Marcel Dunaiski

Danilo Silva, Monika Moir, Cheryl Baxter et al.

Data management can be a complex challenge in fields such as bioinformatics and health sciences, which continuously generate extensive heterogeneous datasets. In the context of collaborative global health initiatives, secure storage and sharing of data are crucial to support impactful research. However, the absence of a unified data management platform complicates efficient data exchange and governance within these initiatives. In this paper, we introduce the design process of OpenHealth Lake, a data management prototype platform based on a data lakehouse architecture, data federation, and the FAIR principles. The platform is designed using open-source tools, guided by system requirements identified in previously published studies and complemented by insights from the existing literature. The current prototype platform comprises a user-friendly website, an open API, Python and R packages, allowing users to interact with the platform in multiple ways. Through a user study that included participants with varying technical backgrounds, we showed that our proposed data management prototype is both usable and useful. Our prototype design showcases the adaptability, scalability, and reproducibility of a lakehouse system that can be used by any organisation. It is designed as a flexible and complementary approach that allows organisations to customise data management systems to their specific requirements and resources, including cloud-based or self-hosted storage choices.

Dylan Marx, Marcel Dunaiski

Large Language Models (LLMs) remain vulnerable to jailbreak attempts that circumvent safety guardrails. We investigate whether multi-turn conversations using low-resource African languages (Afrikaans, Kiswahili, isiXhosa, and isiZulu) can bypass safety mechanisms across commercial LLMs. We translated prompts from existing datasets and evaluated ChatGPT, Claude, DeepSeek, Gemini, and Grok through automated testing and human red-teaming with native speakers. Single-turn translation attacks proved ineffective, while multi-turn conversations achieved English harmful response rates from 52.7% (Claude 3.5 Haiku) to 83.6% (GPT-4o-mini), Afrikaans from 60.0% (Claude 3.5 Haiku) to 78.2% (GPT-4o-mini), and Kiswahili from 41.8% (Claude 3.5 Haiku) to 70.9% (DeepSeek). Human red-teaming increased jailbreak rates compared to automated methods. Over all evaluated languages, the average jailbreak rate increased from 59.8% to 75.8%, with improvements of +20.0% (Afrikaans), +12.7% (isiZulu), +12.3% (isiXhosa), and +1% (Kiswahili), demonstrating that poor translation quality limits jailbreak success. These findings suggest that vulnerabilities in LLMs persist in multilingual contexts and that translation quality is the critical factor determining jailbreak success in low-resource languages.

Ruan Visser, Trienko Grobler, Marcel Dunaiski

Subword regularization methods such as BPE dropout are typically applied only during fine-tuning, while pretraining is usually done with deterministic tokenization. This creates a potential segmentation mismatch between pretraining and fine-tuning. We investigate whether applying BPE dropout during pretraining improves downstream performance in low-resource NLP. We train monolingual and bilingual BERT models on downsampled subsets of English, German, French, Spanish, Kiswahili, and isiXhosa, and evaluate them on XNLI, PAWS-X, PAN-X, and MasakhaNER 2.0. Across tasks, the best results are typically obtained when stochastic tokenization is applied during both pretraining and fine-tuning, whereas applying BPE dropout only during fine-tuning can underperform deterministic tokenization in smaller-data settings. This disadvantage diminishes as fine-tuning data increases, while the benefits of pretraining-time BPE dropout are largest when either pretraining or fine-tuning data is scarce. The benefits of BPE dropout are often attributed to better compositional representations, especially for rare words. To examine this, we measure morphological boundary alignment under BPE dropout and find only modest improvements in expected alignment, while better-aligned segmentations remain rare. This suggests that fine-tuning alone may provide limited exposure to such segmentations, whereas stochastic tokenization during pretraining exposes the model to them more consistently. We further show that selectively introducing morphologically aligned segmentations during fine-tuning improves performance mainly for models pretrained without BPE dropout. Overall, these findings suggest that exposure to better-aligned segmentations may contribute to the downstream benefits of applying BPE dropout during pretraining.

Jaco du Toit, Herman Redelinghuys, Marcel Dunaiski

Hierarchical Text Classification (HTC) is a natural language processing task with the objective to classify text documents into a set of classes from a structured class hierarchy. Many HTC approaches have been proposed which attempt to leverage the class hierarchy information in various ways to improve classification performance. Machine learning-based classification approaches require large amounts of training data and are most-commonly compared through three established benchmark datasets, which include the Web Of Science (WOS), Reuters Corpus Volume 1 Version 2 (RCV1-V2) and New York Times (NYT) datasets. However, apart from the RCV1-V2 dataset which is well-documented, these datasets are not accompanied with detailed description methodologies. In this paper, we introduce three new HTC benchmark datasets in the domain of research publications which comprise the titles and abstracts of papers from the Web of Science publication database. We first create two baseline datasets which use existing journal-and citation-based classification schemas. Due to the respective shortcomings of these two existing schemas, we propose an approach which combines their classifications to improve the reliability and robustness of the dataset. We evaluate the three created datasets with a clustering-based analysis and show that our proposed approach results in a higher quality dataset where documents that belong to the same class are semantically more similar compared to the other datasets. Finally, we provide the classification performance of four state-of-the-art HTC approaches on these three new datasets to provide baselines for future studies on machine learning-based techniques for scientific publication classification.

Jaco du Toit, Marcel Dunaiski

Hierarchical text classification (HTC) is a natural language processing task which has the objective of categorising text documents into a set of classes from a predefined structured class hierarchy. Recent HTC approaches use various techniques to incorporate the hierarchical class structure information with the natural language understanding capabilities of pre-trained language models (PLMs) to improve classification performance. Furthermore, using topic models along with PLMs to extract features from text documents has been shown to be an effective approach for multi-label text classification tasks. The rationale behind the combination of these feature extractor models is that the PLM captures the finer-grained contextual and semantic information while the topic model obtains high-level representations which consider the corpus of documents as a whole. In this paper, we use a HTC approach which uses a PLM and a topic model to extract features from text documents which are used to train a classification model. Our objective is to determine whether the combination of the features extracted from the two models is beneficial to HTC performance in general. In our approach, the extracted features are passed through separate convolutional layers whose outputs are combined and passed to a label-wise attention mechanisms which obtains label-specific document representations by weighing the most important features for each class separately. We perform comprehensive experiments on three HTC benchmark datasets and show that using the features extracted from the topic model generally decreases classification performance compared to only using the features obtained by the PLM. In contrast to previous work, this shows that the incorporation of features extracted from topic models for text classification tasks should not be assumed beneficial.