Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 2412.04072

Boundary-Guided Learning for Gene Expression Prediction in Spatial Transcriptomics

Mingcheng Qu·Yuncong Wu·Donglin Di·Anyang Su·Tonghua Su·Yang Song·Lei Fan
View original source ↗Read source document ↗Export metadata ↓

Abstract

Spatial transcriptomics (ST) has emerged as an advanced technology that provides spatial context to gene expression. Recently, deep learning-based methods have shown the capability to predict gene expression from WSI data using ST data. Existing approaches typically extract features from images and the neighboring regions using pretrained models, and then develop methods to fuse this information to generate the final output. However, these methods often fail to account for the cellular structure similarity, cellular density and the interactions within the microenvironment. In this paper, we propose a framework named BG-TRIPLEX, which leverages boundary information extracted from pathological images as guiding features to enhance gene expression prediction from WSIs. Specifically, our model consists of three branches: the spot, in-context and global branches. In the spot and in-context branches, boundary information, including edge and nuclei characteristics, is extracted using pretrained models. These boundary features guide the learning of cellular morphology and the characteristics of microenvironment through Multi-Head Cross-Attention. Finally, these features are integrated with global features to predict the final output. Extensive experiments were conducted on three public ST datasets. The results demonstrate that our BG-TRIPLEX consistently outperforms existing methods in terms of Pearson Correlation Coefficient (PCC). This method highlights the crucial role of boundary features in understanding the complex interactions between WSI and gene expression, offering a promising direction for future research.

Explore related subjects

cs.LG

Keep this discovery

BibTeXRIS

Mingcheng Qu, Yuncong Wu, Donglin Di, Anyang Su, Tonghua Su, Yang Song, Lei Fan. 2024-12-05. Boundary-Guided Learning for Gene Expression Prediction in Spatial Transcriptomics. https://arxiv.org/abs/2412.04072

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↗