Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 2407.16984

scGHSOM: Hierarchical clustering and visualization of single-cell and CRISPR data using growing hierarchical SOM

Shang-Jung Wen·Jia-Ming Chang·Fang Yu
View original source ↗Read source document ↗Export metadata ↓

Abstract

High-dimensional single-cell data poses significant challenges in identifying underlying biological patterns due to the complexity and heterogeneity of cellular states. We propose a comprehensive gene-cell dependency visualization via unsupervised clustering, Growing Hierarchical Self-Organizing Map (GHSOM), specifically designed for analyzing high-dimensional single-cell data like single-cell sequencing and CRISPR screens. GHSOM is applied to cluster samples in a hierarchical structure such that the self-growth structure of clusters satisfies the required variations between and within. We propose a novel Significant Attributes Identification Algorithm to identify features that distinguish clusters. This algorithm pinpoints attributes with minimal variation within a cluster but substantial variation between clusters. These key attributes can then be used for targeted data retrieval and downstream analysis. Furthermore, we present two innovative visualization tools: Cluster Feature Map and Cluster Distribution Map. The Cluster Feature Map highlights the distribution of specific features across the hierarchical structure of GHSOM clusters. This allows for rapid visual assessment of cluster uniqueness based on chosen features. The Cluster Distribution Map depicts leaf clusters as circles on the GHSOM grid, with circle size reflecting cluster data size and color customizable to visualize features like cell type or other attributes. We apply our analysis to three single-cell datasets and one CRISPR dataset (cell-gene database) and evaluate clustering methods with internal and external CH and ARI scores. GHSOM performs well, being the best performer in internal evaluation (CH=4.2). In external evaluation, GHSOM has the third-best performance of all methods.

Explore related subjects

cs.LGcs.IRq-bio.GN

Keep this discovery

BibTeXRIS

Shang-Jung Wen, Jia-Ming Chang, Fang Yu. 2024-07-24. scGHSOM: Hierarchical clustering and visualization of single-cell and CRISPR data using growing hierarchical SOM. https://arxiv.org/abs/2407.16984

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

AUC Maximization from Biased Positive-unlabeled Data with Confidence

Maximizing the area under the receiver operating characteristic curve (AUC) is a standard approach to imbalanced binary classification. Although positive and negative data are required for maximizing the AUC, negative data are often difficult to collect in some real-world applications due to privacy concerns or the need for specialized expertise to annotate them. Thus, AUC maximization from positive and unlabeled (PU) data has been attracting attention. Existing methods assume that labeled positive data are unbiased samples from the true positive distribution. However, this ideal assumption is often violated in practice. In this paper, we propose a method to maximize the AUC from biased PU data. To address the bias, our key idea is to exploit {\it confidence}, i.e., the probability that an instance is positive, associated with the small number of labeled positive data. We derive an estimator of the AUC risk using biased PU data with confidence, enabling AUC maximization under such bias. We further show that the rewritten AUC risk induces a Bayes-optimal AUC ranking even when the available confidence is any strictly increasing transformation of the true posterior probability. We experimentally show the effectiveness of our method on eight real-world datasets.

cs.LG↗
arXiv2026

Measuring the Value of World-Model Updates: A Counterfactual Utility Protocol for Continual Adaptation

Continual world models must decide whether new data justify changing the model. Fixed replay schedules and prediction-error triggers specify when to update, but neither reveals the value of an individual update: one deployment run cannot show how the same model would have performed at that moment had it held its parameters. We introduce the fork ledger, which branches a deployment stream at pre-registered decision points into matched update and hold continuations under common random numbers. It evaluates both continuations on the same episodes and records $\Delta R = R_{\mathrm{update}} - R_{\mathrm{hold}}$. Always applying one fixed update mechanism lowers return on all three simulated control tasks: CartPole ($-144.0$; checkpoint-bootstrap $95\%$ CI $[-185.4,-116.1]$, against a converged return near $650$), Walker ($-82.8$; $[-101.1,-61.7]$) and Cheetah ($-18.6$; $[-29.0,-6.6]$). Divergence is an outcome of applying the update, so the estimand counts every attempted fork; restricted to the $693$ of $720$ that did not collapse, CartPole and Walker are unchanged in sign ($-113.4$ and $-82.1$) and Cheetah becomes unresolved ($-3.9$; $[-17.5,+13.0]$). The task is the unit of inference: each contributes $240$ attempted forks over five pretrained checkpoints crossed with two drift directions. The ledger makes counterfactual utility observable for a fixed mechanism, allowing triggers to be judged by the updates they select rather than by surprise detection alone.

cs.LG↗
arXiv2026

When More Is Not Better: Component Anti-Synergy in a P300 Speller

P300 brain-computer interface (BCI) spellers can provide hands-free communication for people with severe motor impairments. Modern pipelines combine multiple individually promising components, often assuming that 'more-is-better'. We tested this assumption using a four-component full-factorial experiment varying the inclusion of Euclidean Alignment (EA), xDAWN spatial filtering, subject calibration, and language model priors on a public P300 dataset. Performance was evaluated using accuracy, repetitions, and information transfer rate (ITR) with mixed-effects models. Results show that the value of components is conditional rather than additive. Calibration was the strongest singular contributor, while EA compensated for its absence in zero-calibration settings. Adding independently useful components could also reduce performance, revealing component anti-synergy. Contrary to conventional wisdom, LM support was not universally beneficial: its effect depends strongly on the strength of the underlying EEG pipeline, while results from a larger LM showed a similar pattern. Together, these findings challenge maximal 'all-on' pipeline design and highlight the value of selecting spatial and language-support components according to the quality of available EEG evidence.

cs.LG↗