Advanced bioimaging technologies have enabled the large-scale acquisition of multidimensional data, yet effective metadata management and interoperability remain significant challenges. To address these issues, we propose a new ontology-driven framework for the Systems Science of Biological Dynamics Database (SSBD) that adopts a two-tier architecture. The core layer provides a class-centric structure referencing existing biomedical ontologies, supporting both SSBD:repository -- which focuses on rapid dataset publication with minimal metadata -- and SSBD:database, which is enhanced with biological and imaging-related annotations. Meanwhile, the instance layer represents actual imaging dataset information as Resource Description Framework individuals that are explicitly linked to the core classes. This layered approach aligns flexible instance data with robust ontological classes, enabling seamless integration and advanced semantic queries. By coupling flexibility with rigor, the SSBD Ontology promotes interoperability, data reuse, and the discovery of novel biological mechanisms. Moreover, our solution aligns with the Recommended Metadata for Biological Images guidelines and fosters compatibility. Ultimately, our approach contributes to establishing a Findable, Accessible, Interoperable, and Reusable data ecosystem within the bioimaging community.

This paper aims to address a gap in major Islamic topics by developing an ontology for the Book of Purification in Islam. Many authoritative Islamic texts begin with the Book of Purification, as it is essential for performing prayer (the second pillar of Islam after Shahadah, the profession of faith) and other religious duties such as Umrah and Hajj. The ontology development strategy followed six key steps: (1) domain identification, (2) knowledge acquisition, (3) conceptualization, (4) classification, (5) integration and implementation, and (6) ontology generation. This paper includes examples of the constructed tables and classifications. The focus is on the design and analysis phases, as technical implementation is beyond the scope of this study. However, an initial implementation is provided to illustrate the steps of the proposed strategy. The developed ontology ensures reusability by formally defining and encoding the key concepts, attributes, and relationships related to the Book of Purification. This structured representation is intended to support knowledge sharing and reuse.

Out-of-distribution (OOD) detection in deep learning has traditionally been framed as a binary task, where samples are either classified as belonging to the known classes or marked as OOD, with little attention given to the semantic relationships between OOD samples and the in-distribution (ID) classes. We propose a framework for detecting and classifying OOD samples in a given class hierarchy. Specifically, we aim to predict OOD data to their correct internal nodes of the class hierarchy, whereas the known ID classes should be predicted as their corresponding leaf nodes. Our approach leverages the class hierarchy to create a probabilistic model and we implement this model by using networks trained for ID classification at multiple hierarchy depths. We conduct experiments on three datasets with predefined class hierarchies and show the effectiveness of our method. Our code is available at https://github.com/walline/prohoc.

In many large-scale classification problems, classes are organized in a known hierarchy, typically represented as a tree expressing the inclusion of classes in superclasses. We introduce a loss for this type of supervised hierarchical classification. It utilizes the knowledge of the hierarchy to assign each example not only to a class but also to all encompassing superclasses. Applicable to any feedforward architecture with a softmax output layer, this loss is a proper scoring rule, in that its expectation is minimized by the true posterior class probabilities. This property allows us to simultaneously pursue consistent classification objectives between superclasses and fine-grained classes, and eliminates the need for a performance trade-off between different granularities. We conduct an experimental study on three reference benchmarks, in which we vary the size of the training sets to cover a diverse set of learning scenarios. Our approach does not entail any significant additional computational cost compared with the loss of cross-entropy. It improves accuracy and reduces the number of coarse errors, with predicted labels that are distant from ground-truth labels in the tree.

Ontological commitment, i.e., used concepts, relations, and assumptions, are a corner stone of qualitative reasoning (QR) models. The state-of-the-art for processing raw inputs, though, are deep neural networks (DNNs), nowadays often based off from multimodal foundation models. These automatically learn rich representations of concepts and respective reasoning. Unfortunately, the learned qualitative knowledge is opaque, preventing easy inspection, validation, or adaptation against available QR models. So far, it is possible to associate pre-defined concepts with latent representations of DNNs, but extractable relations are mostly limited to semantic similarity. As a next step towards QR for validation and verification of DNNs: Concretely, we propose a method that extracts the learned superclass hierarchy from a multimodal DNN for a given set of leaf concepts. Under the hood we (1) obtain leaf concept embeddings using the DNN's textual input modality; (2) apply hierarchical clustering to them, using that DNNs encode semantic similarities via vector distances; and (3) label the such-obtained parent concepts using search in available ontologies from QR. An initial evaluation study shows that meaningful ontological class hierarchies can be extracted from state-of-the-art foundation models. Furthermore, we demonstrate how to validate and verify a DNN's learned representations against given ontologies. Lastly, we discuss potential future applications in the context of QR.

