arXiv subjects

Qian Shi

Publications and source records attributed to Qian Shi.

At least 19 recordsLinked to original sources

arXiv2026

Systematic Literature Reviews With Two Multi-Agentic Systems And Human-In-The-Loop

Systematic literature review of clinical trials drives regulatory decision-making, but conventional screening and extraction are time-consuming, labor-intensive, and vulnerable to study selection bias. We propose two fit-to-purpose multi-agentic systems (MAS) for systematic literature review, with human-in-the-loop. The screening MAS uses multiple LLM agents with heterogeneous personas and multiround cross-review, and uniformly improves accuracy over a single-LLM baseline. The extraction MAS combines standardization, an iterative correction loop, and retrieval-based context control to ensure accuracy and scalability. Both MAS are specifically designed to support Human-In-The-Loop which is essential for clinical decisions. The novelty of the proposed approach lies in the system architecture rather than in any single foundation tools: the system can naturally benefit from future improvements in the underlying tools, for instance, stronger LLM agents, retrieval engines, image recognition methods, etc. As a real-world application, a published network meta-analysis is reproduced by the MAS. The result recovers all trials from the original study and identifies additional eligible trials missed by manual review, leading to updated clinical conclusions.

stat.AP↗

arXiv2026

EvoEGF-Mol: Evolving Exponential Geodesic Flow for Structure-based Drug Design

Structure-Based Drug Design (SBDD) aims to discover bioactive ligands. Conventional approaches construct probability paths separately in Euclidean and probabilistic spaces for continuous atomic coordinates and discrete chemical categories, leading to a mismatch with the underlying statistical manifolds. We address this issue by representing molecules using composite exponential-family distributions, where coordinates and categories are represented within a unified natural parameter space to evolve synchronously along exponential geodesics under the Fisher-Rao metric. To avoid the instantaneous trajectory collapse induced by geodesics directly targeting Dirac distributions, we propose Evolving Exponential Geodesic Flow for SBDD (EvoEGF-Mol), which replaces static Dirac targets with dynamically concentrating distributions and is trained with a progressive-parameter-refinement architecture. Our model approaches a reference-level PoseBusters passing rate (93.4%) on CrossDock, demonstrating remarkable geometric precision and interaction fidelity, while achieving superior performance over baseline methods on real-world MolGenBench tasks for bioactive scaffold recovery. Code is available at https://github.com/BLEACH366/EvoEGF-Mol.

cs.LG↗

arXiv2025

Single-cell identification with quantum-enhanced nuclear magnetic resonance

Identification of individual cells within heterogeneous populations is essential for biomedical research and clinical diagnostics. Conventional labeling-based sorting methods, such as fluorescence-activated cell sorting and magnetic-activated cell sorting, enable precise sorting when reliable markers are available. However, their applicability is limited in cells lacking defined markers or sensitive to labeling, as labeling can compromise cellular viability and function. We present a single-cell identification approach using quantum-enhanced NMR with diamond nitrogen-vacancy centers for label-free detection of intracellular proton ($^1$H) signals. Using this method, we distinguish two human tumor cell lines by their proton spin-lattice ($T_1$) relaxation times, which serve as a cell-intrinsic physicochemical signature. It lays the groundwork for label-free sorting applications in rare cell analysis, personalized medicine, and single-cell diagnostics.

quant-ph↗

arXiv2025

SynthIPD: training-free synthetic individual patient data generation

Individual patient data (IPD) are essential for statistical inference in clinical research. However, privacy concerns, high data-sharing costs, and restrictive access often make IPD unavailable. Conventional synthetic data generation usually relies on black box models such as generative adversial networks. These methods, however, requires a large piece of IPD for model training, may be ungeneralizable and lacks interpretability. This paper introduces an assumption-lean, three-step methodology for generating synthetic IPD with survival endpoints only based on published clinical trial articles. The method mainly leverages Kaplan-Meier (KM) curves with at-risk/censoring information and subgroup-level summary statistics. It digitizes the KM curve using Scalable Vector Graphics (SVG) beyond pixel accuracy and then generates synthetic covariates based on the statistics. We illustrate the method's potential through $2$ detailed case studies and simulation studies. The method offers important implications, enabling high-fidelity IPD generation to support evidence-based medical decisions.

stat.AP↗

arXiv2025

MolPIF: A Parameter Interpolation Flow Model for Molecule Generation

Motivation: Structure-based drug design (SBDD) has advanced with deep generative models, but bridging the gap between continuous atomic coordinates and discrete atom types remains a challenge. Current approaches, such as diffusion and flow matching models, often fail to unify these heterogeneous modalities, relying on separate strategies or ill-fitting Euclidean metrics for discrete variables. This lack of a consistent framework limits generative models' ability to capture the geometric and chemical structure of protein-ligand complexes. Results: We present MolPIF, a parameter interpolation flow mechanism designed to unify the generation of continuous and discrete molecular variables. Unlike traditional flow models that operate in sample space, MolPIF interpolates between distributions in the parameter space, theoretically recovering Wasserstein-2 optimal transport for continuous coordinates and establishing Fisher-Rao geodesics for discrete atom types. We further incorporate a geometry-enhanced learning strategy to improve the capture of atomic contexts. Extensive evaluations on the CrossDocked2020 dataset demonstrate that MolPIF outperforms baselines in binding affinity, chemical validity, geometric fidelity and chemical space coverage. Additionally, MolPIF exhibits versatility in lead optimization and offers flexible prior distribution selection (such as Laplace), establishing a robust paradigm for SBDD. Availability: Source code is freely available at https://github.com/BLEACH366/MolPIF. Supplementary information: Supplementary data are available at Bioinformatics.

