home und Smart Living ist durch die zunehmende Vernetzung des häuslichen Anwendungsfelds mit der Digitalisierung des Stromnetzes, alternativen Möglichkeiten der Energiegewinnung und -speicherung und neuer Mobilitätskonzepte geprägt und zu einem unverzichtbaren Bestandteil privaten wie unternehmerischen Handelns geworden.
UX-Professionals stehen vor der Aufgabe ihre Fertigkeiten und Kenntnisse kontinuierlich auszubauen. Eine Möglichkeit dies zu tun sind Communities of Practice, also Gemeinschaften von Personen mit ähnlichen Aufgaben und Schwerpunkten sowie einem gemeinsamen Interesse an Lösungen. Sie agieren weitgehend selbstorganisiert und dienen dem Austausch und der gegenseitigen Unterstützung. So entstehen ein gemeinsamer Wissensschatz sowie ein Netzwerk zwischen allen UX-Interessierten. Der Aufbau einer Community of Practice für UX-Professionals wurde in einem mittelständigen Unternehmen über 18 Monate begleitet und ausgewertet. Die Ergebnisse führten zu Handlungsempfehlungen, um Hindernisse beim Aufbau zu reduzieren und einen Mehrwert für alle Beteiligten herbeizuführen.
Die Entwicklung intelligenter Technologien zur Unterstützung im Alltag und in den eigenen vier Wänden begleitet unsere Gesellschaft schon seit dem Zeitalter des Personal Computers. Mit dem Aufkommen des Internet der Dinge und begünstigt durch immer kleiner und günstiger werdende Hardware ergeben sich neue Potenziale, die das Thema Smart Home attraktiver als je zuvor werden lassen. Eine Vielzahl der aktuell im Markt verfügbaren Lösungen adressiert die Bedürfnisse Komfort, Sicherheit und effiziente Energienutzung. Die versprochene Intelligenz – smartness, wie sie der Begriff selbst suggeriert – wird vor allem bei Lösungen im privaten Nachrüstbereich überwiegend durch die Interaktion der Nutzer selbst und entsprechende regelbasierte Konfigurationen erzeugt. Diese notwendige Art der Interaktion und die damit verbundenen Aufwände sind jedoch von starker Bedeutung für das gesamte Nutzungserlebnis Smart Home und führen nicht selten zu Frustration oder gar Resignation in der Nutzung.
Getrieben durch kleiner und günstiger werdende Sensoren und der damit verbundenen Messbarmachung immer weiter reichender Teile des Alltages, hat sich die Gestaltung von Verbrauchsvisualisierunen bzw. Verbrauchsfeedbacksystemen zur Unterstützung von nachhaltigem Verhalten zu einem sehr aktiven Forschungsfeld entwickelt.
The detection of human skin in images is a very desirable feature for applications such as biometric face recognition, which is becoming more frequently used for, e.g., automated border or access control. However, distinguishing real skin from other materials based on imagery captured in the visual spectrum alone and in spite of varying skin types and lighting conditions can be dicult and unreliable. Therefore, spoofing attacks with facial disguises or masks are still a serious problem for state of the art face recognition algorithms. This dissertation presents a novel approach for reliable skin detection based on spectral remission properties in the short-wave infrared (SWIR) spectrum and proposes a cross-modal method that enhances existing solutions for face verification to ensure the authenticity of a face even in the presence of partial disguises or masks. Furthermore, it presents a reference design and the necessary building blocks for an active multispectral camera system that implements this approach, as well as an in-depth evaluation. The system acquires four-band multispectral images within T = 50ms. Using a machine-learning-based classifier, it achieves unprecedented skin detection accuracy, even in the presence of skin-like materials used for spoofing attacks. Paired with a commercial face recognition software, the system successfully rejected all evaluated attempts to counterfeit a foreign face.
