arXiv subjects

Zhi Wei

Publications and source records attributed to Zhi Wei.

13 recordsLinked to original sources

arXiv2026

HiST: A Hierarchical Sparse Transformer for Cross-Modal Spatial Transcriptomics Modeling

Spatial transcriptomics (ST) links gene expression with tissue morphology but remains expensive and low-throughput, motivating surrogates that infer expression from routine histology. Whole-slide H&E-to-ST inference pairs a gigapixel image with gene measurements at a sparse, irregular set of locations, making multiscale modeling challenging without incurring dense-grid overhead or quadratic token mixing. We propose HiST, a hierarchical sparse transformer that treats measured locations as a lattice-indexed sparse field and builds a dyadic encoder--decoder directly on the active tissue footprint. HiST combines sparse window attention for local geometric correspondence with resolution-changing operators for rapid multiscale context integration. For a fixed window size, the dominant runtime and memory scale with the number of observed locations rather than the dense slide area. To mitigate slide-specific acquisition variation, HiST adds a bottlenecked global conditioning pathway via a \emph{slide calibration token} that summarizes slide-level context and conditions local representations. On a multi-organ benchmark spanning diverse tissues and acquisition sources, HiST improves predictive performance over recent baselines while reducing runtime and peak memory.

cs.CV↗

arXiv2026

INST-Align: Implicit Neural Alignment for Spatial Transcriptomics via Canonical Expression Fields

Spatial transcriptomics (ST) measures mRNA expression while preserving spatial organization, but multi-slice analysis faces two coupled difficulties: large non-rigid deformations across slices and inter-slice batch effects when alignment and integration are treated independently. We present INST-Align, an unsupervised pairwise framework that couples a coordinate-based deformation network with a shared Canonical Expression Field, an implicit neural representation mapping spatial coordinates to expression embeddings, for joint alignment and reconstruction. A two-phase training strategy first establishes a stable canonical embedding space and then jointly optimizes deformation and spatial-feature matching, enabling mutually constrained alignment and representation learning. Cross-slice parameter sharing of the canonical field regularizes ambiguous correspondences and absorbs batch variation. Across nine datasets, INST-Align achieves state-of-the-art mean OT Accuracy (0.702), NN Accuracy (0.719), and Chamfer distance, with Chamfer reductions of up to 94.9\% on large-deformation sections relative to the strongest baseline. The framework also yields biologically meaningful spatial embeddings and coherent 3D tissue reconstruction. The code will be released after review phase.

cs.CV↗

arXiv2025

Selective Conformal Risk Control

Reliable uncertainty quantification is essential for deploying machine learning systems in high-stakes domains. Conformal prediction provides distribution-free coverage guarantees but often produces overly large prediction sets, limiting its practical utility. To address this issue, we propose \textit{Selective Conformal Risk Control} (SCRC), a unified framework that integrates conformal prediction with selective classification. The framework formulates uncertainty control as a two-stage problem: the first stage selects confident samples for prediction, and the second stage applies conformal risk control on the selected subset to construct calibrated prediction sets. We develop two algorithms under this framework. The first, SCRC-T, preserves exchangeability by computing thresholds jointly over calibration and test samples, offering exact finite-sample guarantees. The second, SCRC-I, is a calibration-only variant that provides PAC-style probabilistic guarantees while being more computational efficient. Experiments on two public datasets show that both methods achieve the target coverage and risk levels, with nearly identical performance, while SCRC-I exhibits slightly more conservative risk control but superior computational practicality. Our results demonstrate that selective conformal risk control offers an effective and efficient path toward compact, reliable uncertainty quantification.

cs.LG↗

arXiv2025

Clustering with Communication: A Variational Framework for Single Cell Representation Learning

Single-cell RNA sequencing (scRNA-seq) has revealed complex cellular heterogeneity, but recent studies emphasize that understanding biological function also requires modeling cell-cell communication (CCC), the signaling interactions mediated by ligand-receptor pairs that coordinate cellular behavior. Tools like CellChat have demonstrated that CCC plays a critical role in processes such as cell differentiation, tissue regeneration, and immune response, and that transcriptomic data inherently encodes rich information about intercellular signaling. We propose CCCVAE, a novel variational autoencoder framework that incorporates CCC signals into single-cell representation learning. By leveraging a communication-aware kernel derived from ligand-receptor interactions and a sparse Gaussian process, CCCVAE encodes biologically informed priors into the latent space. Unlike conventional VAEs that treat each cell independently, CCCVAE encourages latent embeddings to reflect both transcriptional similarity and intercellular signaling context. Empirical results across four scRNA-seq datasets show that CCCVAE improves clustering performance, achieving higher evaluation scores than standard VAE baselines. This work demonstrates the value of embedding biological priors into deep generative models for unsupervised single-cell analysis.

