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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.
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.
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.
In recent years, the ability of intelligent systems to be understood by developers and users has received growing attention. This holds in particular for social robots, which are supposed to act autonomously in the vicinity of human users and are known to raise peculiar, often unrealistic attributions and expectations. However, explainable models that, on the one hand, allow a robot to generate lively and autonomous behavior and, on the other, enable it to provide human-compatible explanations for this behavior are missing. In order to develop such a self-explaining autonomous social robot, we have equipped a robot with own needs that autonomously trigger intentions and proactive behavior, and form the basis for understandable self-explanations. Previous research has shown that undesirable robot behavior is rated more positively after receiving an explanation. We thus aim to equip a social robot with the capability to automatically generate verbal explanations of its own behavior, by tracing its internal decision-making routes. The goal is to generate social robot behavior in a way that is generally interpretable, and therefore explainable on a socio-behavioral level increasing users' understanding of the robot's behavior. In this article, we present a social robot interaction architecture, designed to autonomously generate social behavior and self-explanations. We set out requirements for explainable behavior generation architectures and propose a socio-interactive framework for behavior explanations in social human-robot interactions that enables explaining and elaborating according to users' needs for explanation that emerge within an interaction. Consequently, we introduce an interactive explanation dialog flow concept that incorporates empirically validated explanation types. These concepts are realized within the interaction architecture of a social robot, and integrated with its dialog processing modules. We present the components of this interaction architecture and explain their integration to autonomously generate social behaviors as well as verbal self-explanations. Lastly, we report results from a qualitative evaluation of a working prototype in a laboratory setting, showing that (1) the robot is able to autonomously generate naturalistic social behavior, and (2) the robot is able to verbally self-explain its behavior to the user in line with users' requests.
Selection Performance and Reliability of Eye and Head Gaze Tracking Under Varying Light Conditions
(2024)
Dieses Dokument präsentiert eine Zusammenfassung der Dissertation der Autorin. In dieser Dissertation [Ha20] wurde ein neuartiger und hybrider Ansatz für die Scha ̈tzung der Intensität von Gesichtsmuskelbewegungen (Action Unit (AU)) vorgeschlagen und validiert. Dieser Ansatz basiert auf einer Gauß’schen Zustandsschätzung und kombiniert ein verformbares, AU-basiertes Gesichtsformmodell, ein viskoelastisches Modell der Gesichtsmuskelbewegung, mehrere erscheinungsbasierten AU-Klassifikatoren und eine Methode zur Erkennung von Gesichtspunkten. Es wurden mehrere Erweiterungen vorgeschlagen und in das Zustandsschätzungs-Framework integriert, um mit den personenspezifischen Eigenschaften sowie technischen und praktischen Herausforderungen umzugehen.Die mit der vorgeschlagenen Methode erzeugten AU-Intensitätsschätzungen wurden für die automatische Erkennung von Schmerzen und für die Analyse von Fahrerablenkung eingesetzt.
Robust Identification and Segmentation of the Outer Skin Layers in Volumetric Fingerprint Data
(2022)
Despite the long history of fingerprint biometrics and its use to authenticate individuals, there are still some unsolved challenges with fingerprint acquisition and presentation attack detection (PAD). Currently available commercial fingerprint capture devices struggle with non-ideal skin conditions, including soft skin in infants. They are also susceptible to presentation attacks, which limits their applicability in unsupervised scenarios such as border control. Optical coherence tomography (OCT) could be a promising solution to these problems. In this work, we propose a digital signal processing chain for segmenting two complementary fingerprints from the same OCT fingertip scan: One fingerprint is captured as usual from the epidermis (“outer fingerprint”), whereas the other is taken from inside the skin, at the junction between the epidermis and the underlying dermis (“inner fingerprint”). The resulting 3D fingerprints are then converted to a conventional 2D grayscale representation from which minutiae points can be extracted using existing methods. Our approach is device-independent and has been proven to work with two different time domain OCT scanners. Using efficient GPGPU computing, it took less than a second to process an entire gigabyte of OCT data. To validate the results, we captured OCT fingerprints of 130 individual fingers and compared them with conventional 2D fingerprints of the same fingers. We found that both the outer and inner OCT fingerprints were backward compatible with conventional 2D fingerprints, with the inner fingerprint generally being less damaged and, therefore, more reliable.
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.
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.
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.
BACKGROUND
Given the unreliable self-report in patients with dementia, pain assessment should also rely on the observation of pain behaviors, such as facial expressions. Ideal observers should be well trained and should observe the patient continuously in order to pick up any pain-indicative behavior; which are requisitions beyond realistic possibilities of pain care. Therefore, the need for video-based pain detection systems has been repeatedly voiced. Such systems would allow for constant monitoring of pain behaviors and thereby allow for a timely adjustment of pain management in these fragile patients, who are often undertreated for pain.
METHODS
In this road map paper we describe an interdisciplinary approach to develop such a video-based pain detection system. The development starts with the selection of appropriate video material of people in pain as well as the development of technical methods to capture their faces. Furthermore, single facial motions are automatically extracted according to an international coding system. Computer algorithms are trained to detect the combination and timing of those motions, which are pain-indicative.
RESULTS/CONCLUSION
We hope to encourage colleagues to join forces and to inform end-users about an imminent solution of a pressing pain-care problem. For the near future, implementation of such systems can be foreseen to monitor immobile patients in intensive and postoperative care situations.
Modern GPUs come with dedicated hardware to perform ray/triangle intersections and bounding volume hierarchy (BVH) traversal. While the primary use case for this hardware is photorealistic 3D computer graphics, with careful algorithm design scientists can also use this special-purpose hardware to accelerate general-purpose computations such as point containment queries. This article explains the principles behind these techniques and their application to vector field visualization of large simulation data using particle tracing.
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.
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.