Explainable AI (XAI) is critical for ensuring transparency, accountability, and trust in machine learning systems as black-box models are increasingly deployed within high-stakes domains. Among XAI methods, Shapley values are widely used for their fairness and consistency axioms. However, prevalent Shapley value approximation methods commonly rely on abstract baselines or computationally intensive calculations, which can limit their interpretability and scalability. To address such challenges, we propose Pairwise Shapley Values, a novel framework that grounds feature attributions in explicit, human-relatable comparisons between pairs of data instances proximal in feature space. Our method introduces pairwise reference selection combined with single-value imputation to deliver intuitive, model-agnostic explanations while significantly reducing computational overhead. Here, we demonstrate that Pairwise Shapley Values enhance interpretability across diverse regression and classification scenarios--including real estate pricing, polymer property prediction, and drug discovery datasets. We conclude that the proposed methods enable more transparent AI systems and advance the real-world applicability of XAI.

Learning the undirected graph structure of a Markov network from data is a problem that has received a lot of attention during the last few decades. As a result of the general applicability of the model class, a myriad of methods have been developed in parallel in several research fields. Recently, as the size of the considered systems has increased, the focus of new methods has been shifted towards the high-dimensional domain. In particular, the introduction of the pseudo-likelihood function has pushed the limits of score-based methods originally based on the likelihood. At the same time, an array of methods based on simple pairwise tests have been developed to meet the challenges set by the increasingly large data sets in computational biology. Apart from being applicable on high-dimensional problems, methods based on the pseudo-likelihood and pairwise tests are fundamentally very different. In this work, we perform an extensive numerical study comparing the different types of methods on data generated by binary pairwise Markov networks. For sampling large networks, we use a parallelizable Gibbs sampler based on sparse restricted Boltzmann machines. Our results show that pairwise methods can be more accurate than pseudo-likelihood methods in settings often encountered in high-dimensional structure learning.

Protein structure prediction has been a "grand challenge" problem in the structure biology over the last few decades. Protein quality assessment plays a very important role in protein structure prediction. In the paper, we propose a new protein quality assessment method which can predict both local and global quality of the protein 3D structural models. Our method uses both multi and single model quality assessment method for global quality assessment, and uses chemical, physical, geometrical features, and global quality score for local quality assessment. CASP9 targets are used to generate the features for local quality assessment. We evaluate the performance of our local quality assessment method on CASP10, which is comparable with two stage-of-art QA methods based on the average absolute distance between the real and predicted distance. In addition, we blindly tested our method on CASP11, and the good performance shows that combining single and multiple model quality assessment method could be a good way to improve the accuracy of model quality assessment, and the random forest technique could be used to train a good local quality assessment model.