arXiv subjects

Ulf Leser

Publications and source records attributed to Ulf Leser.

At least 37 records · Page 2Linked to original sources

arXiv2024

Motiflets -- Simple and Accurate Detection of Motifs in Time Series

A time series motif intuitively is a short time series that repeats itself approximately the same within a larger time series. Such motifs often represent concealed structures, such as heart beats in an ECG recording, the riff in a pop song, or sleep spindles in EEG sleep data. Motif discovery (MD) is the task of finding such motifs in a given input series. As there are varying definitions of what exactly a motif is, a number of different algorithms exist. As central parameters they all take the length l of the motif and the maximal distance r between the motif's occurrences. In practice, however, especially suitable values for r are very hard to determine upfront, and found motifs show a high variability even for very similar r values. Accordingly, finding an interesting motif requires extensive trial-and-error. In this paper, we present a different approach to the MD problem. We define k-Motiflets as the set of exactly k occurrences of a motif of length l, whose maximum pairwise distance is minimal. This turns the MD problem upside-down: The central parameter of our approach is not the distance threshold r, but the desired number of occurrence k of the motif, which we show is considerably more intuitive and easier to set. Based on this definition, we present exact and approximate algorithms for finding k-Motiflets and analyze their complexity. To further ease the use of our method, we describe statistical tools to automatically determine meaningful values for its input parameters. By evaluation on several real-world data sets and comparison to four SotA MD algorithms, we show that our proposed algorithm is both quantitatively superior to its competitors, finding larger motif sets at higher similarity, and qualitatively better, leading to clearer and easier to interpret motifs without any need for manual tuning.

cs.LG↗

arXiv2024

HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools

With the exponential growth of the life science literature, biomedical text mining (BTM) has become an essential technology for accelerating the extraction of insights from publications. Identifying named entities (e.g., diseases, drugs, or genes) in texts and their linkage to reference knowledge bases are crucial steps in BTM pipelines to enable information aggregation from different documents. However, tools for these two steps are rarely applied in the same context in which they were developed. Instead, they are applied in the wild, i.e., on application-dependent text collections different from those used for the tools' training, varying, e.g., in focus, genre, style, and text type. This raises the question of whether the reported performance of BTM tools can be trusted for downstream applications. Here, we report on the results of a carefully designed cross-corpus benchmark for named entity extraction, where tools were applied systematically to corpora not used during their training. Based on a survey of 28 published systems, we selected five for an in-depth analysis on three publicly available corpora encompassing four different entity types. Comparison between tools results in a mixed picture and shows that, in a cross-corpus setting, the performance is significantly lower than the one reported in an in-corpus setting. HunFlair2 showed the best performance on average, being closely followed by PubTator. Our results indicate that users of BTM tools should expect diminishing performances when applying them in the wild compared to original publications and show that further research is necessary to make BTM tools more robust.

cs.CL↗

arXiv2024

BELHD: Improving Biomedical Entity Linking with Homonoym Disambiguation

Biomedical entity linking (BEL) is the task of grounding entity mentions to a knowledge base (KB). A popular approach to the task are name-based methods, i.e. those identifying the most appropriate name in the KB for a given mention, either via dense retrieval or autoregressive modeling. However, as these methods directly return KB names, they cannot cope with homonyms, i.e. different KB entities sharing the exact same name. This significantly affects their performance, especially for KBs where homonyms account for a large amount of entity mentions (e.g. UMLS and NCBI Gene). We therefore present BELHD (Biomedical Entity Linking with Homonym Disambiguation), a new name-based method that copes with this challenge. Specifically, BELHD builds upon the BioSyn (Sung et al.,2020) model introducing two crucial extensions. First, it performs a preprocessing of the KB in which it expands homonyms with an automatically chosen disambiguating string, thus enforcing unique linking decisions. Second, we introduce candidate sharing, a novel strategy to select candidates for contrastive learning that enhances the overall training signal. Experiments with 10 corpora and five entity types show that BELHD improves upon state-of-the-art approaches, achieving the best results in 6 out 10 corpora with an average improvement of 4.55pp recall@1. Furthermore, the KB preprocessing is orthogonal to the core prediction model and thus can also improve other methods, which we exemplify for GenBioEL (Yuan et al, 2022), a generative name-based BEL approach. Code is available at: link added upon publication.

