What sorts of structure might enable a learner to discover classes from unlabeled data? Traditional approaches rely on feature-space similarity and heroic assumptions on the data. In this paper, we introduce unsupervised learning under Latent Label Shift (LLS), where the label marginals $p_d(y)$ shift but the class conditionals $p(x|y)$ do not.

Single-cell RNA sequencing technologies have revolutionized our understanding of cellular heterogeneity, yet computational methods often struggle to balance performance with biological interpretability. Embedded topic models have been widely used for interpretable single-cell embedding learning. However, these models suffer from the potential problem of interpretation collapse, where topics semantically collapse towards each other, resulting in redundant topics and incomplete capture of biological variation. Furthermore, the rise of single-cell foundation models creates opportunities to harness external biological knowledge for guiding model embeddings. Here, we present scE2TM, an external knowledge-guided embedded topic model that provides a high-quality cell embedding and interpretation for scRNA-seq analysis. Through embedding clustering regularization method, each topic is constrained to be the center of a separately aggregated gene cluster, enabling it to capture unique biological information. Across 20 scRNA-seq datasets, scE2TM achieves superior clustering performance compared with seven state-of-the-art methods. A comprehensive interpretability benchmark further shows that scE2TM-learned topics exhibit higher diversity and stronger consistency with underlying biological pathways. Modeling interferon-stimulated PBMCs, scE2TM simulates topic perturbations that drive control cells toward stimulated-like transcriptional states, faithfully mirroring experimental interferon responses. In melanoma, scE2TM identifies malignant-specific topics and extrapolates them to unseen patient data, revealing gene programs associated with patient survival.

Many users and contributors of large open-source projects report software defects or enhancement requests (known as bug reports) to the issue-tracking systems. However, they sometimes report issues that have already been reported. First, they may not have time to do sufficient research on existing bug reports. Second, they may not possess the right expertise in that specific area to realize that an existing bug report is essentially elaborating on the same matter, perhaps with a different wording. In this paper, we propose a novel approach based on machine learning methods that can automatically detect duplicate bug reports in an open bug repository based on the textual data in the reports. We present six alternative methods: Topic modeling, Gaussian Naive Bayes, deep learning, time-based organization, clustering, and summarization using a generative pre-trained transformer large language model. Additionally, we introduce a novel threshold-based approach for duplicate identification, in contrast to the conventional top-k selection method that has been widely used in the literature. Our approach demonstrates promising results across all the proposed methods, achieving accuracy rates ranging from the high 70%'s to the low 90%'s. We evaluated our methods on a public dataset of issues belonging to an Eclipse open-source project.

Interpretable topic modeling is essential for tracking how research interests evolve within co-author communities. In scientific corpora, where novelty is prized, identifying underrepresented niche topics is particularly important. However, contemporary models built from dense transformer embeddings tend to miss rare topics and therefore also fail to capture smooth temporal alignment. We propose a geometric method that integrates multimodal text and co-author network data, using Hellinger distances and Ward's linkage to construct a hierarchical topic dendrogram. This approach captures both local and global structure, supporting multiscale learning across semantic and temporal dimensions. Our method effectively identifies rare-topic structure and visualizes smooth topic drift over time. Experiments highlight the strength of interpretable bag-of-words models when paired with principled geometric alignment.

We propose new algorithms for topic modeling when the number of topics is unknown.

In topic modeling, many algorithms that guarantee identifiability of the topics have been developed under the premise that there exist anchor words -- i.e., words that only appear (with positive probability) in one topic. Follow-up work has resorted to three or higher-order statistics of the data corpus to relax the anchor word assumption. Reliable estimates of higher-order statistics are hard to obtain, however, and the identification of topics under those models hinges on uncorrelatedness of the topics, which can be unrealistic. This paper revisits topic modeling based on second-order moments, and proposes an anchor-free topic mining framework. The proposed approach guarantees the identification of the topics under a much milder condition compared to the anchor-word assumption, thereby exhibiting much better robustness in practice. The associated algorithm only involves one eigen-decomposition and a few small linear programs. This makes it easy to implement and scale up to very large problem instances. Experiments using the TDT2 and Reuters-21578 corpus demonstrate that the proposed anchor-free approach exhibits very favorable performance (measured using coherence, similarity count, and clustering accuracy metrics) compared to the prior art.

The associated algorithm only involves one eigen-decomposition and a few small linear programs.

The original paper of Blei et al. (2003) (see also Hofmann (1999)) contains early hints about a convex

Sparse autoencoders (SAEs) are used to analyze embeddings, but their role and practical value are debated. We propose a new perspective on SAEs by demonstrating that they can be naturally understood as topic models. We extend Latent Dirichlet Allocation to embedding spaces and derive the SAE objective as a maximum a posteriori estimator under this model. This view implies SAE features are thematic components rather than steerable directions. Based on this, we introduce SAE-TM, a topic modeling framework that: (1) trains an SAE to learn reusable topic atoms, (2) interprets them as word distributions on downstream data, and (3) merges them into any number of topics without retraining. SAE-TM yields more coherent topics than strong baselines on text and image datasets while maintaining diversity. Finally, we analyze thematic structure in image datasets and trace topic changes over time in Japanese woodblock prints. Our work positions SAEs as effective tools for large-scale thematic analysis across modalities. Code and data will be released upon publication.