Neural Architecture for Online Ensemble Continual Learning

Continual learning with an increasing number of classes is a challenging task. The difficulty rises when each example is presented exactly once, which requires the model to learn online. Recent methods with classic parameter optimization procedures have been shown to struggle in such setups or have limitations like non-differentiable components or memory buffers. For this reason, we present the fully differentiable ensemble method that allows us to efficiently train an ensemble of neural networks in the end-to-end regime. The proposed technique achieves SOTA results without a memory buffer and clearly outperforms the reference methods. The conducted experiments have also shown a significant increase in the performance for small ensembles, which demonstrates the capability of obtaining relatively high classification accuracy with a reduced number of classifiers

Similarity-based Memory Enhanced Joint Entity and Relation Extraction

Document-level joint entity and relation extraction is a challenging information extraction problem that requires a unified approach where a single neural network performs four sub-tasks: mention detection, coreference resolution, entity classification, and relation extraction. Existing methods often utilize a sequential multi-task learning approach, in which the arbitral decomposition causes the current task to depend only on the previous one, missing the possible existence of the more complex relationships between them. In this paper, we present a multi-task learning framework with bidirectional memory-like dependency between tasks to address those drawbacks and perform the joint problem more accurately. Our empirical studies show that the proposed approach outperforms the existing methods and achieves state-of-the-art results on the BioCreative V CDR corpus

Classical Out-of-Distribution Detection Methods Benchmark in Text Classification Tasks

State-of-the-art models can perform well in controlled environments, but they often struggle when presented with out-of-distribution (OOD) examples, making OOD detection a critical component of NLP systems. In this paper, we focus on highlighting the limitations of existing approaches to OOD detection in NLP. Specifically, we evaluated eight OOD detection methods that are easily integrable into existing NLP systems and require no additional OOD data or model modifications. One of our contributions is providing a well-structured research environment that allows for full reproducibility of the results. Additionally, our analysis shows that existing OOD detection methods for NLP tasks are not yet sufficiently sensitive to capture all samples characterized by various types of distributional shifts. Particularly challenging testing scenarios arise in cases of background shift and randomly shuffled word order within in domain texts. This highlights the need for future work to develop more effective OOD detection approaches for the NLP problems, and our work provides a well-defined foundation for further research in this area.Comment: 11 pages, 3 figures, Association for Computational Linguistic

Domain-Agnostic Neural Architecture for Class Incremental Continual Learning in Document Processing Platform

Production deployments in complex systems require ML architectures to be highly efficient and usable against multiple tasks. Particularly demanding are classification problems in which data arrives in a streaming fashion and each class is presented separately. Recent methods with stochastic gradient learning have been shown to struggle in such setups or have limitations like memory buffers, and being restricted to specific domains that disable its usage in real-world scenarios. For this reason, we present a fully differentiable architecture based on the Mixture of Experts model, that enables the training of high-performance classifiers when examples from each class are presented separately. We conducted exhaustive experiments that proved its applicability in various domains and ability to learn online in production environments. The proposed technique achieves SOTA results without a memory buffer and clearly outperforms the reference methods.Comment: arXiv admin note: text overlap with arXiv:2211.1496

Computer vision-based automated peak picking applied to protein NMR spectra

Motivation: A detailed analysis of multidimensional NMR spectra of macromolecules requires the identification of individual resonances (peaks). This task can be tedious and time-consuming and often requires support by experienced users. Automated peak picking algorithms were introduced more than 25 years ago, but there are still major deficiencies/flaws that often prevent complete and error free peak picking of biological macromolecule spectra. The major challenges of automated peak picking algorithms is both the distinction of artifacts from real peaks particularly from those with irregular shapes and also picking peaks in spectral regions with overlapping resonances which are very hard to resolve by existing computer algorithms. In both of these cases a visual inspection approach could be more effective than a ‘blind' algorithm. Results: We present a novel approach using computer vision (CV) methodology which could be better adapted to the problem of peak recognition. After suitable ‘training' we successfully applied the CV algorithm to spectra of medium-sized soluble proteins up to molecular weights of 26 kDa and to a 130 kDa complex of a tetrameric membrane protein in detergent micelles. Our CV approach outperforms commonly used programs. With suitable training datasets the application of the presented method can be extended to automated peak picking in multidimensional spectra of nucleic acids or carbohydrates and adapted to solid-state NMR spectra. Availability and implementation: CV-Peak Picker is available upon request from the authors. Contact: [email protected]; [email protected]; [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin