Ioanna Gemou

Ioanna Gemou, Matteo Gamba, Randall Balestriero et al.

Counterfactual explanations seek small, semantically meaningful changes to an input that alter a model's prediction, and are widely used to interpret and audit machine learning systems. In modern vision, language, and multimodal systems, pretrained encoders map inputs to representation spaces, and downstream classifier heads impose decision boundaries within those spaces. As a result, the feasibility and distance of nearby counterfactuals depend on boundary placement relative to the data. Yet models with similar predictive performance can differ substantially in whether such changes are achievable and how far representations must move. This work examines this variation using a standardized local search probe across several pretrained encoders and linear classifier heads. Results show that despite similar predictive performance, models differ substantially in their counterfactual behavior. Under fixed representations, varying only the classifier head alters counterfactual outcomes while leaving predictive performance largely unchanged. This variation is explained by the interaction of decision-boundary proximity and local data support, which jointly determine whether prediction changes are both feasible and lie in regions supported by the data, and can also improve counterfactual search within fixed models. Together, these findings identify counterfactual behavior as a distinct dimension beyond predictive performance and show that it can be altered without changing accuracy, with implications for model selection, robustness, and the reliability of counterfactual methods.

Tassallah Abdullahi, Ioanna Gemou, Nihal V. Nayak et al.

Biomedical knowledge graphs (KGs) encode rich, structured information critical for drug discovery tasks, but extracting meaningful insights from large-scale KGs remains challenging due to their complex structure. Existing biomedical subgraph retrieval methods are tailored for graph neural networks (GNNs), limiting compatibility with other paradigms, including large language models (LLMs). We introduce K-Paths, a model-agnostic retrieval framework that extracts structured, diverse, and biologically meaningful multi-hop paths from dense biomedical KGs. These paths enable the prediction of unobserved drug-drug and drug-disease interactions, including those involving entities not seen during training, thus supporting inductive reasoning. K-Paths is training-free and employs a diversity-aware adaptation of Yen's algorithm to extract the K shortest loopless paths between entities in a query, prioritizing biologically relevant and relationally diverse connections. These paths serve as concise, interpretable reasoning chains that can be directly integrated with LLMs or GNNs to improve generalization, accuracy, and enable explainable inference. Experiments on benchmark datasets show that K-Paths improves zero-shot reasoning across state-of-the-art LLMs. For instance, Tx-Gemma 27B improves by 19.8 and 4.0 F1 points on interaction severity prediction and drug repurposing tasks, respectively. Llama 70B achieves gains of 8.5 and 6.2 points on the same tasks. K-Paths also boosts the training efficiency of EmerGNN, a state-of-the-art GNN, by reducing the KG size by 90% while maintaining predictive performance. Beyond efficiency, K-Paths bridges the gap between KGs and LLMs, enabling scalable and explainable LLM-augmented scientific discovery. We release our code and the retrieved paths as a benchmark for inductive reasoning.

Ioanna Gemou, Evangelos Lamprou

Accurate disease prediction is vital for timely intervention, effective treatment, and reducing medical complications. While symbolic AI has been applied in healthcare, its adoption remains limited due to the effort required for constructing high-quality knowledge bases. This work introduces McCoy, a framework that combines Large Language Models (LLMs) with Answer Set Programming (ASP) to overcome this barrier. McCoy orchestrates an LLM to translate medical literature into ASP code, combines it with patient data, and processes it using an ASP solver to arrive at the final diagnosis. This integration yields a robust, interpretable prediction framework that leverages the strengths of both paradigms. Preliminary results show McCoy has strong performance on small-scale disease diagnosis tasks.