Concepts Worth Having: Refining VLM-Guided Concept Bottleneck Models with Minimal Annotations

Concept Bottleneck Models (CBMs) aim to improve interpretability in Deep Learning by structuring predictions through human-understandable concepts, but they provide no way to verify whether learned concepts align with the human's intended meaning, hurting interpretability. We introduce Prototype-Grounded Concept Models (PGCMs), which ground concepts in learned visual prototypes: image parts that serve as explicit evidence for the concepts. This grounding enables direct inspection of concept semantics and supports targeted human intervention at the prototype level to correct misalignments. Empirically, PGCMs achieve similar predictive performance as state-of-the-art CBMs while substantially improving transparency, interpretability, and intervenability.

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.

Recently impressive performance has been achieved in Concept Bottleneck Models (CBM) by utilizing the image-text alignment learned by a large pre-trained vision-language model (i.e. CLIP). However, there exist two key limitations in concept modeling. Existing methods often suffer from pre-training biases, manifested as granularity misalignment or reliance on structural priors. Moreover, fine-tuning with Binary Cross-Entropy (BCE) loss treats each concept independently, which ignores mutual exclusivity among concepts, leading to suboptimal alignment. To address these limitations, we propose Concept-wise Attention for Fine-grained Concept Bottleneck Models (CoAt-CBM), a novel framework that achieves adaptive fine-grained image-concept alignment and high interpretability. Specifically, CoAt-CBM employs learnable concept-wise visual queries to adaptively obtain fine-grained concept-wise visual embeddings, which are then used to produce a concept score vector. Then, a novel concept contrastive optimization guides the model to handle the relative importance of the concept scores, enabling concept predictions to faithfully reflect the image content and improved alignment. Extensive experiments demonstrate that CoAt-CBM consistently outperforms state-of-the-art methods. The codes will be available upon acceptance.