Advances in computer graphics enable us to create digital images of astonishing complexity and realism. However, processing resources are still a limiting factor. Hence, many costly but desirable aspects of realism are often not accounted for, including global illumination, accurate depth of field and motion blur, spectral effects, etc. especially in real‐time rendering. At the same time, there is a strong trend towards more pixels per display due to larger displays, higher pixel densities or larger fields of view. Further observable trends in current display technology include more bits per pixel (high dynamic range, wider color gamut/fidelity), increasing refresh rates (better motion depiction), and an increasing number of displayed views per pixel (stereo, multi‐view, all the way to holographic or lightfield displays). These developments cause significant unsolved technical challenges due to aspects such as limited compute power and bandwidth. Fortunately, the human visual system has certain limitations, which mean that providing the highest possible visual quality is not always necessary. In this report, we present the key research and models that exploit the limitations of perception to tackle visual quality and workload alike. Moreover, we present the open problems and promising future research targeting the question of how we can minimize the effort to compute and display only the necessary pixels while still offering a user full visual experience.
Females are influenced more than males by visual cues during many spatial orientation tasks; but females rely more heavily on gravitational cues during visual-vestibular conflict. Are there gender biases in the relative contributions of vision, gravity and the internal representation of the body to the perception of upright? And might any such biases be affected by low gravity? 16 participants (8 female) viewed a highly polarized visual scene tilted ±112° while lying supine on the European Space Agency's short-arm human centrifuge. The centrifuge was rotated to simulate 24 logarithmically spaced g-levels along the long axis of the body (0.04-0.5g at ear-level). The perception of upright was measured using the Oriented Character Recognition Test (OCHART). OCHART uses the ambiguous symbol "p" shown in different orientations. Participants decided whether it was a "p" or a "d" from which the perceptual upright (PU) can be calculated for each visual/gravity combination. The relative contribution of vision, gravity and the internal representation of the body were then calculated. Experiments were repeated while upright. The relative contribution of vision on the PU was less in females compared to males (t=-18.48, p≤0.01). Females placed more emphasis on the gravity cue instead (f:28.4%, m:24.9%) while body weightings were constant (f:63.0%, m:63.2%). When upright (1g) in this and other studies (e.g., Barnett-Cowan et al. 2010, EJN, 31,1899) females placed more emphasis on vision in this task than males. The reduction in weight allocated by females to vision when in simulated low-gravity conditions compared to when upright under normal gravity may be related to similar female behaviour in response to other instances of visual-vestibular conflict. Why this is the case and at which point the perceptual change happens requires further research.
In this paper, we provide a participatory design study of a mobile health platform for older adults that provides an integrative perspective on health data collected from different devices and apps. We illustrate the diversity and complexity of older adults’ perspectives in the context of health and technology use, the challenges which follow on for the design of mobile health platforms that support active and healthy ageing (AHA) and our approach to addressing these challenges through a participatory design (PD) process. Interviews were conducted with older adults aged 65+ in a two-month study with the goal of understanding perspectives on health and technologies for AHA support. We identified challenges and derived design ideas for a mobile health platform called “My-AHA”. For researchers in this field, the structured documentation of our procedures and results, as well as the implications derived provide valuable insights for the design of mobile health platforms for older adults.
Background: Virtual reality combined with spherical treadmills is used across species for studying neural circuits underlying navigation.
New Method: We developed an optical flow-based method for tracking treadmil ball motion in real-time using a single high-resolution camera.
Results: Tracking accuracy and timing were determined using calibration data. Ball tracking was performed at 500 Hz and integrated with an open source game engine for virtual reality projection. The projection was updated at 120 Hz with a latency with respect to ball motion of 30 ± 8 ms.
Comparison: with Existing Method(s) Optical flow based tracking of treadmill motion is typically achieved using optical mice. The camera-based optical flow tracking system developed here is based on off-the-shelf components and offers control over the image acquisition and processing parameters. This results in flexibility with respect to tracking conditions – such as ball surface texture, lighting conditions, or ball size – as well as camera alignment and calibration.
Conclusions: A fast system for rotational ball motion tracking suitable for virtual reality animal behavior across different scales was developed and characterized.
