Organizations: Department of Intelligent Systems, Tilburg University, 5037 AB Tilburg, The Netherlands · Information Systems Group, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands · Department of Industrial Engineering, Faculty of Engineering, Universidad de Talca, Campus Curic´o, Curic´o 3340000, Chile
Abstract
Concept Bottleneck Models (CBMs) route predictions exclusively through a clinically grounded concept layer, binding interpretability to concept-label consistency. When a dataset contains concept-level inconsistencies, identical concept profiles mapped to conflicting diagnosis labels create an unresolvable bottleneck that imposes a hard ceiling on achievable accuracy. In this paper, we apply rough set theory to the Derm7pt dermoscopy benchmark and characterize the full extent and clinical structure of this inconsistency. Among 305 unique concept profiles formed by the 7 dermoscopic criteria of the 7-point melanoma checklist, 50 (16.4%) are inconsistent, spanning 306 images (30.3% of the dataset). This yields a theoretical accuracy ceiling of 92.1%, independent of backbone architecture or training strategy for CBMs that exclusively operate with hard concepts. In addition, we characterize the conflict-severity distribution, identify the clinical features most responsible for boundary ambiguity, and evaluate two filtering strategies with quantified effects on dataset composition and CBM interpretability. Symmetric removal of all boundary-region images yields Derm7pt+, a fully consistent benchmark subset of 705 images with perfect quality of classification and no hard accuracy ceiling. Building on this filtered dataset, we present a hard CBM evaluated across 19 backbone architectures from the EfficientNet, DenseNet, ResNet, and Wide ResNet families. Under symmetric filtering, explored for completeness, EfficientNet-B5 achieves the best label F1 score (0.85) and label accuracy (0.90) on the held-out test set, with a concept accuracy of 0.70. Under asymmetric filtering, EfficientNet-B7 leads across all four metrics, reaching a label F1 score of 0.82 and concept accuracy of 0.70. These results establish reproducible baselines for concept-consistent CBM evaluation on dermoscopic data.
Concept Bottleneck Models (CBMs) provide an intrinsically interpretable alternative to post-hoc explanations. However, existing CBMs often rely on predefined concept vocabularies or supervised annotations, lack explicit concept grounding, and summarize each concept with a single image-level score -- discarding spatial recurrence and inter-concept dependencies. We propose a Graph-based Concept Bottleneck Model (G-CBM), an intrinsically interpretable framework that performs unsupervised concept discovery via Non-negative Matrix Factorization (NMF) and represents the discovered concepts as nodes in a per-image concept-graph representation. G-CBM matches region-level features to these concept nodes -- providing concept grounding and capturing concept recurrence across the image -- and applies a \emph{tunable concept filtering threshold} τ to suppress weak region-level features. A Graph Attention Network (GAT) then performs concept-level reasoning by modeling nonlinear dependencies across nodes. Across ImageNet, HAM10000, PH2, and Derm7pt, G-CBM achieves an average relative AUC improvement of 3.7% over a ResNet-50 baseline. Concept filtering frequently improves predictive performance while inducing selective concept use, achieving peak AUC of 0.96 on PH2 with only 2 of 10 concepts and 0.92 on HAM10000 with 3.8 of 9 concepts. On dermoscopy benchmarks, G-CBM is competitive with supervised approaches requiring external annotations. Deletion/insertion analyses with random ablation controls show that the learned concept ranking faithfully reflects model predictions.
In many machine learning problems, there may exist multiple models that achieve nearly identical predictive performance while relying on fundamentally different internal logic. However, standard training procedures produce a single model, offering no practical way to explore alternatives that may better suit downstream needs. The set of these equally accurate models is known as the Rashomon set. Exploring the Rashomon set is particularly challenging in large and complex hypothesis spaces, such as Concept Bottleneck Models (CBMs), which are widely used in computer vision to make predictions through intermediate, human-understandable concepts. In this paper, we provide a method for efficiently exploring the Rashomon set of CBMs. Our framework introduces a specialized parallel adapter-based construction, combined with a checkpointing scheme and a concept diversity objective, to generate multiple equally accurate CBMs from a single training process. Empirical results show that our method finds models with better diversity than baselines while using much less memory. We further demonstrate that access to these diverse yet accurate CBMs enables trustworthy model selection, resolution of inter-class confusion, and reliable abstention in decision-making.
Concept bottleneck models predict outcomes from high-level concepts detected in inputs. Although concepts provide a simple way to reap benefits from interpretability, very few datasets include concept labels. This limits researchers' ability to determine which problems are suitable for these models, isolate the factors that drive their performance or lead to failures, or uncover which algorithms perform well. In this paper, we develop synthetic benchmarks for concept-bottleneck models, focusing on their two main use cases: decision support, in which models assist humans in making better decisions, and automation, in which models handle routine tasks without supervision. Our benchmarks can generate labeled datasets while controlling for properties that affect performance, including data modality, concept choice, annotation quality, and completeness. We demonstrate how the benchmarks can be used to evaluate representative classes of concept bottleneck models. Our demonstrations show how the benchmarks can diagnose failure modes and guide follow-up testing.
Julian Skirzynski, Harry Cheon, Shreyas Kadekodi +2