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ReadBouncer
(2022)
Motivation:
Nanopore sequencers allow targeted sequencing of interesting nucleotide sequences by rejecting other sequences from individual pores. This feature facilitates the enrichment of low-abundant sequences by depleting overrepresented ones in-silico. Existing tools for adaptive sampling either apply signal alignment, which cannot handle human-sized reference sequences, or apply read mapping in sequence space relying on fast graphical processing units (GPU) base callers for real-time read rejection. Using nanopore long-read mapping tools is also not optimal when mapping shorter reads as usually analyzed in adaptive sampling applications.
Results:
Here, we present a new approach for nanopore adaptive sampling that combines fast CPU and GPU base calling with read classification based on Interleaved Bloom Filters. ReadBouncer improves the potential enrichment of low abundance sequences by its high read classification sensitivity and specificity, outperforming existing tools in the field. It robustly removes even reads belonging to large reference sequences while running on commodity hardware without GPUs, making adaptive sampling accessible for in-field researchers. Readbouncer also provides a user-friendly interface and installer files for end-users without a bioinformatics background.
TRIPOD
(2021)
Inertial measurement units (IMUs) enable easy to operate and low-cost data recording for gait analysis. When combined with treadmill walking, a large number of steps can be collected in a controlled environment without the need of a dedicated gait analysis laboratory. In order to evaluate existing and novel IMU-based gait analysis algorithms for treadmill walking, a reference dataset that includes IMU data as well as reliable ground truth measurements for multiple participants and walking speeds is needed. This article provides a reference dataset consisting of 15 healthy young adults who walked on a treadmill at three different speeds. Data were acquired using seven IMUs placed on the lower body, two different reference systems (Zebris FDMT-HQ and OptoGait), and two RGB cameras. Additionally, in order to validate an existing IMU-based gait analysis algorithm using the dataset, an adaptable modular data analysis pipeline was built. Our results show agreement between the pressure-sensitive Zebris and the photoelectric OptoGait system (r = 0.99), demonstrating the quality of our reference data. As a use case, the performance of an algorithm originally designed for overground walking was tested on treadmill data using the data pipeline. The accuracy of stride length and stride time estimations was comparable to that reported in other studies with overground data, indicating that the algorithm is equally applicable to treadmill data. The Python source code of the data pipeline is publicly available, and the dataset will be provided by the authors upon request, enabling future evaluations of IMU gait analysis algorithms without the need of recording new data.
Generative adversarial networks (GANs) have been broadly applied to a wide range of application domains since their proposal. In this thesis, we propose several methods that aim to tackle different existing problems in GANs. Particularly, even though GANs are generally able to generate high-quality samples, the diversity of the generated set is often sub-optimal. Moreover, the common increase of the number of models in the original GANs framework, as well as their architectural sizes, introduces additional costs. Additionally, even though challenging, the proper evaluation of a generated set is an important direction to ultimately improve the generation process in GANs. We start by introducing two diversification methods that extend the original GANs framework to multiple adversaries to stimulate sample diversity in a generated set. Then, we introduce a new post-training compression method based on Monte Carlo methods and importance sampling to quantize and prune the weights and activations of pre-trained neural networks without any additional training. The previous method may be used to reduce the memory and computational costs introduced by increasing the number of models in the original GANs framework. Moreover, we use a similar procedure to quantize and prune gradients during training, which also reduces the communication costs between different workers in a distributed training setting. We introduce several topology-based evaluation methods to assess data generation in different settings, namely image generation and language generation. Our methods retrieve both single-valued and double-valued metrics, which, given a real set, may be used to broadly assess a generated set or separately evaluate sample quality and sample diversity, respectively. Moreover, two of our metrics use locality-sensitive hashing to accurately assess the generated sets of highly compressed GANs. The analysis of the compression effects in GANs paves the way for their efficient employment in real-world applications. Given their general applicability, the methods proposed in this thesis may be extended beyond the context of GANs. Hence, they may be generally applied to enhance existing neural networks and, in particular, generative frameworks.
