Laurie Burchell, Ona De Gibert Bonet, Nikolay Arefyev, Mikko Aulamo, Marta Bañón, Pinzhen Chen, Mariia Fedorova, Liane Guillou, Barry Haddow, Jan Hajič, Jindřich Helcl, Erik Henriksson, Mateusz Klimaszewski, Ville Komulainen, Andrey Kutuzov, Joona Kytöniemi, Veronika Laippala, Petter Mæhlum, Bhavitvya Malik, Farrokh Mehryary, Vladislav Mikhailov, Nikita Moghe, Amanda Myntti, Dayyán O’Brien, Stephan Oepen, Proyag Pal, Jousia Piha, Sampo Pyysalo, Gema Ramírez-Sánchez, David Samuel, Pavel Stepachev, Jörg Tiedemann, Dušan Variš, Tereza Vojtěchová, Jaume Zaragoza-Bernabeu. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

We describe the progress of the High Performance Language Technologies (HPLT) project, a 3-year EU-funded project that started in September 2022. We focus on the up-to-date results on the release of free text datasets derived from web crawls, one of the central objectives of the project. The second release used a revised processing pipeline, and an enlarged set of input crawls. From 4.5 petabytes of web crawls we extracted 7.6T tokens of monolingual text in 193 languages, plus 380 million parallel sentences in 51 language pairs. We also release MultiHPLT, a cross-combination of the parallel data, which produces 1,275 pairs, as well as releasing the containing documents for all parallel sentences in order to enable research in document-level MT. We report changes in the pipeline, analysis and evaluation results for the second parallel data release based on machine translation systems. All datasets are released under a permissive CC0 licence.

MOTIVATION: Understanding biological processes relies heavily on curated knowledge of physical interactions between proteins. Yet, a notable gap remains between the information stored in databases of curated knowledge and the plethora of interactions documented in the scientific literature. RESULTS: To bridge this gap, we introduce ComplexTome, a manually annotated corpus designed to facilitate the development of text-mining methods for the extraction of complex formation relationships among biomedical entities targeting the downstream semantics of the physical interaction subnetwork of the STRING database. This corpus comprises 1287 documents with ∼3500 relationships. We train a novel relation extraction model on this corpus and find that it can highly reliably identify physical protein interactions (F1-score = 82.8%). We additionally enhance the model's capabilities through unsupervised trigger word detection and apply it to extract relations and trigger words for these relations from all open publications in the domain literature. This information has been fully integrated into the latest version of the STRING database. AVAILABILITY AND IMPLEMENTATION: We provide the corpus, code, and all results produced by the large-scale runs of our systems biomedical on literature via Zenodo https://doi.org/10.5281/zenodo.8139716, Github https://github.com/farmeh/ComplexTome_extraction, and the latest version of STRING database https://string-db.org/.

Over the past decade, the demand for automated protein function prediction has increased due to the volume of newly sequenced proteins. In this paper, we address the function prediction task by developing an ensemble system automatically assigning Gene Ontology (GO) terms to the given input protein sequence. We develop an ensemble system which combines the GO predictions made by random forest (RF) and neural network (NN) classifiers. Both RF and NN models rely on features derived from BLAST sequence alignments, taxonomy and protein signature analysis tools. In addition, we report on experiments with a NN model that directly analyzes the amino acid sequence as its sole input, using a convolutional layer. The Swiss-Prot database is used as the training and evaluation data. In the CAFA3 evaluation, which relies on experimental verification of the functional predictions, our submitted ensemble model demonstrates competitive performance ranking among top-10 best-performing systems out of over 100 submitted systems. In this paper, we evaluate and further improve the CAFA3-submitted system. Our machine learning models together with the data pre-processing and feature generation tools are publicly available as an open source software at https://github.com/TurkuNLP/CAFA3.

Objective: We executed the Social Media Mining for Health (SMM4H) 2017 shared tasks to enable the community-driven development and large-scale evaluation of automatic text processing methods for the classification and normalization of health-related text from social media. An additional objective was to publicly release manually annotated data. Materials and Methods: We organized 3 independent subtasks: automatic classification of self-reports of 1) adverse drug reactions (ADRs) and 2) medication consumption, from medication-mentioning tweets, and 3) normalization of ADR expressions. Training data consisted of 15 717 annotated tweets for (1), 10 260 for (2), and 6650 ADR phrases and identifiers for (3); and exhibited typical properties of social-media-based health-related texts. Systems were evaluated using 9961, 7513, and 2500 instances for the 3 subtasks, respectively. We evaluated performances of classes of methods and ensembles of system combinations following the shared tasks. Results: Among 55 system runs, the best system scores for the 3 subtasks were 0.435 (ADR class F1-score) for subtask-1, 0.693 (micro-averaged F1-score over two classes) for subtask-2, and 88.5% (accuracy) for subtask-3. Ensembles of system combinations obtained best scores of 0.476, 0.702, and 88.7%, outperforming individual systems. Discussion: Among individual systems, support vector machines and convolutional neural networks showed high performance. Performance gains achieved by ensembles of system combinations suggest that such strategies may be suitable for operational systems relying on difficult text classification tasks (eg, subtask-1). Conclusions: Data imbalance and lack of context remain challenges for natural language processing of social media text. Annotated data from the shared task have been made available as reference standards for future studies (http://dx.doi.org/10.17632/rxwfb3tysd.1).