MOTIVATION: In precision oncology (PO), clinicians aim to find the best treatment for any patient based on their molecular characterization. A major bottleneck is the manual annotation and evaluation of individual variants, for which usually a range of knowledge bases are screened. To incorporate and integrate the vast information of different databases, fast and accurate methods for harmonizing databases with different types of information are necessary. An essential step for harmonization in PO includes the normalization of tumor entities as well as therapy options for patients. SUMMARY: preon is a fast and accurate library for the normalization of drug names and cancer types in large-scale data integration. AVAILABILITY AND IMPLEMENTATION: preon is implemented in Python and freely available via the PyPI repository. Source code and the data underlying this article are available in GitHub at https://github.com/ermshaua/preon/.

Ubiquitous sensors today emit high frequency streams of numerical measurements that reflect properties of human, animal, industrial, commercial, and natural processes. Shifts in such processes, e.g. caused by external events or internal state changes, manifest as changes in the recorded signals. The task of streaming time series segmentation (STSS) is to partition the stream into consecutive variable-sized segments that correspond to states of the observed processes or entities. The partition operation itself must in performance be able to cope with the input frequency of the signals. We introduce ClaSS, a novel, efficient, and highly accurate algorithm for STSS. ClaSS assesses the homogeneity of potential partitions using self-supervised time series classification and applies statistical tests to detect significant change points (CPs). In our experimental evaluation using two large benchmarks and six real-world data archives, we found ClaSS to be significantly more precise than eight state-of-the-art competitors. Its space and time complexity is independent of segment sizes and linear only in the sliding window size. We also provide ClaSS as a window operator with an average throughput of 1 k data points per second for the Apache Flink streaming engine.

Abstract 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 hyper-parameters 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.

The study of biological or physical processes often results in long sequences of temporally-ordered values, aka time series (TS). Changes in the observed processes, e.g. as a cause of natural events or internal state changes, result in changes of the measured values. Time series segmentation (TSS) tries to find such changes in TS to deduce changes in the underlying process. TSS is typically approached as an unsupervised learning problem aiming at the identification of segments distinguishable by some statistical property. We present ClaSP, a novel and highly accurate method for TSS. ClaSP hierarchically splits a TS into two parts, where each split point is determined by training a binary TS classifier for each possible split point and selecting the one with highest accuracy, i.e., the one that is best at identifying subsequences to be from either of the partitions. In our experimental evaluation using a benchmark of 98 datasets, we show that ClaSP outperforms the state-of-the-art in terms of accuracy and is also faster than the second best method. We highlight properties of ClaSP using several real-life time series.