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arXiv2023

The Common Workflow Scheduler Interface: Status Quo and Future Plans

Nowadays, many scientific workflows from different domains, such as Remote Sensing, Astronomy, and Bioinformatics, are executed on large computing infrastructures managed by resource managers. Scientific workflow management systems (SWMS) support the workflow execution and communicate with the infrastructures' resource managers. However, the communication between SWMS and resource managers is complicated by a) inconsistent interfaces between SMWS and resource managers and b) the lack of support for workflow dependencies and workflow-specific properties. To tackle these issues, we developed the Common Workflow Scheduler Interface (CWSI), a simple yet powerful interface to exchange workflow-related information between a SWMS and a resource manager, making the resource manager workflow-aware. The first prototype implementations show that the CWSI can reduce the makespan already with simple but workflow-aware strategies up to 25%. In this paper, we show how existing workflow resource management research can be integrated into the CWSI.

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arXiv2023

Large Language Models to the Rescue: Reducing the Complexity in Scientific Workflow Development Using ChatGPT

Scientific workflow systems are increasingly popular for expressing and executing complex data analysis pipelines over large datasets, as they offer reproducibility, dependability, and scalability of analyses by automatic parallelization on large compute clusters. However, implementing workflows is difficult due to the involvement of many black-box tools and the deep infrastructure stack necessary for their execution. Simultaneously, user-supporting tools are rare, and the number of available examples is much lower than in classical programming languages. To address these challenges, we investigate the efficiency of Large Language Models (LLMs), specifically ChatGPT, to support users when dealing with scientific workflows. We performed three user studies in two scientific domains to evaluate ChatGPT for comprehending, adapting, and extending workflows. Our results indicate that LLMs efficiently interpret workflows but achieve lower performance for exchanging components or purposeful workflow extensions. We characterize their limitations in these challenging scenarios and suggest future research directions.

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arXiv2023

Lotaru: Locally Predicting Workflow Task Runtimes for Resource Management on Heterogeneous Infrastructures

Many resource management techniques for task scheduling, energy and carbon efficiency, and cost optimization in workflows rely on a-priori task runtime knowledge. Building runtime prediction models on historical data is often not feasible in practice as workflows, their input data, and the cluster infrastructure change. Online methods, on the other hand, which estimate task runtimes on specific machines while the workflow is running, have to cope with a lack of measurements during start-up. Frequently, scientific workflows are executed on heterogeneous infrastructures consisting of machines with different CPU, I/O, and memory configurations, further complicating predicting runtimes due to different task runtimes on different machine types. This paper presents Lotaru, a method for locally predicting the runtimes of scientific workflow tasks before they are executed on heterogeneous compute clusters. Crucially, our approach does not rely on historical data and copes with a lack of training data during the start-up. To this end, we use microbenchmarks, reduce the input data to quickly profile the workflow locally, and predict a task's runtime with a Bayesian linear regression based on the gathered data points from the local workflow execution and the microbenchmarks. Due to its Bayesian approach, Lotaru provides uncertainty estimates that can be used for advanced scheduling methods on distributed cluster infrastructures. In our evaluation with five real-world scientific workflows, our method outperforms two state-of-the-art runtime prediction baselines and decreases the absolute prediction error by more than 12.5%. In a second set of experiments, the prediction performance of our method, using the predicted runtimes for state-of-the-art scheduling, carbon reduction, and cost prediction, enables results close to those achieved with perfect prior knowledge of runtimes.

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arXiv2023

BELB: a Biomedical Entity Linking Benchmark

Biomedical entity linking (BEL) is the task of grounding entity mentions to a knowledge base. It plays a vital role in information extraction pipelines for the life sciences literature. We review recent work in the field and find that, as the task is absent from existing benchmarks for biomedical text mining, different studies adopt different experimental setups making comparisons based on published numbers problematic. Furthermore, neural systems are tested primarily on instances linked to the broad coverage knowledge base UMLS, leaving their performance to more specialized ones, e.g. genes or variants, understudied. We therefore developed BELB, a Biomedical Entity Linking Benchmark, providing access in a unified format to 11 corpora linked to 7 knowledge bases and spanning six entity types: gene, disease, chemical, species, cell line and variant. BELB greatly reduces preprocessing overhead in testing BEL systems on multiple corpora offering a standardized testbed for reproducible experiments. Using BELB we perform an extensive evaluation of six rule-based entity-specific systems and three recent neural approaches leveraging pre-trained language models. Our results reveal a mixed picture showing that neural approaches fail to perform consistently across entity types, highlighting the need of further studies towards entity-agnostic models.

cs.CL↗

arXiv2023

How Workflow Engines Should Talk to Resource Managers: A Proposal for a Common Workflow Scheduling Interface