Computer graphics research strives to synthesize images of a high visual realism that are indistinguishable from real visual experiences. While modern image synthesis approaches enable to create digital images of astonishing complexity and beauty, processing resources remain a limiting factor. Here, rendering efficiency is a central challenge involving a trade-off between visual fidelity and interactivity. For that reason, there is still a fundamental difference between the perception of the physical world and computer-generated imagery. At the same time, advances in display technologies drive the development of novel display devices. The dynamic range, the pixel densities, and refresh rates are constantly increasing. Display systems enable a larger visual field to be addressed by covering a wider field-of-view, due to either their size or in the form of head-mounted devices. Currently, research prototypes are ranging from stereo and multi-view systems, head-mounted devices with adaptable lenses, up to retinal projection, and lightfield/holographic displays. Computer graphics has to keep step with, as driving these devices presents us with immense challenges, most of which are currently unsolved. Fortunately, the human visual system has certain limitations, which means that providing the highest possible visual quality is not always necessary. Visual input passes through the eye’s optics, is filtered, and is processed at higher level structures in the brain. Knowledge of these processes helps to design novel rendering approaches that allow the creation of images at a higher quality and within a reduced time-frame. This thesis presents the state-of-the-art research and models that exploit the limitations of perception in order to increase visual quality but also to reduce workload alike - a concept we call perception-driven rendering. This research results in several practical rendering approaches that allow some of the fundamental challenges of computer graphics to be tackled. By using different tracking hardware, display systems, and head-mounted devices, we show the potential of each of the presented systems. The capturing of specific processes of the human visual system can be improved by combining multiple measurements using machine learning techniques. Different sampling, filtering, and reconstruction techniques aid the visual quality of the synthesized images. An in-depth evaluation of the presented systems including benchmarks, comparative examination with image metrics as well as user studies and experiments demonstrated that the methods introduced are visually superior or on the same qualitative level as ground truth, whilst having a significantly reduced computational complexity.
In mathematical modeling by means of performance models, the Fitness-Fatigue Model (FF-Model) is a common approach in sport and exercise science to study the training performance relationship. The FF-Model uses an initial basic level of performance and two antagonistic terms (for fitness and fatigue). By model calibration, parameters are adapted to the subject’s individual physical response to training load. Although the simulation of the recorded training data in most cases shows useful results when the model is calibrated and all parameters are adjusted, this method has two major difficulties. First, a fitted value as basic performance will usually be too high. Second, without modification, the model cannot be simply used for prediction. By rewriting the FF-Model such that effects of former training history can be analyzed separately – we call those terms preload – it is possible to close the gap between a more realistic initial performance level and an athlete's actual performance level without distorting other model parameters and increase model accuracy substantially. Fitting error of the preload-extended FF-Model is less than 32% compared to the error of the FF-Model without preloads. Prediction error of the preload-extended FF-Model is around 54% of the error of the FF-Model without preloads.
This work addresses the issue of finding an optimal flight zone for a side-by-side tracking and following Unmanned Aerial Vehicle(UAV) adhering to space-restricting factors brought upon by a dynamic Vector Field Extraction (VFE) algorithm. The VFE algorithm demands a relatively perpendicular field of view of the UAV to the tracked vehicle, thereby enforcing the space-restricting factors which are distance, angle and altitude. The objective of the UAV is to perform side-by-side tracking and following of a lightweight ground vehicle while acquiring high quality video of tufts attached to the side of the tracked vehicle. The recorded video is supplied to the VFE algorithm that produces the positions and deformations of the tufts over time as they interact with the surrounding air, resulting in an airflow model of the tracked vehicle. The present limitations of wind tunnel tests and computational fluid dynamics simulation suggest the use of a UAV for real world evaluation of the aerodynamic properties of the vehicle’s exterior. The novelty of the proposed approach is alluded to defining the specific flight zone restricting factors while adhering to the VFE algorithm, where as a result we were capable of formalizing a locally-static and a globally-dynamic geofence attached to the tracked vehicle and enclosing the UAV.
