arXiv subjects

Sebastian Josef Vollmer

Publications and source records attributed to Sebastian Josef Vollmer.

6 recordsLinked to original sources

arXiv2026

Linear-LLM-SCM: Benchmarking LLMs for Coefficient Elicitation in Linear-Gaussian Causal Models

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 framework for evaluating LLMs on Linear Gaussian structural causal model parametrization when a directed acyclic graph (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 with seven real-world DAGs effect ground truth illustrate limitations of LLMs as quantitative causal parameterizers. Across most models, we observe variability in coefficient estimates and sensitivity to structural perturbations. We open-sourced the framework to further encourage the community to work on studies toward the use of LLM for causal effect elicitation in safety-critical domain, e.g., healthcare.

cs.LG↗

arXiv2026

Reimagining Anomalies: What If Anomalies Were Normal?

Deep learning-based methods have achieved a breakthrough in image anomaly detection, but their complexity introduces a considerable challenge to understanding why an instance is predicted to be anomalous. We introduce a novel explanation method that generates multiple alternative modifications for each anomaly, capturing diverse concepts of anomalousness. Each modification is trained to be perceived as normal by the anomaly detector. The method provides a semantic explanation of the mechanism that triggered the detector, allowing users to explore ``what-if scenarios.'' Qualitative and quantitative analyses across various image datasets demonstrate that applying this method to state-of-the-art detectors provides high-quality semantic explanations.

cs.CV↗

arXiv2025

Co-Exploration and Co-Exploitation via Shared Structure in Multi-Task Bandits

We propose a novel Bayesian framework for efficient exploration in contextual multi-task multi-armed bandit settings, where the context is only observed partially and dependencies between reward distributions are induced by latent context variables. In order to exploit these structural dependencies, our approach integrates observations across all tasks and learns a global joint distribution, while still allowing personalised inference for new tasks. In this regard, we identify two key sources of epistemic uncertainty, namely structural uncertainty in the latent reward dependencies across arms and tasks, and user-specific uncertainty due to incomplete context and limited interaction history. To put our method into practice, we represent the joint distribution over tasks and rewards using a particle-based approximation of a log-density Gaussian process. This representation enables flexible, data-driven discovery of both inter-arm and inter-task dependencies without prior assumptions on the latent variables. Empirically, we demonstrate that our method outperforms baselines such as hierarchical model bandits, especially in settings with model misspecification or complex latent heterogeneity.

cs.LG↗

arXiv2025

MEDAKA: Construction of Biomedical Knowledge Graphs Using Large Language Models

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.

cs.AI↗

arXiv2025

Rethinking Cancer Gene Identification through Graph Anomaly Analysis

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.

cs.CE↗

arXiv2024

Graph Agnostic Causal Bayesian Optimisation

We study the problem of globally optimising a target variable of an unknown causal graph on which a sequence of soft or hard interventions can be performed. The problem of optimising the target variable associated with a causal graph is formalised as Causal Bayesian Optimisation (CBO). We study the CBO problem under the cumulative regret objective with unknown causal graphs for two settings, namely structural causal models with hard interventions and function networks with soft interventions. We propose Graph Agnostic Causal Bayesian Optimisation (GACBO), an algorithm that actively discovers the causal structure that contributes to achieving optimal rewards. GACBO seeks to balance exploiting the actions that give the best rewards against exploring the causal structures and functions. To the best of our knowledge, our work is the first to study causal Bayesian optimization with cumulative regret objectives in scenarios where the graph is unknown or partially known. We show our proposed algorithm outperforms baselines in simulated experiments and real-world applications.

cs.LG↗