Scientific workflow management systems (SWMSs) and resource managers together ensure that tasks are scheduled on provisioned resources so that all dependencies are obeyed, and some optimization goal, such as makespan minimization, is achieved. In practice, however, there is no clear separation of scheduling responsibilities between an SWMS and a resource manager because there exists no agreed-upon separation of concerns between their different components. This has two consequences. First, the lack of a standardized API to exchange scheduling information between SWMSs and resource managers hinders portability. It incurs costly adaptations when a component should be replaced by a different one (e.g., an SWMS with another SWMS on the same resource manager). Second, due to overlapping functionalities, current installations often actually have two schedulers, both making partial scheduling decisions under incomplete information, leading to suboptimal workflow scheduling. In this paper, we propose a simple REST interface between SWMSs and resource managers, which allows any SWMS to pass dynamic workflow information to a resource manager, enabling maximally informed scheduling decisions. We provide an implementation of this API as an example, using Nextflow as an SWMS and Kubernetes as a resource manager. Our experiments with nine real-world workflows show that this strategy reduces makespan by up to 25.1% and 10.8% on average compared to the standard Nextflow/Kubernetes configuration. Furthermore, a more widespread implementation of this API would enable leaner code bases, a simpler exchange of components of workflow systems, and a unified place to implement new scheduling algorithms.

cs.DC↗

arXiv2023

Validity Constraints for Data Analysis Workflows

Porting a scientific data analysis workflow (DAW) to a cluster infrastructure, a new software stack, or even only a new dataset with some notably different properties is often challenging. Despite the structured definition of the steps (tasks) and their interdependencies during a complex data analysis in the DAW specification, relevant assumptions may remain unspecified and implicit. Such hidden assumptions often lead to crashing tasks without a reasonable error message, poor performance in general, non-terminating executions, or silent wrong results of the DAW, to name only a few possible consequences. Searching for the causes of such errors and drawbacks in a distributed compute cluster managed by a complex infrastructure stack, where DAWs for large datasets typically are executed, can be tedious and time-consuming. We propose validity constraints (VCs) as a new concept for DAW languages to alleviate this situation. A VC is a constraint specifying some logical conditions that must be fulfilled at certain times for DAW executions to be valid. When defined together with a DAW, VCs help to improve the portability, adaptability, and reusability of DAWs by making implicit assumptions explicit. Once specified, VC can be controlled automatically by the DAW infrastructure, and violations can lead to meaningful error messages and graceful behaviour (e.g., termination or invocation of repair mechanisms). We provide a broad list of possible VCs, classify them along multiple dimensions, and compare them to similar concepts one can find in related fields. We also provide a first sketch for VCs' implementation into existing DAW infrastructures.

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arXiv2023

WEASEL 2.0 -- A Random Dilated Dictionary Transform for Fast, Accurate and Memory Constrained Time Series Classification

A time series is a sequence of sequentially ordered real values in time. Time series classification (TSC) is the task of assigning a time series to one of a set of predefined classes, usually based on a model learned from examples. Dictionary-based methods for TSC rely on counting the frequency of certain patterns in time series and are important components of the currently most accurate TSC ensembles. One of the early dictionary-based methods was WEASEL, which at its time achieved SotA results while also being very fast. However, it is outperformed both in terms of speed and accuracy by other methods. Furthermore, its design leads to an unpredictably large memory footprint, making it inapplicable for many applications. In this paper, we present WEASEL 2.0, a complete overhaul of WEASEL based on two recent advancements in TSC: Dilation and ensembling of randomized hyper-parameter settings. These two techniques allow WEASEL 2.0 to work with a fixed-size memory footprint while at the same time improving accuracy. Compared to 15 other SotA methods on the UCR benchmark set, WEASEL 2.0 is significantly more accurate than other dictionary methods and not significantly worse than the currently best methods. Actually, it achieves the highest median accuracy over all data sets, and it performs best in 5 out of 12 problem classes. We thus believe that WEASEL 2.0 is a viable alternative for current TSC and also a potentially interesting input for future ensembles.

