Avtar Singh

Marzieh Haghighi, Mario C. Cruz, Erin Weisbart et al.

Various strategies for label-scarce object detection have been explored by the computer vision research community. These strategies mainly rely on assumptions that are specific to natural images and not directly applicable to the biological and biomedical vision domains. For example, most semi-supervised learning strategies rely on a small set of labeled data as a confident source of ground truth. In many biological vision applications, however, the ground truth is unknown and indirect information might be available in the form of noisy estimations or orthogonal evidence. In this work, we frame a crucial problem in spatial transcriptomics - decoding barcodes from In-Situ-Sequencing (ISS) images - as a semi-supervised object detection (SSOD) problem. Our proposed framework incorporates additional available sources of information into a semi-supervised learning framework in the form of privileged information. The privileged information is incorporated into the teacher's pseudo-labeling in a teacher-student self-training iteration. Although the available privileged information could be data domain specific, we have introduced a general strategy of pseudo-labeling enhanced by privileged information (PLePI) and exemplified the concept using ISS images, as well on the COCO benchmark using extra evidence provided by CLIP.

Ying Yuan, Xing-Yue Monica Ge, Aaron Archer Waterman et al.

Large-scale single-cell and Perturb-seq investigations routinely involve clustering cells and subsequently annotating each cluster with Gene-Ontology (GO) terms to elucidate the underlying biological programs. However, both stages, resolution selection and functional annotation, are inherently subjective, relying on heuristics and expert curation. We present HYPOGENEAGENT, a large language model (LLM)-driven framework, transforming cluster annotation into a quantitatively optimizable task. Initially, an LLM functioning as a gene-set analyst analyzes the content of each gene program or perturbation module and generates a ranked list of GO-based hypotheses, accompanied by calibrated confidence scores. Subsequently, we embed every predicted description with a sentence-embedding model, compute pair-wise cosine similarities, and let the agent referee panel score (i) the internal consistency of the predictions, high average similarity within the same cluster, termed intra-cluster agreement (ii) their external distinctiveness, low similarity between clusters, termed inter-cluster separation. These two quantities are combined to produce an agent-derived resolution score, which is maximized when clusters exhibit simultaneous coherence and mutual exclusivity. When applied to a public K562 CRISPRi Perturb-seq dataset as a preliminary test, our Resolution Score selects clustering granularities that exhibit alignment with known pathway compared to classical metrics such silhouette score, modularity score for gene functional enrichment summary. These findings establish LLM agents as objective adjudicators of cluster resolution and functional annotation, thereby paving the way for fully automated, context-aware interpretation pipelines in single-cell multi-omics studies.