CoFeeMOOC-v.2
(2021)
Providing adequate support to MOOC participants is often a challenging task due to massiveness of the learners’ population and the asynchronous communication among peers and MOOC practitioners. This workshop aims at discussing common learners’ problems reported in the literature and reflect on designing adequate feedback interventions with the use of learning data. Our aim is three-fold: a) to pinpoint MOOC aspects that impact the planning of feedback, b) to explore the use of learning data in designing feedback strategies, and c) to propose design guidelines for developing and delivering scaffolding interventions for personalized feedback in MOOCs. To do so, we will carry out hands-on activities that aim to involve participants in interpreting learning data and using them to design adaptive feedback. This workshop appeals to researchers, practitioners and MOOC stakeholders who aim to providing contextualized scaffolding. We envision that this workshop will provide insights for bridging the gap between pedagogical theory and practice when it comes to feedback interventions in MOOCs.
This work presents a new design for programming environments that promote the exploration of domain-specific software artifacts and the construction of graphical tools for such program comprehension tasks. In complex software projects, tool building is essential because domain- or task-specific tools can support decision making by representing concerns concisely with low cognitive effort. In contrast, generic tools can only support anticipated scenarios, which usually align with programming language concepts or well-known project domains.
However, the creation and modification of interactive tools is expensive because the glue that connects data to graphics is hard to find, change, and test. Even if valuable data is available in a common format and even if promising visualizations could be populated, programmers have to invest many resources to make changes in the programming environment. Consequently, only ideas of predictably high value will be implemented. In the non-graphical, command-line world, the situation looks different and inspiring: programmers can easily build their own tools as shell scripts by configuring and combining filter programs to process data.
We propose a new perspective on graphical tools and provide a concept to build and modify such tools with a focus on high quality, low effort, and continuous adaptability. That is, (1) we propose an object-oriented, data-driven, declarative scripting language that reduces the amount of and governs the effects of glue code for view-model specifications, and (2) we propose a scalable UI-design language that promotes short feedback loops in an interactive, graphical environment such as Morphic known from Self or Squeak/Smalltalk systems.
We implemented our concept as a tool building environment, which we call VIVIDE, on top of Squeak/Smalltalk and Morphic. We replaced existing code browsing and debugging tools to iterate within our solution more quickly. In several case studies with undergraduate and graduate students, we observed that VIVIDE can be applied to many domains such as live language development, source-code versioning, modular code browsing, and multi-language debugging. Then, we designed a controlled experiment to measure the effect on the time to build tools. Several pilot runs showed that training is crucial and, presumably, takes days or weeks, which implies a need for further research.
As a result, programmers as users can directly work with tangible representations of their software artifacts in the VIVIDE environment. Tool builders can write domain-specific scripts to populate views to approach comprehension tasks from different angles. Our novel perspective on graphical tools can inspire the creation of new trade-offs in modularity for both data providers and view designers.
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.
Developing highly skilled researchers is essential to accelerate the economic progress of developing countries such as Cambodia in South East Asia. While there is continuing research investigating Cambodia’s potential to cultivate such a workforce, the circumstances of undergraduate students in public provincial universities do not receive ample attention. This is crucial as numerous multinational corporations are participating via foreign direct investments in special economic zones at the border provinces and need talented human resources in Cambodia as well as in neighboring Southeast Asian countries such as Thailand and Vietnam. Student’s research capability growth starts with one’s belief in their capacity to use the necessary information tools and their potential to succeed in research. In this research paper, we look at how such beliefs, specifically research self-efficacy and information literacy, can be developed through a short-term intervention that uses MOOCs and assess their long-term effects. Our previous research has shown that short-term training intervention has immediate positive effects on the undergraduate students’ self-efficacies in Cambodian public provincial universities. In this paper, we present the follow-up study results conducted sixteen months after the said short-term training intervention. Results reveal that from follow-up evaluations that while student’s self-efficacies were significantly higher than before the short-term intervention was completed, they were lower than immediately after the intervention. Thus, while perfunctory interventions such as merely introducing the students to MOOCs and other relevant research tools over as little as three weeks can have significant positive effects, efforts must be made to sustain the benefits gained. This implication is essential to developing countries such as Cambodia that need low-cost solutions with immediate positive results in developing human resources to conduct research, particularly in areas far from more developed capital cities.