cs.LG↗

arXiv2022

ClaSP -- Parameter-free Time Series Segmentation

The study of natural and human-made processes often results in long sequences of temporally-ordered values, aka time series (TS). Such processes often consist of multiple states, e.g. operating modes of a machine, such that state changes in the observed processes result in changes in the distribution of shape of the measured values. Time series segmentation (TSS) tries to find such changes in TS post-hoc to deduce changes in the data-generating process. TSS is typically approached as an unsupervised learning problem aiming at the identification of segments distinguishable by some statistical property. Current algorithms for TSS require domain-dependent hyper-parameters to be set by the user, make assumptions about the TS value distribution or the types of detectable changes which limits their applicability. Common hyperparameters are the measure of segment homogeneity and the number of change points, which are particularly hard to tune for each data set. We present ClaSP, a novel, highly accurate, hyper-parameter-free and domain-agnostic method for TSS. ClaSP hierarchically splits a TS into two parts. A change point is determined by training a binary TS classifier for each possible split point and selecting the one split that is best at identifying subsequences to be from either of the partitions. ClaSP learns its main two model-parameters from the data using two novel bespoke algorithms. In our experimental evaluation using a benchmark of 107 data sets, we show that ClaSP outperforms the state of the art in terms of accuracy and is fast and scalable. Furthermore, we highlight properties of ClaSP using several real-world case studies.

cs.LG↗

arXiv2022

Reshi: Recommending Resources for Scientific Workflow Tasks on Heterogeneous Infrastructures

Scientific workflows typically comprise a multitude of different processing steps which often are executed in parallel on different partitions of the input data. These executions, in turn, must be scheduled on the compute nodes of the computational infrastructure at hand. This assignment is complicated by the facts that (a) tasks typically have highly heterogeneous resource requirements and (b) in many infrastructures, compute nodes offer highly heterogeneous resources. In consequence, predictions of the runtime of a given task on a given node, as required by many scheduling algorithms, are often rather imprecise, which can lead to sub-optimal scheduling decisions. We propose Reshi, a method for recommending task-node assignments during workflow execution that can cope with heterogeneous tasks and heterogeneous nodes. Reshi approaches the problem as a regression task, where task-node pairs are modeled as feature vectors over the results of dedicated micro benchmarks and past task executions. Based on these features, Reshi trains a regression tree model to rank and recommend nodes for each ready-to-run task, which can be used as input to a scheduler. For our evaluation, we benchmarked 27 AWS machine types using three representative workflows. We compare Reshi's recommendations with three state-of-the-art schedulers. Our evaluation shows that Reshi outperforms HEFT by a mean makespan reduction of 7.18% and 18.01% assuming a mean task runtime prediction error of 15%.

cs.DC↗

arXiv2022

Lotaru: Locally Estimating Runtimes of Scientific Workflow Tasks in Heterogeneous Clusters

Many scientific workflow scheduling algorithms need to be informed about task runtimes a-priori to conduct efficient scheduling. In heterogeneous cluster infrastructures, this problem becomes aggravated because these runtimes are required for each task-node pair. Using historical data is often not feasible as logs are typically not retained indefinitely and workloads as well as infrastructure changes. In contrast, online methods, which predict task runtimes on specific nodes while the workflow is running, have to cope with the lack of example runs, especially during the start-up. In this paper, we present Lotaru, a novel online method for locally estimating task runtimes in scientific workflows on heterogeneous clusters. Lotaru first profiles all nodes of a cluster with a set of short-running and uniform microbenchmarks. Next, it runs the workflow to be scheduled on the user's local machine with drastically reduced data to determine important task characteristics. Based on these measurements, Lotaru learns a Bayesian linear regression model to predict a task's runtime given the input size and finally adjusts the predicted runtime specifically for each task-node pair in the cluster based on the micro-benchmark results. Due to its Bayesian approach, Lotaru can also compute robust uncertainty estimates and provides them as an input for advanced scheduling methods. Our evaluation with five real-world scientific workflows and different datasets shows that Lotaru significantly outperforms the baselines in terms of prediction errors for homogeneous and heterogeneous clusters.

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arXiv2022

A probabilistic view on rupture predictability: all earthquakes evolve similarly

Ruptures of the largest earthquakes can last between a few seconds and several minutes. An early assessment of the final earthquake size is essential for early warning systems. However, it is still unclear when in the rupture history this final size can be predicted. Here we introduce a probabilistic view of rupture evolution - how likely is the event to become large - allowing for a clear and well-founded answer with implications for earthquake physics and early warning. We apply our approach to real time magnitude estimation based on either moment rate functions or broadband teleseismic P arrivals. In both cases, we find strong and principled evidence against early rupture predictability because differentiation between differently sized ruptures only occurs once half of the rupture has been observed. Even then, it is impossible to foresee future asperities. Our results hint towards a universal initiation behavior for small and large ruptures.