cs.LG↗

arXiv2025

Enhancing TCR-Peptide Interaction Prediction with Pretrained Language Models and Molecular Representations

Understanding the binding specificity between T-cell receptors (TCRs) and peptide-major histocompatibility complexes (pMHCs) is central to immunotherapy and vaccine development. However, current predictive models struggle with generalization, especially in data-scarce settings and when faced with novel epitopes. We present LANTERN (Large lAnguage model-powered TCR-Enhanced Recognition Network), a deep learning framework that combines large-scale protein language models with chemical representations of peptides. By encoding TCR \b{eta}-chain sequences using ESM-1b and transforming peptide sequences into SMILES strings processed by MolFormer, LANTERN captures rich biological and chemical features critical for TCR-peptide recognition. Through extensive benchmarking against existing models such as ChemBERTa, TITAN, and NetTCR, LANTERN demonstrates superior performance, particularly in zero-shot and few-shot learning scenarios. Our model also benefits from a robust negative sampling strategy and shows significant clustering improvements via embedding analysis. These results highlight the potential of LANTERN to advance TCR-pMHC binding prediction and support the development of personalized immunotherapies.

q-bio.QM↗

arXiv2025

Two-stage Risk Control with Application to Ranked Retrieval

Practical machine learning systems often operate in multiple sequential stages, as seen in ranking and recommendation systems, which typically include a retrieval phase followed by a ranking phase. Effectively assessing prediction uncertainty and ensuring effective risk control in such systems pose significant challenges due to their inherent complexity. To address these challenges, we developed two-stage risk control methods based on the recently proposed learn-then-test (LTT) and conformal risk control (CRC) frameworks. Unlike the methods in prior work that address multiple risks, our approach leverages the sequential nature of the problem, resulting in reduced computational burden. We provide theoretical guarantees for our proposed methods and design novel loss functions tailored for ranked retrieval tasks. The effectiveness of our approach is validated through experiments on two large-scale, widely-used datasets: MSLR-Web and Yahoo LTRC.

cs.IR↗

arXiv2024

DaLPSR: Leverage Degradation-Aligned Language Prompt for Real-World Image Super-Resolution

Image super-resolution pursuits reconstructing high-fidelity high-resolution counterpart for low-resolution image. In recent years, diffusion-based models have garnered significant attention due to their capabilities with rich prior knowledge. The success of diffusion models based on general text prompts has validated the effectiveness of textual control in the field of text2image. However, given the severe degradation commonly presented in low-resolution images, coupled with the randomness characteristics of diffusion models, current models struggle to adequately discern semantic and degradation information within severely degraded images. This often leads to obstacles such as semantic loss, visual artifacts, and visual hallucinations, which pose substantial challenges for practical use. To address these challenges, this paper proposes to leverage degradation-aligned language prompt for accurate, fine-grained, and high-fidelity image restoration. Complementary priors including semantic content descriptions and degradation prompts are explored. Specifically, on one hand, image-restoration prompt alignment decoder is proposed to automatically discern the degradation degree of LR images, thereby generating beneficial degradation priors for image restoration. On the other hand, much richly tailored descriptions from pretrained multimodal large language model elicit high-level semantic priors closely aligned with human perception, ensuring fidelity control for image restoration. Comprehensive comparisons with state-of-the-art methods have been done on several popular synthetic and real-world benchmark datasets. The quantitative and qualitative analysis have demonstrated that the proposed method achieves a new state-of-the-art perceptual quality level. Related source codes and pre-trained parameters were public in https://github.com/puppy210/DaLPSR.

cs.CV↗

arXiv2024

Conformal Risk Control for Ordinal Classification

As a natural extension to the standard conformal prediction method, several conformal risk control methods have been recently developed and applied to various learning problems. In this work, we seek to control the conformal risk in expectation for ordinal classification tasks, which have broad applications to many real problems. For this purpose, we firstly formulated the ordinal classification task in the conformal risk control framework, and provided theoretic risk bounds of the risk control method. Then we proposed two types of loss functions specially designed for ordinal classification tasks, and developed corresponding algorithms to determine the prediction set for each case to control their risks at a desired level. We demonstrated the effectiveness of our proposed methods, and analyzed the difference between the two types of risks on three different datasets, including a simulated dataset, the UTKFace dataset and the diabetic retinopathy detection dataset.

cs.LG↗

arXiv2020

DeepVar: An End-to-End Deep Learning Approach for Genomic Variant Recognition in Biomedical Literature

We consider the problem of Named Entity Recognition (NER) on biomedical scientific literature, and more specifically the genomic variants recognition in this work. Significant success has been achieved for NER on canonical tasks in recent years where large data sets are generally available. However, it remains a challenging problem on many domain-specific areas, especially the domains where only small gold annotations can be obtained. In addition, genomic variant entities exhibit diverse linguistic heterogeneity, differing much from those that have been characterized in existing canonical NER tasks. The state-of-the-art machine learning approaches in such tasks heavily rely on arduous feature engineering to characterize those unique patterns. In this work, we present the first successful end-to-end deep learning approach to bridge the gap between generic NER algorithms and low-resource applications through genomic variants recognition. Our proposed model can result in promising performance without any hand-crafted features or post-processing rules. Our extensive experiments and results may shed light on other similar low-resource NER applications.

