David Antony Selby

Kanta Yamaoka, Sumantrak Mukherjee, Thomas Gärtner et al.

Large language models (LLMs) have shown potential in identifying qualitative causal relations, but their ability to perform quantitative causal reasoning -- estimating effect sizes that parametrize functional relationships -- remains underexplored in continuous domains. We introduce Linear-LLM-SCM, a plug-and-play benchmarking framework for evaluating LLMs on linear Gaussian structural causal model (SCM) parametrization when the DAG is given. The framework decomposes a DAG into local parent-child sets and prompts an LLM to produce a regression-style structural equation per node, which is aggregated and compared against available ground-truth parameters. Our experiments show several challenges in such benchmarking tasks, namely, strong stochasticity in the results in some of the models and susceptibility to DAG misspecification via spurious edges in the continuous domains. Across models, we observe substantial variability in coefficient estimates for some settings and sensitivity to structural and semantic perturbations, highlighting current limitations of LLMs as quantitative causal parameterizers. We also open-sourced the benchmarking framework so that researchers can utilize their DAGs and any off-the-shelf LLMs plug-and-play for evaluation in their domains effortlessly.

Asmita Sengupta, David Antony Selby, Sebastian Josef Vollmer et al.

Knowledge graphs (KGs) are increasingly used to represent biomedical information in structured, interpretable formats. However, existing biomedical KGs often focus narrowly on molecular interactions or adverse events, overlooking the rich data found in drug leaflets. In this work, we present (1) a hackable, end-to-end pipeline to create KGs from unstructured online content using a web scraper and an LLM; and (2) a curated dataset, MEDAKA, generated by applying this method to publicly available drug leaflets. The dataset captures clinically relevant attributes such as side effects, warnings, contraindications, ingredients, dosage guidelines, storage instructions and physical characteristics. We evaluate it through manual inspection and with an LLM-as-a-Judge framework, and compare its coverage with existing biomedical KGs and databases. We expect MEDAKA to support tasks such as patient safety monitoring and drug recommendation. The pipeline can also be used for constructing KGs from unstructured texts in other domains. Code and dataset are available at https://github.com/medakakg/medaka.

Selina Heller, Mohamed Ibrahim, David Antony Selby et al.

Decision conferences are structured, collaborative meetings that bring together experts from various fields to address complex issues and reach a consensus on recommendations for future actions or policies. These conferences often rely on facilitated discussions to ensure productive dialogue and collective agreement. Recently, Large Language Models (LLMs) have shown significant promise in simulating real-world scenarios, particularly through collaborative multi-agent systems that mimic group interactions. In this work, we present a novel LLM-based multi-agent system designed to simulate decision conferences, specifically focusing on detecting agreement among the participant agents. To achieve this, we evaluate six distinct LLMs on two tasks: stance detection, which identifies the position an agent takes on a given issue, and stance polarity detection, which identifies the sentiment as positive, negative, or neutral. These models are further assessed within the multi-agent system to determine their effectiveness in complex simulations. Our results indicate that LLMs can reliably detect agreement even in dynamic and nuanced debates. Incorporating an agreement-detection agent within the system can also improve the efficiency of group debates and enhance the overall quality and coherence of deliberations, making them comparable to real-world decision conferences regarding outcome and decision-making. These findings demonstrate the potential for LLM-based multi-agent systems to simulate group decision-making processes. They also highlight that such systems could be instrumental in supporting decision-making with expert elicitation workshops across various domains.

Yujing Ke, Kevin George, Kathan Pandya et al.

Identifying novel hypotheses is essential to scientific research, yet this process risks being overwhelmed by the sheer volume and complexity of available information. Existing automated methods often struggle to generate novel and evidence-grounded hypotheses, lack robust iterative refinement and rarely undergo rigorous temporal evaluation for future discovery potential. To address this, we propose BioDisco, a multi-agent framework that draws upon language model-based reasoning and a dual-mode evidence system (biomedical knowledge graphs and automated literature retrieval) for grounded novelty, integrates an internal scoring and feedback loop for iterative refinement, and validates performance through pioneering temporal and human evaluations and a Bradley-Terry paired comparison model to provide statistically-grounded assessment. Our evaluations demonstrate superior novelty and significance over ablated configurations representative of existing agentic architectures. Designed for flexibility and modularity, BioDisco allows seamless integration of custom language models or knowledge graphs, and can be run with just a few lines of code. We anticipate researchers using this practical tool as a catalyst for the discovery of new hypotheses.

Yilong Zang, Lingfei Ren, Yue Li et al.

Graph neural networks (GNNs) have shown promise in integrating protein-protein interaction (PPI) networks for identifying cancer genes in recent studies. However, due to the insufficient modeling of the biological information in PPI networks, more faithfully depiction of complex protein interaction patterns for cancer genes within the graph structure remains largely unexplored. This study takes a pioneering step toward bridging biological anomalies in protein interactions caused by cancer genes to statistical graph anomaly. We find a unique graph anomaly exhibited by cancer genes, namely weight heterogeneity, which manifests as significantly higher variance in edge weights of cancer gene nodes within the graph. Additionally, from the spectral perspective, we demonstrate that the weight heterogeneity could lead to the "flattening out" of spectral energy, with a concentration towards the extremes of the spectrum. Building on these insights, we propose the HIerarchical-Perspective Graph Neural Network (HIPGNN) that not only determines spectral energy distribution variations on the spectral perspective, but also perceives detailed protein interaction context on the spatial perspective. Extensive experiments are conducted on two reprocessed datasets STRINGdb and CPDB, and the experimental results demonstrate the superiority of HIPGNN.

Siyi Sun, David Antony Selby, Yunchuan Huang et al.

Missing data imputation in tabular datasets remains a pivotal challenge in data science and machine learning, particularly within socioeconomic research. However, real-world socioeconomic datasets are typically subject to strict data protection protocols, which often prohibit public sharing, even for synthetic derivatives. This severely limits the reproducibility and accessibility of benchmark studies in such settings. Further, there are very few publicly available synthetic datasets. Thus, there is limited availability of benchmarks for systematic evaluation of imputation methods on socioeconomic datasets, whether real or synthetic. In this study, we utilize the World Bank's publicly available synthetic dataset, Synthetic Data for an Imaginary Country, which closely mimics a real World Bank household survey while being fully public, enabling broad access for methodological research. With this as a starting point, we derived the IMAGIC-500 dataset: we select a subset of 500k individuals across approximately 100k households with 19 socioeconomic features, designed to reflect the hierarchical structure of real-world household surveys. This paper introduces a comprehensive missing data imputation benchmark on IMAGIC-500 under various missing mechanisms (MCAR, MAR, MNAR) and missingness ratios (10\%, 20\%, 30\%, 40\%, 50\%). Our evaluation considers the imputation accuracy for continuous and categorical variables, computational efficiency, and impact on downstream predictive tasks, such as estimating educational attainment at the individual level. The results highlight the strengths and weaknesses of statistical, traditional machine learning, and deep learning imputation techniques, including recent diffusion-based methods. The IMAGIC-500 dataset and benchmark aim to facilitate the development of robust imputation algorithms and foster reproducible social science research.