arXiv subjects

Sydney Anuyah

Publications and source records attributed to Sydney Anuyah.

8 recordsLinked to original sources

arXiv2026

PubMedCausal: A Span-Level Annotated Corpus for Causal Relation Extraction in Biomedical Text

Causal relation extraction (CRE) is central to biomedical text mining, but current resources often conflate causal relations with broader associations, restrict annotation to sentence-level examples, or focus mainly on explicit causal cues. This limits their usefulness for evaluating whether models can recover causal claims as they are actually expressed in biomedical text. We introduce PubMedCausal, a span-level annotated corpus for biomedical CRE built from PubMed abstracts. The corpus contains 30,000 paragraph-level rows, including 3,945 causal rows and 6,491 adjudicated cause--effect pairs. Each causal relation is annotated with full-text cause and effect spans, causality type, and sententiality, enabling evaluation of both causal detection and full-span causal extraction. We benchmark discriminative encoders and open-source generative models across detection and extraction settings. For causal detection, biomedical encoders are strongest, with PubMedBERT reaching an F$_1$ score of 0.7391. For span-level extraction, the best generative baseline is DeepSeek-R1-32B with few-shot prompting, reaching a Cosine Pair F$_1$ of 0.6765. We further test transfer learning by evaluating PubMedCausal-trained encoders on external causal relation datasets, showing that the resource supports cross-dataset evaluation. Our results show that biomedical CRE remains difficult under class imbalance, long causal spans, implicit causality, inter-sentential relations, and prompt sensitivity. Code and Data can be found here: https://github.com/josiahpaul07/PubMedCausal_Exp

cs.CL↗

arXiv2026

Domain-Specific Knowledge Graphs in RAG-Enhanced Healthcare LLMs

Large Language Models (LLMs) generate fluent answers but can struggle with trustworthy, domain-specific reasoning. We evaluate whether domain knowledge graphs (KGs) improve Retrieval-Augmented Generation (RAG) for healthcare by constructing three PubMed-derived graphs: $\mathbb{G}_1$ (T2DM), $\mathbb{G}_2$ (Alzheimer's disease), and $\mathbb{G}_3$ (AD+T2DM). We design two probes: Probe 1 targets merged AD T2DM knowledge, while Probe 2 targets the intersection of $\mathbb{G}_1$ and $\mathbb{G}_2$. Seven instruction-tuned LLMs are tested across retrieval sources {No-RAG, $\mathbb{G}_1$, $\mathbb{G}_2$, $\mathbb{G}_1$ + $\mathbb{G}_2$, $\mathbb{G}_3$, $\mathbb{G}_1$+$\mathbb{G}_2$ + $\mathbb{G}_3$} and three decoding temperatures. Results show that scope alignment between probe and KG is decisive: precise, scope-matched retrieval (notably $\mathbb{G}_2$) yields the most consistent gains, whereas indiscriminate graph unions often introduce distractors that reduce accuracy. Larger models frequently match or exceed KG-RAG with a No-RAG baseline on Probe 1, indicating strong parametric priors, whereas smaller/mid-sized models benefit more from well-scoped retrieval. Temperature plays a secondary role; higher values rarely help. We conclude that precision-first, scope-matched KG-RAG is preferable to breadth-first unions, and we outline practical guidelines for graph selection, model sizing, and retrieval/reranking. Code and Data available here - https://github.com/sydneyanuyah/RAGComparison

cs.CL↗

arXiv2026

Benchmarking LLMs for Pairwise Causal Discovery in Biomedical and Multi-Domain Contexts

The safe deployment of large language models (LLMs) in high-stakes fields like biomedicine, requires them to be able to reason about cause and effect. We investigate this ability by testing 13 open-source LLMs on a fundamental task: pairwise causal discovery (PCD) from text. Our benchmark, using 12 diverse datasets, evaluates two core skills: 1) \textbf{Causal Detection} (identifying if a text contains a causal link) and 2) \textbf{Causal Extraction} (pulling out the exact cause and effect phrases). We tested various prompting methods, from simple instructions (zero-shot) to more complex strategies like Chain-of-Thought (CoT) and Few-shot In-Context Learning (FICL). The results show major deficiencies in current models. The best model for detection, DeepSeek-R1-Distill-Llama-70B, only achieved a mean score of 49.57\% ($C_{detect}$), while the best for extraction, Qwen2.5-Coder-32B-Instruct, reached just 47.12\% ($C_{extract}$). Models performed best on simple, explicit, single-sentence relations. However, performance plummeted for more difficult (and realistic) cases, such as implicit relationships, links spanning multiple sentences, and texts containing multiple causal pairs. We provide a unified evaluation framework, built on a dataset validated with high inter-annotator agreement ($κ\ge 0.758$), and make all our data, code, and prompts publicly available to spur further research. \href{https://github.com/sydneyanuyah/CausalDiscovery}{Code available here: https://github.com/sydneyanuyah/CausalDiscovery}

cs.CL↗

arXiv2025

Automated Knowledge Graph Construction using Large Language Models and Sentence Complexity Modelling