cs.CL↗

arXiv2018

A Blended Deep Learning Approach for Predicting User Intended Actions

User intended actions are widely seen in many areas. Forecasting these actions and taking proactive measures to optimize business outcome is a crucial step towards sustaining the steady business growth. In this work, we focus on pre- dicting attrition, which is one of typical user intended actions. Conventional attrition predictive modeling strategies suffer a few inherent drawbacks. To overcome these limitations, we propose a novel end-to-end learning scheme to keep track of the evolution of attrition patterns for the predictive modeling. It integrates user activity logs, dynamic and static user profiles based on multi-path learning. It exploits historical user records by establishing a decaying multi-snapshot technique. And finally it employs the precedent user intentions via guiding them to the subsequent learning procedure. As a result, it addresses all disadvantages of conventional methods. We evaluate our methodology on two public data repositories and one private user usage dataset provided by Adobe Creative Cloud. The extensive experiments demonstrate that it can offer the appealing performance in comparison with several existing approaches as rated by different popular metrics. Furthermore, we introduce an advanced interpretation and visualization strategy to effectively characterize the periodicity of user activity logs. It can help to pinpoint important factors that are critical to user attrition and retention and thus suggests actionable improvement targets for business practice. Our work will provide useful insights into the prediction and elucidation of other user intended actions as well.

cs.LG↗

arXiv2016

A Noise-Filtering Approach for Cancer Drug Sensitivity Prediction

Accurately predicting drug responses to cancer is an important problem hindering oncologists' efforts to find the most effective drugs to treat cancer, which is a core goal in precision medicine. The scientific community has focused on improving this prediction based on genomic, epigenomic, and proteomic datasets measured in human cancer cell lines. Real-world cancer cell lines contain noise, which degrades the performance of machine learning algorithms. This problem is rarely addressed in the existing approaches. In this paper, we present a noise-filtering approach that integrates techniques from numerical linear algebra and information retrieval targeted at filtering out noisy cancer cell lines. By filtering out noisy cancer cell lines, we can train machine learning algorithms on better quality cancer cell lines. We evaluate the performance of our approach and compare it with an existing approach using the Area Under the ROC Curve (AUC) on clinical trial data. The experimental results show that our proposed approach is stable and also yields the highest AUC at a statistically significant level.

cs.LG↗

arXiv2014

An empirical Bayes testing procedure for detecting variants in analysis of next generation sequencing data

Because of the decreasing cost and high digital resolution, next-generation sequencing (NGS) is expected to replace the traditional hybridization-based microarray technology. For genetics study, the first-step analysis of NGS data is often to identify genomic variants among sequenced samples. Several statistical models and tests have been developed for variant calling in NGS study. The existing approaches, however, are based on either conventional Bayesian or frequentist methods, which are unable to address the multiplicity and testing efficiency issues simultaneously. In this paper, we derive an optimal empirical Bayes testing procedure to detect variants for NGS study. We utilize the empirical Bayes technique to exploit the across-site information among many testing sites in NGS data. We prove that our testing procedure is valid and optimal in the sense of rejecting the maximum number of nonnulls while the Bayesian false discovery rate is controlled at a given nominal level. We show by both simulation studies and real data analysis that our testing efficiency can be greatly enhanced over the existing frequentist approaches that fail to pool and utilize information across the multiple testing sites.

stat.AP↗

arXiv2008

A hidden spatial-temporal Markov random field model for network-based analysis of time course gene expression data

Microarray time course (MTC) gene expression data are commonly collected to study the dynamic nature of biological processes. One important problem is to identify genes that show different expression profiles over time and pathways that are perturbed during a given biological process. While methods are available to identify the genes with differential expression levels over time, there is a lack of methods that can incorporate the pathway information in identifying the pathways being modified/activated during a biological process. In this paper we develop a hidden spatial-temporal Markov random field (hstMRF)-based method for identifying genes and subnetworks that are related to biological processes, where the dependency of the differential expression patterns of genes on the networks are modeled over time and over the network of pathways. Simulation studies indicated that the method is quite effective in identifying genes and modified subnetworks and has higher sensitivity than the commonly used procedures that do not use the pathway structure or time dependency information, with similar false discovery rates. Application to a microarray gene expression study of systemic inflammation in humans identified a core set of genes on the KEGG pathways that show clear differential expression patterns over time. In addition, the method confirmed that the TOLL-like signaling pathway plays an important role in immune response to endotoxins.

stat.AP↗