arXiv subjects

Yikun Zhang

Publications and source records attributed to Yikun Zhang.

31 records · Page 2Linked to original sources

arXiv2025

Mode and Ridge Estimation in Euclidean and Directional Product Spaces: A Mean Shift Approach

The set of local modes and density ridge lines are important summary characteristics of the data-generating distribution. In this work, we focus on estimating local modes and density ridges from point cloud data in a product space combining two or more Euclidean and/or directional metric spaces. Specifically, our approach extends the (subspace constrained) mean shift algorithm to such product spaces, addressing potential challenges in the generalization process. We establish the algorithmic convergence of the proposed methods, along with practical implementation guidelines. Experiments on simulated and real-world datasets demonstrate the effectiveness of our proposed methods.

stat.ML↗

arXiv2025

Doubly Robust Inference on Causal Derivative Effects for Continuous Treatments

Statistical methods for causal inference with continuous treatments mainly focus on estimating the mean potential outcome function, commonly known as the dose-response curve. However, it is often not the dose-response curve but its derivative function that signals the treatment effect. In this paper, we investigate nonparametric inference on the derivative of the dose-response curve with and without the positivity condition. Under the positivity and other regularity conditions, we propose a doubly robust (DR) inference method for estimating the derivative of the dose-response curve using kernel smoothing. When the positivity condition is violated, we demonstrate the inconsistency of conventional inverse probability weighting (IPW) and DR estimators, and introduce novel bias-corrected IPW and DR estimators. In all settings, our DR estimator achieves asymptotic normality at the standard nonparametric rate of convergence with nonparametric efficiency guarantees. Additionally, our approach reveals an interesting connection to nonparametric support and level set estimation problems. Finally, we demonstrate the applicability of our proposed estimators through simulations and a case study of evaluating a job training program.

stat.ME↗

arXiv2025

Atomas: Hierarchical Alignment on Molecule-Text for Unified Molecule Understanding and Generation

Molecule-and-text cross-modal representation learning has emerged as a promising direction for enhancing the quality of molecular representation, thereby improving performance in various scientific fields. However, most approaches employ a global alignment approach to learn the knowledge from different modalities that may fail to capture fine-grained information, such as molecule-and-text fragments and stereoisomeric nuances, which is crucial for downstream tasks. Furthermore, it is incapable of modeling such information using a similar global alignment strategy due to the lack of annotations about the fine-grained fragments in the existing dataset. In this paper, we propose Atomas, a hierarchical molecular representation learning framework that jointly learns representations from SMILES strings and text. We design a Hierarchical Adaptive Alignment model to automatically learn the fine-grained fragment correspondence between two modalities and align these representations at three semantic levels. Atomas's end-to-end training framework supports understanding and generating molecules, enabling a wider range of downstream tasks. Atomas achieves superior performance across 12 tasks on 11 datasets, outperforming 11 baseline models thus highlighting the effectiveness and versatility of our method. Scaling experiments further demonstrate Atomas's robustness and scalability. Moreover, visualization and qualitative analysis, validated by human experts, confirm the chemical relevance of our approach. Codes are released on https://github.com/yikunpku/Atomas.

q-bio.QM↗

arXiv2025

Nonparametric Inference on Dose-Response Curves Without the Positivity Condition

Existing statistical methods in causal inference often assume the positivity condition, where every individual has some chance of receiving any treatment level regardless of covariates. This assumption could be violated in observational studies with continuous treatments. In this paper, we develop identification and estimation theories for causal effects with continuous treatments (i.e., dose-response curves) without relying on the positivity condition. Our approach identifies and estimates the derivative of the treatment effect for each observed sample, integrating it to the treatment level of interest to mitigate bias from the lack of positivity. The method is grounded in a weaker assumption, satisfied by additive confounding models. We propose a fast and reliable numerical recipe for computing our integral estimator in practice and derive its asymptotic properties. To enable valid inference on the dose-response curve and its derivative, we use the nonparametric bootstrap and establish its consistency. The performances of our proposed estimators are validated through simulation studies and an analysis of the effect of air pollution exposure (PM$_{2.5}$) on cardiovascular mortality rates.

