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Chang Yu

Chang Yu appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

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Computer VisionGenomicsMachine LearningApplicationsMethodologyPopulations and Evolution

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Published work

7 published item(s)

preprint2026arXiv

Clarifying identification and estimation of treatment effects in the Sequential Parallel Comparison Design

Sequential parallel comparison design (SPCD) clinical trials aim to adjust active treatment effect estimates for placebo response to minimize the impact of placebo responders on the estimates. This is potentially accomplished using a two stage design by measuring treatment effects among all participants during the first stage, then classifying some placebo arm participants as placebo non-responders who will be re-randomized in the second stage. In this paper, we use causal inference tools to clarify under what assumptions treatment effects can be identified in SPCD trials and what effects the conventional estimators target at each stage of the SPCD trial. We further illustrate the highly influential impact of placebo response misclassification on the second stage estimate. We conclude that the conventional SPCD estimators do not target meaningful treatment effects.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Revisiting Randomization in Greedy Model Search

Feature subsampling is a core component of random forests and other ensemble methods. While recent theory suggests that this randomization acts solely as a variance reduction mechanism analogous to ridge regularization, these results largely rely on base learners optimized via ordinary least squares. We investigate the effects of feature subsampling on greedy forward selection, a model that better captures the adaptive nature of decision trees. Assuming an orthogonal design, we prove that ensembling with feature subsampling can reduce both bias and variance, contrasting with the pure variance reduction of convex base learners. More precisely, we show that both the training error and degrees of freedom can be non-monotonic in the subsampling rate, breaking the analogy with standard shrinkage methods like the lasso or ridge regression. Furthermore, we characterize the exact asymptotic behavior of the estimator, showing that it adaptively reweights OLS coefficients based on their rank, with weights that are well-approximated by a logistic function. These results elucidate the distinct role of algorithmic randomization when interleaved with greedy optimization.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

scHelix: Asymmetric Dual-Stream Integration via Explicit Gene-Level Disentanglement

A critical challenge in single-cell RNA sequencing (scRNA-seq) integration is resolving the tension between eliminating batch effects and maintaining biological fidelity. While recent evidence indicates that batch effects manifest heterogeneously across genes, most existing methods process the transcriptome uniformly, frequently resulting in over-correction and loss of subtle biological signals. To address this, we present scHelix, a dataset-adaptive framework that fundamentally changes how features are processed by explicitly partitioning genes into domain-invariant Anchors and domain-sensitive Variants at the input level. scHelix utilizes a dual-stream sparse diffusion encoder equipped with stop-gradient graph caching to efficiently learn multi-scale structural representations. The core of our approach is a novel asymmetric Align-Refine-Fuse protocol: the unstable Variant stream is first aligned to the robust topology of the Anchor stream, followed by a conservative refinement phase where the Anchor stream absorbs denoised details via bounded residual gating. This divide-and-conquer architecture prevents shortcut learning and ensures robust batch removal without compromising the integrity of biological clusters. Extensive benchmarking demonstrates that scHelix outperforms state-of-the-art methods.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Beyond 3DMM: Learning to Capture High-fidelity 3D Face Shape

3D Morphable Model (3DMM) fitting has widely benefited face analysis due to its strong 3D priori. However, previous reconstructed 3D faces suffer from degraded visual verisimilitude due to the loss of fine-grained geometry, which is attributed to insufficient ground-truth 3D shapes, unreliable training strategies and limited representation power of 3DMM. To alleviate this issue, this paper proposes a complete solution to capture the personalized shape so that the reconstructed shape looks identical to the corresponding person. Specifically, given a 2D image as the input, we virtually render the image in several calibrated views to normalize pose variations while preserving the original image geometry. A many-to-one hourglass network serves as the encode-decoder to fuse multiview features and generate vertex displacements as the fine-grained geometry. Besides, the neural network is trained by directly optimizing the visual effect, where two 3D shapes are compared by measuring the similarity between the multiview images rendered from the shapes. Finally, we propose to generate the ground-truth 3D shapes by registering RGB-D images followed by pose and shape augmentation, providing sufficient data for network training. Experiments on several challenging protocols demonstrate the superior reconstruction accuracy of our proposal on the face shape.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

HP-Capsule: Unsupervised Face Part Discovery by Hierarchical Parsing Capsule Network

Capsule networks are designed to present the objects by a set of parts and their relationships, which provide an insight into the procedure of visual perception. Although recent works have shown the success of capsule networks on simple objects like digits, the human faces with homologous structures, which are suitable for capsules to describe, have not been explored. In this paper, we propose a Hierarchical Parsing Capsule Network (HP-Capsule) for unsupervised face subpart-part discovery. When browsing large-scale face images without labels, the network first encodes the frequently observed patterns with a set of explainable subpart capsules. Then, the subpart capsules are assembled into part-level capsules through a Transformer-based Parsing Module (TPM) to learn the compositional relations between them. During training, as the face hierarchy is progressively built and refined, the part capsules adaptively encode the face parts with semantic consistency. HP-Capsule extends the application of capsule networks from digits to human faces and takes a step forward to show how the neural networks understand homologous objects without human intervention. Besides, HP-Capsule gives unsupervised face segmentation results by the covered regions of part capsules, enabling qualitative and quantitative evaluation. Experiments on BP4D and Multi-PIE datasets show the effectiveness of our method.

0 citations0 reviewsNo code linkedOpen access
preprint2013arXiv

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners including BarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60 percent. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1 percent FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides a scoring scheme same as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.

0 citations0 reviewsNo code linkedOpen access
preprint2013arXiv

YHap: software for probabilistic assignment of Y haplogroups from population re-sequencing data

Y haplogroup analyses are an important component of genealogical reconstruction, population genetic analyses, medical genetics and forensics. These fields are increasingly moving towards use of low-coverage, high throughput sequencing. However, there is as yet no software available for using sequence data to assign Y haplogroup groups probabilistically, such that the posterior probability of assignment fully reflects the information present in the data, and borrows information across all samples sequenced from a population. YHap addresses this problem.

0 citations0 reviewsNo code linkedOpen access