We introduce CoDe-KG, an open-source, end-to-end pipeline for extracting sentence-level knowledge graphs by combining robust coreference resolution with syntactic sentence decomposition. Using our model, we contribute a dataset of over 150,000 knowledge triples, which is open source. We also contribute a training corpus of 7248 rows for sentence complexity, 190 rows of gold human annotations for co-reference resolution using open source lung-cancer abstracts from PubMed, 900 rows of gold human annotations for sentence conversion policies, and 398 triples of gold human annotations. We systematically select optimal prompt-model pairs across five complexity categories, showing that hybrid chain-of-thought and few-shot prompting yields up to 99.8% exact-match accuracy on sentence simplification. On relation extraction (RE), our pipeline achieves 65.8% macro-F1 on REBEL, an 8-point gain over the prior state of the art, and 75.7% micro-F1 on WebNLG2, while matching or exceeding performance on Wiki-NRE and CaRB. Ablation studies demonstrate that integrating coreference and decomposition increases recall on rare relations by over 20%. Code and dataset are available at https://github.com/KaushikMahmud/CoDe-KG_EMNLP_2025

cs.CL↗

arXiv2025

What does making money have to do with crime?: A dive into the National Crime Victimization survey

In this short article, I leverage the National Crime Victimization Survey from 1992 to 2022 to examine how income, education, employment, and key demographic factors shape the type of crime victims experience (violent vs property). Using balanced classification splits and logistic regression models evaluated by F1-score, there is an isolation of the socioeconomic drivers of victimization "Group A" models and then an introduction of demographic factors such as age, gender, race, and marital status controls called "Group B" models. The results consistently proves that higher income and education lower the odds of violent relative to property crime, while men younger individuals and racial minorities face disproportionately higher violentcrime risks. On the geographic spectrum, the suburban models achieve the strongest predictive performance with an accuracy of 0.607 and F1 of 0.590, urban areas benefit from adding education and employment predictors and crime in rural areas are still unpredictable using these current factors. The patterns found in this study shows the need for specific interventions like educational investments in metropolitan settings economic support in rural communities and demographicaware prevention strategies.

physics.soc-ph↗

arXiv2025

An Empirical Study of Causal Relation Extraction Transfer: Design and Data

We conduct an empirical analysis of neural network architectures and data transfer strategies for causal relation extraction. By conducting experiments with various contextual embedding layers and architectural components, we show that a relatively straightforward BioBERT-BiGRU relation extraction model generalizes better than other architectures across varying web-based sources and annotation strategies. Furthermore, we introduce a metric for evaluating transfer performance, $F1_{phrase}$ that emphasizes noun phrase localization rather than directly matching target tags. Using this metric, we can conduct data transfer experiments, ultimately revealing that augmentation with data with varying domains and annotation styles can improve performance. Data augmentation is especially beneficial when an adequate proportion of implicitly and explicitly causal sentences are included.

cs.CL↗

arXiv2024

Advancing clinical trial outcomes using deep learning and predictive modelling: bridging precision medicine and patient-centered care

The integration of artificial intelligence [AI] into clinical trials has revolutionized the process of drug development and personalized medicine. Among these advancements, deep learning and predictive modelling have emerged as transformative tools for optimizing clinical trial design, patient recruitment, and real-time monitoring. This study explores the application of deep learning techniques, such as convolutional neural networks [CNNs] and transformerbased models, to stratify patients, forecast adverse events, and personalize treatment plans. Furthermore, predictive modelling approaches, including survival analysis and time-series forecasting, are employed to predict trial outcomes, enhancing efficiency and reducing trial failure rates. To address challenges in analysing unstructured clinical data, such as patient notes and trial protocols, natural language processing [NLP] techniques are utilized for extracting actionable insights. A custom dataset comprising structured patient demographics, genomic data, and unstructured text is curated for training and validating these models. Key metrics, including precision, recall, and F1 scores, are used to evaluate model performance, while trade-offs between accuracy and computational efficiency are examined to identify the optimal model for clinical deployment. This research underscores the potential of AI-driven methods to streamline clinical trial workflows, improve patient-centric outcomes, and reduce costs associated with trial inefficiencies. The findings provide a robust framework for integrating predictive analytics into precision medicine, paving the way for more adaptive and efficient clinical trials. By bridging the gap between technological innovation and real-world applications, this study contributes to advancing the role of AI in healthcare, particularly in fostering personalized care and improving overall trial success rates.

cs.LG↗

arXiv2024

Understanding Graph Databases: A Comprehensive Tutorial and Survey

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

cs.DB↗