physics.geo-ph↗

arXiv2021

A Community Roadmap for Scientific Workflows Research and Development

The landscape of workflow systems for scientific applications is notoriously convoluted with hundreds of seemingly equivalent workflow systems, many isolated research claims, and a steep learning curve. To address some of these challenges and lay the groundwork for transforming workflows research and development, the WorkflowsRI and ExaWorks projects partnered to bring the international workflows community together. This paper reports on discussions and findings from two virtual "Workflows Community Summits" (January and April, 2021). The overarching goals of these workshops were to develop a view of the state of the art, identify crucial research challenges in the workflows community, articulate a vision for potential community efforts, and discuss technical approaches for realizing this vision. To this end, participants identified six broad themes: FAIR computational workflows; AI workflows; exascale challenges; APIs, interoperability, reuse, and standards; training and education; and building a workflows community. We summarize discussions and recommendations for each of these themes.

cs.DC↗

arXiv2021

Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development

Scientific workflows are a cornerstone of modern scientific computing, and they have underpinned some of the most significant discoveries of the last decade. Many of these workflows have high computational, storage, and/or communication demands, and thus must execute on a wide range of large-scale platforms, from large clouds to upcoming exascale HPC platforms. Workflows will play a crucial role in the data-oriented and post-Moore's computing landscape as they democratize the application of cutting-edge research techniques, computationally intensive methods, and use of new computing platforms. As workflows continue to be adopted by scientific projects and user communities, they are becoming more complex. Workflows are increasingly composed of tasks that perform computations such as short machine learning inference, multi-node simulations, long-running machine learning model training, amongst others, and thus increasingly rely on heterogeneous architectures that include CPUs but also GPUs and accelerators. The workflow management system (WMS) technology landscape is currently segmented and presents significant barriers to entry due to the hundreds of seemingly comparable, yet incompatible, systems that exist. Another fundamental problem is that there are conflicting theoretical bases and abstractions for a WMS. Systems that use the same underlying abstractions can likely be translated between, which is not the case for systems that use different abstractions. More information: https://workflowsri.org/summits/technical

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arXiv2021

Earthquake magnitude and location estimation from real time seismic waveforms with a transformer network

Precise real time estimates of earthquake magnitude and location are essential for early warning and rapid response. While recently multiple deep learning approaches for fast assessment of earthquakes have been proposed, they usually rely on either seismic records from a single station or from a fixed set of seismic stations. Here we introduce a new model for real-time magnitude and location estimation using the attention based transformer networks. Our approach incorporates waveforms from a dynamically varying set of stations and outperforms deep learning baselines in both magnitude and location estimation performance. Furthermore, it outperforms a classical magnitude estimation algorithm considerably and shows promising performance in comparison to a classical localization algorithm. In this work, we furthermore conduct a comprehensive study of the requirements on training data, the training procedures and the typical failure modes using three diverse and large scale data sets. Our analysis gives several key insights. First, we can precisely pinpoint the effect of large training data; for example, a four times larger training set reduces the required time for real time assessment by a factor of four. Second, the basic model systematically underestimates large magnitude events. This issue can be mitigated by incorporating events from other regions into the training through transfer learning. Third, location estimation is highly precise in areas with sufficient training data, but is strongly degraded for events outside the training distribution. Our analysis suggests that these characteristics are not only present for our model, but for most deep learning models for fast assessment published so far. They result from the black box modeling and their mitigation will likely require imposing physics derived constraints on the neural network.

physics.geo-ph↗

arXiv2021

The transformer earthquake alerting model: A new versatile approach to earthquake early warning

Earthquakes are major hazards to humans, buildings and infrastructure. Early warning methods aim to provide advance notice of incoming strong shaking to enable preventive action and mitigate seismic risk. Their usefulness depends on accuracy, the relation between true, missed and false alerts, and timeliness, the time between a warning and the arrival of strong shaking. Current approaches suffer from apparent aleatoric uncertainties due to simplified modelling or short warning times. Here we propose a novel early warning method, the deep-learning based transformer earthquake alerting model (TEAM), to mitigate these limitations. TEAM analyzes raw, strong motion waveforms of an arbitrary number of stations at arbitrary locations in real-time, making it easily adaptable to changing seismic networks and warning targets. We evaluate TEAM on two regions with high seismic hazard, Japan and Italy, that are complementary in their seismicity. On both datasets TEAM outperforms existing early warning methods considerably, offering accurate and timely warnings. Using domain adaptation, TEAM even provides reliable alerts for events larger than any in the training data, a property of highest importance as records from very large events are rare in many regions.

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