Alex Bogatu

Alex Bogatu, Magdalena Wysocka, Oskar Wysocki et al.

Cytokine release syndrome (CRS), also known as cytokine storm, is one of the most consequential adverse effects of chimeric antigen receptor therapies that have shown promising results in cancer treatment. When emerging, CRS could be identified by the analysis of specific cytokine and chemokine profiles that tend to exhibit similarities across patients. In this paper, we exploit these similarities using machine learning algorithms and set out to pioneer a meta--review informed method for the identification of CRS based on specific cytokine peak concentrations and evidence from previous clinical studies. We argue that such methods could support clinicians in analyzing suspect cytokine profiles by matching them against CRS knowledge from past clinical studies, with the ultimate aim of swift CRS diagnosis. During evaluation with real--world CRS clinical data, we emphasize the potential of our proposed method of producing interpretable results, in addition to being effective in identifying the onset of cytokine storm.

Alex Bogatu, Zili Zhou, Dónal Landers et al.

Entailment trees have been proposed to simulate the human reasoning process of explanation generation in the context of open--domain textual question answering. However, in practice, manually constructing these explanation trees proves a laborious process that requires active human involvement. Given the complexity of capturing the line of reasoning from question to the answer or from claim to premises, the issue arises of how to assist the user in efficiently constructing multi--level entailment trees given a large set of available facts. In this paper, we frame the construction of entailment trees as a sequence of active premise selection steps, i.e., for each intermediate node in an explanation tree, the expert needs to annotate positive and negative examples of premise facts from a large candidate list. We then iteratively fine--tune pre--trained Transformer models with the resulting positive and tightly controlled negative samples and aim to balance the encoding of semantic relationships and explanatory entailment relationships. Experimental evaluation confirms the measurable efficiency gains of the proposed active fine--tuning method in facilitating entailment trees construction: up to 20\% improvement in explanatory premise selection when compared against several alternatives.

Mael Jullien, Alex Bogatu, Harriet Unsworth et al.

Matching patients to clinical trials demands a systematic and reasoned interpretation of documents which require significant expert-level background knowledge, over a complex set of well-defined eligibility criteria. Moreover, this interpretation process needs to operate at scale, over vast knowledge bases of trials. In this paper, we propose a scalable method that extends the capabilities of LLMs in the direction of systematizing the reasoning over sets of medical eligibility criteria, evaluating it in the context of real-world cases. The proposed method overlays a Set-guided reasoning method for LLMs. The proposed framework is evaluated on TREC 2022 Clinical Trials, achieving results superior to the state-of-the-art: NDCG@10 of 0.693 and Precision@10 of 0.73.

Oskar Wysocki, Magdalena Wysocka, Danilo Carvalho et al.

We present BioLunar, developed using the Lunar framework, as a tool for supporting biological analyses, with a particular emphasis on molecular-level evidence enrichment for biomarker discovery in oncology. The platform integrates Large Language Models (LLMs) to facilitate complex scientific reasoning across distributed evidence spaces, enhancing the capability for harmonizing and reasoning over heterogeneous data sources. Demonstrating its utility in cancer research, BioLunar leverages modular design, reusable data access and data analysis components, and a low-code user interface, enabling researchers of all programming levels to construct LLM-enabled scientific workflows. By facilitating automatic scientific discovery and inference from heterogeneous evidence, BioLunar exemplifies the potential of the integration between LLMs, specialised databases and biomedical tools to support expert-level knowledge synthesis and discovery.

Alex Bogatu, Norman W. Paton, Mark Douthwaite et al.

Accurately identifying different representations of the same real-world entity is an integral part of data cleaning and many methods have been proposed to accomplish it. The challenges of this entity resolution task that demand so much research attention are often rooted in the task-specificity and user-dependence of the process. Adopting deep learning techniques has the potential to lessen these challenges. In this paper, we set out to devise an entity resolution method that builds on the robustness conferred by deep autoencoders to reduce human-involvement costs. Specifically, we reduce the cost of training deep entity resolution models by performing unsupervised representation learning. This unveils a transferability property of the resulting model that can further reduce the cost of applying the approach to new datasets by means of transfer learning. Finally, we reduce the cost of labelling training data through an active learning approach that builds on the properties conferred by the use of deep autoencoders. Empirical evaluation confirms the accomplishment of our cost-reduction desideratum while achieving comparable effectiveness with state-of-the-art alternatives.