Crochet is a popular handcraft all over the world. While other techniques such as knitting or weaving have received technical support over the years through machines, crochet is still a purely manual craft. Not just the act of crochet itself is manual but also the process of creating instructions for new crochet patterns, which is barely supported by domain specific digital solutions. This leads to unstructured and often also ambiguous and erroneous pattern instructions. In this report, we propose a concept to digitally represent crochet patterns. This format incorporates crochet techniques which allows domain specific support for crochet pattern designers during the pattern creation and instruction writing process. As contributions, we present a thorough domain analysis, the concept of a graph structure used as domain specific language to specify crochet patterns and a prototype of a projectional editor using the graph as representation format of patterns and a diagramming system to visualize them in 2D and 3D. By analyzing the domain, we learned about crochet techniques and pain points of designers in their pattern creation workflow. These insights are the basis on which we defined the pattern representation. In order to evaluate our concept, we built a prototype by which the feasibility of the concept is shown and we tested the software with professional crochet designers who approved of the concept.
RailChain
(2023)
The RailChain project designed, implemented, and experimentally evaluated a juridical recorder that is based on a distributed consensus protocol. That juridical blockchain recorder has been realized as distributed ledger on board the advanced TrainLab (ICE-TD 605 017) of Deutsche Bahn.
For the project, a consortium consisting of DB Systel, Siemens, Siemens Mobility, the Hasso Plattner Institute for Digital Engineering, Technische Universität Braunschweig, TÜV Rheinland InterTraffic, and Spherity has been formed. These partners not only concentrated competencies in railway operation, computer science, regulation, and approval, but also combined experiences from industry, research from academia, and enthusiasm from startups.
Distributed ledger technologies (DLTs) define distributed databases and express a digital protocol for transactions between business partners without the need for a trusted intermediary. The implementation of a blockchain with real-time requirements for the local network of a railway system (e.g., interlocking or train) allows to log data in the distributed system verifiably in real-time. For this, railway-specific assumptions can be leveraged to make modifications to standard blockchains protocols.
EULYNX and OCORA (Open CCS On-board Reference Architecture) are parts of a future European reference architecture for control command and signalling (CCS, Reference CCS Architecture – RCA). Both architectural concepts outline heterogeneous IT systems with components from multiple manufacturers. Such systems introduce novel challenges for the approved and safety-relevant CCS of railways which were considered neither for road-side nor for on-board systems so far. Logging implementations, such as the common juridical recorder on vehicles, can no longer be realized as a central component of a single manufacturer. All centralized approaches are in question.
The research project RailChain is funded by the mFUND program and gives practical evidence that distributed consensus protocols are a proper means to immutably (for legal purposes) store state information of many system components from multiple manufacturers. The results of RailChain have been published, prototypically implemented, and experimentally evaluated in large-scale field tests on the advanced TrainLab. At the same time, the project showed how RailChain can be integrated into the road-side and on-board architecture given by OCORA and EULYNX.
Logged data can now be analysed sooner and also their trustworthiness is being increased. This enables, e.g., auditable predictive maintenance, because it is ensured that data is authentic and unmodified at any point in time.
The analysis of behavioral models such as Graph Transformation Systems (GTSs) is of central importance in model-driven engineering. However, GTSs often result in intractably large or even infinite state spaces and may be equipped with multiple or even infinitely many start graphs. To mitigate these problems, static analysis techniques based on finite symbolic representations of sets of states or paths thereof have been devised. We focus on the technique of k-induction for establishing invariants specified using graph conditions. To this end, k-induction generates symbolic paths backwards from a symbolic state representing a violation of a candidate invariant to gather information on how that violation could have been reached possibly obtaining contradictions to assumed invariants. However, GTSs where multiple agents regularly perform actions independently from each other cannot be analyzed using this technique as of now as the independence among backward steps may prevent the gathering of relevant knowledge altogether.
In this paper, we extend k-induction to GTSs with multiple agents thereby supporting a wide range of additional GTSs. As a running example, we consider an unbounded number of shuttles driving on a large-scale track topology, which adjust their velocity to speed limits to avoid derailing. As central contribution, we develop pruning techniques based on causality and independence among backward steps and verify that k-induction remains sound under this adaptation as well as terminates in cases where it did not terminate before.