Facial emotion recognition is the task to classify human emotions in face images. It is a difficult task due to high aleatoric uncertainty and visual ambiguity. A large part of the literature aims to show progress by increasing accuracy on this task, but this ignores the inherent uncertainty and ambiguity in the task. In this paper we show that Bayesian Neural Networks, as approximated using MC-Dropout, MC-DropConnect, or an Ensemble, are able to model the aleatoric uncertainty in facial emotion recognition, and produce output probabilities that are closer to what a human expects. We also show that calibration metrics show strange behaviors for this task, due to the multiple classes that can be considered correct, which motivates future work. We believe our work will motivate other researchers to move away from Classical and into Bayesian Neural Networks.
This paper introduces FaceHaptics, a novel haptic display based on a robot arm attached to a head-mounted virtual reality display. It provides localized, multi-directional and movable haptic cues in the form of wind, warmth, moving and single-point touch events and water spray to dedicated parts of the face not covered by the head-mounted display.The easily extensible system, however, can principally mount any type of compact haptic actuator or object. User study 1 showed that users appreciate the directional resolution of cues, and can judge wind direction well, especially when they move their head and wind direction is adjusted dynamically to compensate for head rotations. Study 2 showed that adding FaceHaptics cues to a VR walkthrough can significantly improve user experience, presence, and emotional responses.
Foreword to the Special Section on the Symposium on Virtual and Augmented Reality 2019 (SVR 2019)
(2020)
Kollaborative Industrieroboter werden für produzierende Unternehmen immer kosteneffizienter. Während diese Systeme für den menschlichen Mitarbeiter eine große Hilfe sein können, stellen sie gleichzeitig ein ernstes Gesundheitsrisiko dar, wenn die zwingend notwendigen Sicherheitsmaßnahmen nur unzureichend umgesetzt werden. Herkömmliche Sicherheitseinrichtungen wie Zäune oder Lichtvorhänge bieten einen guten Schutz, aber solch statische Schutzvorrichtungen sind in neuen, hochdynamischen Arbeitsszenarien problematisch.
Im Forschungsprojekt BeyondSPAI wurde ein Funktionsmuster eines Multisensorsystems zur Absicherung solcher dynamischer Arbeitsszenarien entworfen, implementiert und im Feld getestet. Kern des Systems ist eine robuste optische Materialklassifikation, die mit Hilfe eines intelligenten InGaAs-Kamerasystems Haut von anderen typischen Werkstückoberflächen (z.B. Holz, Metalle od. Kunststoffe) unterscheiden kann. Diese einzigartige Eigenschaft wird genutzt, um menschliche Mitarbeiter zuverlässig zu erkennen, so dass ein konventioneller Roboter in Folge als personenbewusster Cobot arbeiten kann.
Das System ist modular und kann leicht mit weiteren Sensoren verschiedenster Art erweitert werden. Es kann an verschiedene Marken von Industrierobotern angepasst werden und lässt sich schnell an bestehenden Robotersystemen integrieren. Die vier vom System bereitgestellten Sicherheitsausgänge können dazu verwendet werden - abhängig von der durchdrungenen Überwachungszone - entweder eine Warnung auszugeben, die Bewegung des Roboters auf eine sichere Geschwindigkeit zu verlangsamen, oder den Roboter sicher anzuhalten. Sobald alle Zonen wieder als „eindeutig frei von Personen“ identifiziert sind, kann der Roboter wieder beschleunigen, seine ursprüngliche Bewegung wiederaufnehmen und die Arbeit fortsetzen.
The majority of biomedical knowledge is stored in structured databases or as unstructured text in scientific publications. This vast amount of information has led to numerous machine learning-based biological applications using either text through natural language processing (NLP) or structured data through knowledge graph embedding models (KGEMs). However, representations based on a single modality are inherently limited. To generate better representations of biological knowledge, we propose STonKGs, a Sophisticated Transformer trained on biomedical text and Knowledge Graphs. This multimodal Transformer uses combined input sequences of structured information from KGs and unstructured text data from biomedical literature to learn joint representations. First, we pre-trained STonKGs on a knowledge base assembled by the Integrated Network and Dynamical Reasoning Assembler (INDRA) consisting of millions of text-triple pairs extracted from biomedical literature by multiple NLP systems. Then, we benchmarked STonKGs against two baseline models trained on either one of the modalities (i.e., text or KG) across eight different classification tasks, each corresponding to a different biological application. Our results demonstrate that STonKGs outperforms both baselines, especially on the more challenging tasks with respect to the number of classes, improving upon the F1-score of the best baseline by up to 0.083. Additionally, our pre-trained model as well as the model architecture can be adapted to various other transfer learning applications. Finally, the source code and pre-trained STonKGs models are available at https://github.com/stonkgs/stonkgs and https://huggingface.co/stonkgs/stonkgs-150k.