stat.ME↗

arXiv2024

Annotation-guided Protein Design with Multi-Level Domain Alignment

The core challenge of de novo protein design lies in creating proteins with specific functions or properties, guided by certain conditions. Current models explore to generate protein using structural and evolutionary guidance, which only provide indirect conditions concerning functions and properties. However, textual annotations of proteins, especially the annotations for protein domains, which directly describe the protein's high-level functionalities, properties, and their correlation with target amino acid sequences, remain unexplored in the context of protein design tasks. In this paper, we propose Protein-Annotation Alignment Generation, PAAG, a multi-modality protein design framework that integrates the textual annotations extracted from protein database for controllable generation in sequence space. Specifically, within a multi-level alignment module, PAAG can explicitly generate proteins containing specific domains conditioned on the corresponding domain annotations, and can even design novel proteins with flexible combinations of different kinds of annotations. Our experimental results underscore the superiority of the aligned protein representations from PAAG over 7 prediction tasks. Furthermore, PAAG demonstrates a significant increase in generation success rate (24.7% vs 4.7% in zinc finger, and 54.3% vs 22.0% in the immunoglobulin domain) in comparison to the existing model. We anticipate that PAAG will broaden the horizons of protein design by leveraging the knowledge from between textual annotation and proteins.

q-bio.QM↗

arXiv2022

Four-dimensional direct detection with Jones space optical full-field recovery

Data centers, the engines of the global Internet, are supported by massive high-speed optical interconnects. In optical fiber communication, the classic direct detection obtains only the intensity of the optical field, while the coherent detection counterpart utilizes both phase and polarization diversities at the expense of beating with a narrow-linewidth and high-stable local oscillator (LO). Herein, we propose and demonstrate a four-dimensional Jones space optical field recovery (4-D JSFR) scheme without LO. The information encoded on the intensity and phase of both polarizations can be captured by the polarization-diversity full-field receiver structure and subsequently extracted through deep neural network-aided field recovery. It achieves similar electrical spectral efficiency as standard intradyne coherent detection. The fully recovered optical field can extend the transmission distance beyond the power fading limitation induced by fiber chromatic dispersion. Furthermore, the LO-free advantage makes 4-D JSFR suitable for monolithic photonic integration, offering a spectrally efficient and cost-effective candidate for large-scale data center applications. Our results could motivate a fundamental paradigm shift in the optical field recovery theory and future optical transceiver design.

physics.optics↗

arXiv2022

SCONCE: A cosmic web finder for spherical and conic geometries

The latticework structure known as the cosmic web provides a valuable insight into the assembly history of large-scale structures. Despite the variety of methods to identify the cosmic web structures, they mostly rely on the assumption that galaxies are embedded in a Euclidean geometric space. Here we present a novel cosmic web identifier called SCONCE (Spherical and CONic Cosmic wEb finder) that inherently considers the 2D (RA,DEC) spherical or the 3D (RA,DEC,$z$) conic geometry. The proposed algorithms in SCONCE generalize the well-known subspace constrained mean shift (SCMS) method and primarily address the predominant filament detection problem. They are intrinsic to the spherical/conic geometry and invariant to data rotations. We further test the efficacy of our method with an artificial cross-shaped filament example and apply it to the SDSS galaxy catalogue, revealing that the 2D spherical version of our algorithms is robust even in regions of high declination. Finally, using N-body simulations from Illustris, we show that the 3D conic version of our algorithms is more robust in detecting filaments than the standard SCMS method under the redshift distortions caused by the peculiar velocities of halos. Our cosmic web finder is packaged in python as SCONCE-SCMS and has been made publicly available.

astro-ph.CO↗

arXiv2022

Linear Convergence of the Subspace Constrained Mean Shift Algorithm: From Euclidean to Directional Data

This paper studies the linear convergence of the subspace constrained mean shift (SCMS) algorithm, a well-known algorithm for identifying a density ridge defined by a kernel density estimator. By arguing that the SCMS algorithm is a special variant of a subspace constrained gradient ascent (SCGA) algorithm with an adaptive step size, we derive the linear convergence of such SCGA algorithm. While the existing research focuses mainly on density ridges in the Euclidean space, we generalize density ridges and the SCMS algorithm to directional data. In particular, we establish the stability theorem of density ridges with directional data and prove the linear convergence of our proposed directional SCMS algorithm.

