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.

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.

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.

Raising the ClaSS of Streaming Time Series Segmentation

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 538 data points per second for the Apache Flink streaming engine.

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.

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.

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 115 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.

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

A 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, 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 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, suitable values for r are very hard to determine upfront, and the found motifs show a high variability. Setting the wrong input value will result in a motif that is not distinguishable from noise. Accordingly, finding an interesting motif with these methods requires extensive trial-and-error. 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: Our central parameter is not the distance threshold r, but the desired size k of a motif set, 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 extensions to automatically determine the right/suitable values for its input parameters. Thus, for the first time, extracting meaningful motif sets without any a-priori knowledge becomes feasible. By evaluating real-world use cases and comparison to 4 state-of-the-art MD algorithms, we show that our proposed algorithm is (a) quantitatively superior, finding larger motif sets at higher similarity, (b) qualitatively better, leading to clearer and easier to interpret motifs, and (c) has the lowest runtime.