We tackle the challenge of predicting models' Out-of-Distribution (OOD) performance using in-distribution (ID) measurements without requiring OOD data. Existing evaluations with "Effective Robustness", which use ID accuracy as an indicator of OOD accuracy, encounter limitations when models are trained with diverse supervision and distributions, such as class labels (Vision Models, VMs, on ImageNet) and textual descriptions (Visual-Language Models, VLMs, on LAION). VLMs often generalize better to OOD data than VMs despite having similar or lower ID performance. To improve the prediction of models' OOD performance from ID measurements, we introduce the Lowest Common Ancestor (LCA)-on-the-Line framework. This approach revisits the established concept of LCA distance, which measures the hierarchical distance between labels and predictions within a predefined class hierarchy, such as WordNet. We assess 75 models using ImageNet as the ID dataset and five significantly shifted OOD variants, uncovering a strong linear correlation between ID LCA distance and OOD top-1 accuracy. Our method provides a compelling alternative for understanding why VLMs tend to generalize better. Additionally, we propose a technique to construct a taxonomic hierarchy on any dataset using K-means clustering, demonstrating that LCA distance is robust to the constructed taxonomic hierarchy. Moreover, we demonstrate that aligning model predictions with class taxonomies, through soft labels or prompt engineering, can enhance model generalization. Open source code in our Project Page: https://elvishelvis.github.io/papers/lca/.

Hierarchical classification aims to sort the object into a hierarchical structure of categories. For example, a bird can be categorized according to a three-level hierarchy of order, family, and species. Existing methods commonly address hierarchical classification by decoupling it into a series of multi-class classification tasks. However, such a multi-task learning strategy fails to fully exploit the correlation among various categories across different levels of the hierarchy. In this paper, we propose Label Hierarchy Transition (LHT), a unified probabilistic framework based on deep learning, to address the challenges of hierarchical classification. The LHT framework consists of a transition network and a confusion loss. The transition network focuses on explicitly learning the label hierarchy transition matrices, which has the potential to effectively encode the underlying correlations embedded within class hierarchies. The confusion loss encourages the classification network to learn correlations across different label hierarchies during training. The proposed framework can be readily adapted to any existing deep network with only minor modifications. We experiment with a series of public benchmark datasets for hierarchical classification problems, and the results demonstrate the superiority of our approach beyond current state-of-the-art methods. Furthermore, we extend our proposed LHT framework to the skin lesion diagnosis task and validate its great potential in computer-aided diagnosis. The code of our method is available at \href{https://github.com/renzhenwang/label-hierarchy-transition}{https://github.com/renzhenwang/label-hierarchy-transition}.

Few-Shot Learning (FSL) is a challenging task, which aims to recognize novel classes with few examples. Recently, lots of methods have been proposed from the perspective of meta-learning and representation learning. However, few works focus on the interpretability of FSL decision process. In this paper, we take a step towards the interpretable FSL by proposing a novel meta-learning based decision tree framework, namely, MetaDT. In particular, the FSL interpretability is achieved from two aspects, i.e., a concept aspect and a visual aspect. On the concept aspect, we first introduce a tree-like concept hierarchy as FSL prior. Then, resorting to the prior, we split each few-shot task to a set of subtasks with different concept levels and then perform class prediction via a model of decision tree. The advantage of such design is that a sequence of high-level concept decisions that lead up to a final class prediction can be obtained, which clarifies the FSL decision process. On the visual aspect, a set of subtask-specific classifiers with visual attention mechanism is designed to perform decision at each node of the decision tree. As a result, a subtask-specific heatmap visualization can be obtained to achieve the decision interpretability of each tree node. At last, to alleviate the data scarcity issue of FSL, we regard the prior of concept hierarchy as an undirected graph, and then design a graph convolution-based decision tree inference network as our meta-learner to infer parameters of the decision tree. Extensive experiments on performance comparison and interpretability analysis show superiority of our MetaDT.

Social media offer plenty of information to perform market research in order to meet the requirements of customers. One way how this research is conducted is that a domain expert gathers and categorizes user-generated content into a complex and fine-grained class structure. In many of such cases, little data meets complex annotations. It is not yet fully understood how this can be leveraged successfully for classification. We examine the classification accuracy of expert labels when used with a) many fine-grained classes and b) few abstract classes. For scenario b) we compare abstract class labels given by the domain expert as baseline and by automatic hierarchical clustering. We compare this to another baseline where the entire class structure is given by a completely unsupervised clustering approach. By doing so, this work can serve as an example of how complex expert annotations are potentially beneficial and can be utilized in the most optimal way for opinion mining in highly specific domains. By exploring across a range of techniques and experiments, we find that automated class abstraction approaches in particular the unsupervised approach performs remarkably well against domain expert baseline on text classification tasks. This has the potential to inspire opinion mining applications in order to support market researchers in practice and to inspire fine-grained automated content analysis on a large scale.