Over the last decades, different kinds of design guides have been created to maintain consistency and usability in interactive system development. However, in the case of spatial applications, practitioners from research and industry either have difficulty finding them or perceive such guides as lacking relevance, practicability, and applicability. This paper presents the current state of scientific research and industry practice by investigating currently used design recommendations for mixed reality (MR) system development. We analyzed and compared 875 design recommendations for MR applications elicited from 89 scientific papers and documentation from six industry practitioners in a literature review. In doing so, we identified differences regarding four key topics: Focus on unique MR design challenges, abstraction regarding devices and ecosystems, level of detail and abstraction of content, and covered topics. Based on that,we contribute to the MR design research by providing three factors for perceived irrelevance and six main implications for design recommendations that are applicable in scientific and industry practice.
Augmented/Virtual Reality (AR/VR) is still a fragmented space to design for due to the rapidly evolving hardware, the interdisciplinarity of teams, and a lack of standards and best practices. We interviewed 26 professional AR/VR designers and developers to shed light on their tasks, approaches, tools, and challenges. Based on their work and the artifacts they generated, we found that AR/VR application creators fulfill four roles: concept developers, interaction designers, content authors, and technical developers. One person often incorporates multiple roles and faces a variety of challenges during the design process from the initial contextual analysis to the deployment. From analysis of their tool sets, methods, and artifacts, we describe critical key challenges. Finally, we discuss the importance of prototyping for the communication in AR/VR development teams and highlight design implications for future tools to create a more usable AR/VR tool chain.
Using Visual and Auditory Cues to Locate Out-of-View Objects in Head-Mounted Augmented Reality
(2021)
When users in virtual reality cannot physically walk and self-motions are instead only visually simulated, spatial updating is often impaired. In this paper, we report on a study that investigated if HeadJoystick, an embodied leaning-based flying interface, could improve performance in a 3D navigational search task that relies on maintaining situational awareness and spatial updating in VR. We compared it to Gamepad, a standard flying interface. For both interfaces, participants were seated on a swivel chair and controlled simulated rotations by physically rotating. They either leaned (forward/backward, right/left, up/down) or used the Gamepad thumbsticks for simulated translation. In a gamified 3D navigational search task, participants had to find eight balls within 5 min. Those balls were hidden amongst 16 randomly positioned boxes in a dark environment devoid of any landmarks. Compared to the Gamepad, participants collected more balls using the HeadJoystick. It also minimized the distance travelled, motion sickness, and mental task demand. Moreover, the HeadJoystick was rated better in terms of ease of use, controllability, learnability, overall usability, and self-motion perception. However, participants rated HeadJoystick could be more physically fatiguing after a long use. Overall, participants felt more engaged with HeadJoystick, enjoyed it more, and preferred it. Together, this provides evidence that leaning-based interfaces like HeadJoystick can provide an affordable and effective alternative for flying in VR and potentially telepresence drones.
Low-Cost In-Hand Slippage Detection and Avoidance for Robust Robotic Grasping with Compliant Fingers
(2021)
Contextual information is widely considered for NLP and knowledge discovery in life sciences since it highly influences the exact meaning of natural language. The scientific challenge is not only to extract such context data, but also to store this data for further query and discovery approaches. Classical approaches use RDF triple stores, which have serious limitations. Here, we propose a multiple step knowledge graph approach using labeled property graphs based on polyglot persistence systems to utilize context data for context mining, graph queries, knowledge discovery and extraction. We introduce the graph-theoretic foundation for a general context concept within semantic networks and show a proof of concept based on biomedical literature and text mining. Our test system contains a knowledge graph derived from the entirety of PubMed and SCAIView data and is enriched with text mining data and domain-specific language data using Biological Expression Language. Here, context is a more general concept than annotations. This dense graph has more than 71M nodes and 850M relationships. We discuss the impact of this novel approach with 27 real-world use cases represented by graph queries. Storing and querying a giant knowledge graph as a labeled property graph is still a technological challenge. Here, we demonstrate how our data model is able to support the understanding and interpretation of biomedical data. We present several real-world use cases that utilize our massive, generated knowledge graph derived from PubMed data and enriched with additional contextual data. Finally, we show a working example in context of biologically relevant information using SCAIView.
ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs
(2022)
While most approaches individually exploit unstructured data from the biomedical literature or structured data from biomedical knowledge graphs, their union can better exploit the advantages of such approaches, ultimately improving representations of biology. Using multimodal transformers for such purposes can improve performance on context dependent classication tasks, as demonstrated by our previous model, the Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs (STonKGs). In this work, we introduce ProtSTonKGs, a transformer aimed at learning all-encompassing representations of protein-protein interactions. ProtSTonKGs presents an extension to our previous work by adding textual protein descriptions and amino acid sequences (i.e., structural information) to the text- and knowledge graph-based input sequence used in STonKGs. We benchmark ProtSTonKGs against STonKGs, resulting in improved F1 scores by up to 0.066 (i.e., from 0.204 to 0.270) in several tasks such as predicting protein interactions in several contexts. Our work demonstrates how multimodal transformers can be used to integrate heterogeneous sources of information, paving the foundation for future approaches that use multiple modalities for biomedical applications.
We describe a systematic approach for rendering time-varying simulation data produced by exa-scale simulations, using GPU workstations. The data sets we focus on use adaptive mesh refinement (AMR) to overcome memory bandwidth limitations by representing interesting regions in space with high detail. Particularly, our focus is on data sets where the AMR hierarchy is fixed and does not change over time. Our study is motivated by the NASA Exajet, a large computational fluid dynamics simulation of a civilian cargo aircraft that consists of 423 simulation time steps, each storing 2.5 GB of data per scalar field, amounting to a total of 4 TB. We present strategies for rendering this time series data set with smooth animation and at interactive rates using current generation GPUs. We start with an unoptimized baseline and step by step extend that to support fast streaming updates. Our approach demonstrates how to push current visualization workstations and modern visualization APIs to their limits to achieve interactive visualization of exa-scale time series data sets.
MOTIVATION
The majority of biomedical knowledge is stored in structured databases or as unstructured text in scientific publications. This vast amount of information has led to numerous machine learning-based biological applications using either text through natural language processing (NLP) or structured data through knowledge graph embedding models (KGEMs). However, representations based on a single modality are inherently limited.
RESULTS
To generate better representations of biological knowledge, we propose STonKGs, a Sophisticated Transformer trained on biomedical text and Knowledge Graphs (KGs). This multimodal Transformer uses combined input sequences of structured information from KGs and unstructured text data from biomedical literature to learn joint representations in a shared embedding space. First, we pre-trained STonKGs on a knowledge base assembled by the Integrated Network and Dynamical Reasoning Assembler (INDRA) consisting of millions of text-triple pairs extracted from biomedical literature by multiple NLP systems. Then, we benchmarked STonKGs against three baseline models trained on either one of the modalities (i.e., text or KG) across eight different classification tasks, each corresponding to a different biological application. Our results demonstrate that STonKGs outperforms both baselines, especially on the more challenging tasks with respect to the number of classes, improving upon the F1-score of the best baseline by up to 0.084 (i.e., from 0.881 to 0.965). Finally, our pre-trained model as well as the model architecture can be adapted to various other transfer learning applications.
AVAILABILITY
We make the source code and the Python package of STonKGs available at GitHub (https://github.com/stonkgs/stonkgs) and PyPI (https://pypi.org/project/stonkgs/). The pre-trained STonKGs models and the task-specific classification models are respectively available at https://huggingface.co/stonkgs/stonkgs-150k and https://zenodo.org/communities/stonkgs.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.