stat.ML↗

arXiv2021

Kernel Smoothing, Mean Shift, and Their Learning Theory with Directional Data

Directional data consist of observations distributed on a (hyper)sphere, and appear in many applied fields, such as astronomy, ecology, and environmental science. This paper studies both statistical and computational problems of kernel smoothing for directional data. We generalize the classical mean shift algorithm to directional data, which allows us to identify local modes of the directional kernel density estimator (KDE). The statistical convergence rates of the directional KDE and its derivatives are derived, and the problem of mode estimation is examined. We also prove the ascending property of the directional mean shift algorithm and investigate a general problem of gradient ascent on the unit hypersphere. To demonstrate the applicability of the algorithm, we evaluate it as a mode clustering method on both simulated and real-world data sets.

stat.ML↗

arXiv2021

Iterative Reconstruction for Low-Dose CT using Deep Gradient Priors of Generative Model

Dose reduction in computed tomography (CT) is essential for decreasing radiation risk in clinical applications. Iterative reconstruction is one of the most promising ways to compensate for the increased noise due to reduction of photon flux. Rather than most existing prior-driven algorithms that benefit from manually designed prior functions or supervised learning schemes, in this work we integrate the data-consistency as a conditional term into the iterative generative model for low-dose CT. At the stage of prior learning, the gradient of data density is directly learned from normal-dose CT images as a prior. Then at the iterative reconstruction stage, the stochastic gradient descent is employed to update the trained prior with annealed and conditional schemes. The distance between the reconstructed image and the manifold is minimized along with data fidelity during reconstruction. Experimental comparisons demonstrated the noise reduction and detail preservation abilities of the proposed method.

eess.IV↗

arXiv2021

The EM Perspective of Directional Mean Shift Algorithm

The directional mean shift (DMS) algorithm is a nonparametric method for pursuing local modes of densities defined by kernel density estimators on the unit hypersphere. In this paper, we show that any DMS iteration can be viewed as a generalized Expectation-Maximization (EM) algorithm; in particular, when the von Mises kernel is applied, it becomes an exact EM algorithm. Under the (generalized) EM framework, we provide a new proof for the ascending property of density estimates and demonstrate the global convergence of directional mean shift sequences. Finally, we give a new insight into the linear convergence of the DMS algorithm.

math.ST↗

arXiv2020

DIRECT-Net: a unified mutual-domain material decomposition network for quantitative dual-energy CT imaging

By acquiring two sets of tomographic measurements at distinct X-ray spectra, the dual-energy CT (DECT) enables quantitative material-specific imaging. However, the conventionally decomposed material basis images may encounter severe image noise amplification and artifacts, resulting in degraded image quality and decreased quantitative accuracy. Iterative DECT image reconstruction algorithms incorporating either the sinogram or the CT image prior information have shown potential advantages in noise and artifact suppression, but with the expense of large computational resource, prolonged reconstruction time, and tedious manual selections of algorithm parameters. To partially overcome these limitations, we develop a domain-transformation enabled end-to-end deep convolutional neural network (DIRECT-Net) to perform high quality DECT material decomposition. Specifically, the proposed DIRECT-Net has immediate accesses to mutual-domain data, and utilizes stacked convolution neural network (CNN) layers for noise reduction and material decomposition. The training data are numerically simulated based on the underlying physics of DECT imaging.The XCAT digital phantom, iodine solutions phantom, and biological specimen are used to validate the performance of DIRECT-Net. The qualitative and quantitative results demonstrate that this newly developed DIRECT-Net is promising in suppressing noise, improving image accuracy, and reducing computation time for future DECT imaging.

physics.med-ph↗

arXiv2020

Dual-energy CT imaging from single-energy CT data with material decomposition convolutional neural network

Dual-energy computed tomography (DECT) is of great significance for clinical practice due to its huge potential to provide material-specific information. However, DECT scanners are usually more expensive than standard single-energy CT (SECT) scanners and thus are less accessible to undeveloped regions. In this paper, we show that the energy-domain correlation and anatomical consistency between standard DECT images can be harnessed by a deep learning model to provide high-performance DECT imaging from fully-sampled low-energy data together with single-view high-energy data, which can be obtained by using a scout-view high-energy image. We demonstrate the feasibility of the approach with contrast-enhanced DECT scans from 5,753 slices of images of twenty-two patients and show its superior performance on DECT applications. The deep learning-based approach could be useful to further significantly reduce the radiation dose of current premium DECT scanners and has the potential to simplify the hardware of DECT imaging systems and to enable DECT imaging using standard SECT scanners.

physics.med-ph↗