cs.LG↗

arXiv2025

Reconstruction of Antarctic sea ice thickness from sparse satellite laser altimetry data using a partial convolutional neural network

The persistent lack of spatially complete Antarctic sea ice thickness (SIT) data at sub-monthly resolution has fundamentally constrained the quantitative understanding of large-scale sea ice mass balance processes. In this study, a pan-Antarctic SIT dataset at 5-day and 12.5 km resolution was developed based on sparse Ice, Cloud and Land Elevation Satellite (ICESat: 2003-2009) and ICESat-2 (2018-2024) along-track laser altimetry SIT retrievals using a deep learning approach. The reconstructed SIT was quantitatively validated against independent upward-looking sonar (ULS) observations and showed higher accuracy than the other four satellite-derived and reanalyzed Antarctic SIT datasets. The temporal evolution of the reconstructed SIT was further validated by ULS and ICESat-2 observations. Consistent seasonal cycles and intra-seasonal tendencies across these datasets confirm the reconstruction's reliability. Beyond advancing the mechanistic understanding of Antarctic sea ice variability and climate linkages, this reconstruction dataset's near-real-time updating capability offers operational value for monitoring and forecasting the Antarctic sea ice state.

physics.geo-ph↗

arXiv2024

P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching

Biological processes, functions, and properties are intricately linked to the ensemble of protein conformations, rather than being solely determined by a single stable conformation. In this study, we have developed P2DFlow, a generative model based on SE(3) flow matching, to predict the structural ensembles of proteins. We specifically designed a valuable prior for the flow process and enhanced the model's ability to distinguish each intermediate state by incorporating an additional dimension to describe the ensemble data, which can reflect the physical laws governing the distribution of ensembles, so that the prior knowledge can effectively guide the generation process. When trained and evaluated on the MD datasets of ATLAS, P2DFlow outperforms other baseline models on extensive experiments, successfully capturing the observable dynamic fluctuations as evidenced in crystal structure and MD simulations. As a potential proxy agent for protein molecular simulation, the high-quality ensembles generated by P2DFlow could significantly aid in understanding protein functions across various scenarios. Code is available at https://github.com/BLEACH366/P2DFlow

physics.bio-ph↗

arXiv2023

Restricted Mean Survival Time Estimation Using Bayesian Nonparametric Dependent Mixture Models

Restricted mean survival time (RMST) is an intuitive summary statistic for time-to-event random variables, and can be used for measuring treatment effects. Compared to hazard ratio, its estimation procedure is robust against the non-proportional hazards assumption. We propose nonparametric Bayeisan (BNP) estimators for RMST using a dependent stick-breaking process prior mixture model that adjusts for mixed-type covariates. The proposed Bayesian estimators can yield both group-level causal estimate and subject-level predictions. Besides, we propose a novel dependent stick-breaking process prior that on average results in narrower credible intervals while maintaining similar coverage probability compared to a dependent probit stick-breaking process prior. We conduct simulation studies to investigate the performance of the proposed BNP RMST estimators compared to existing frequentist approaches and under different Bayesian modeling choices. The proposed framework is applied to estimate the treatment effect of an immuno therapy among KRAS wild-type colorectal cancer patients.

stat.ME↗

arXiv2022

Temperature-dependent behaviors of single spin defects in solids determined with Hz-level precision

Revealing the properties of single spin defects in solids is essential for quantum applications based on solid-state systems. However, it is intractable to investigate the temperature-dependent properties of single defects, due to the low precision for single-defect measurements in contrast to defect ensembles. Here we report that the temperature dependence of the Hamiltonian parameters for single negatively charged nitrogen-vacancy (NV$^{-}$) centers in diamond is precisely measured, and the results find a reasonable agreement with first-principles calculations. Particularly, the hyperfine interactions with randomly distributed $^{13}$C nuclear spins are clearly observed to vary with temperature, and the relevant coefficients are measured with Hz-level precision. The temperature-dependent behaviors are attributed to both thermal expansion and lattice vibrations by first-principles calculations. Our results pave the way for taking nuclear spins as more stable thermometers at nanoscale. The methods developed here for high-precision measurements and first-principles calculations can be further extended to other solid-state spin defects.

quant-ph↗

arXiv2022

Electronically phase separated nano-network in antiferromagnetic insulating LaMnO3/PrMnO3/CaMnO3 tricolor superlattice

Strongly correlated materials often exhibit an electronic phase separation (EPS) phenomena whose domain pattern is random in nature. The ability to control the spatial arrangement of the electronic phases at microscopic scales is highly desirable for tailoring their macroscopic properties and/or designing novel electronic devices. Here we report the formation of EPS nanoscale network in a mono-atomically stacked LaMnO3/CaMnO3/PrMnO3 superlattice grown on SrTiO3 (STO) (001) substrate, which is known to have an antiferromagnetic (AFM) insulating ground state. The EPS nano-network is a consequence of an internal strain relaxation triggered by the structural domain formation of the underlying STO substrate at low temperatures. The same nanoscale network pattern can be reproduced upon temperature cycling allowing us to employ different local imaging techniques to directly compare the magnetic and transport state of a single EPS domain. Our results confirm the one-to-one correspondence between ferromagnetic (AFM) to metallic (insulating) state in manganite. It also represents a significant step in a paradigm shift from passively characterizing EPS in strongly correlated systems to actively engaging in its manipulation.

cond-mat.str-el↗

arXiv2021

Improving Global Forest Mapping by Semi-automatic Sample Labeling with Deep Learning on Google Earth Images

Global forest cover is critical to the provision of certain ecosystem services. With the advent of the google earth engine cloud platform, fine resolution global land cover mapping task could be accomplished in a matter of days instead of years. The amount of global forest cover (GFC) products has been steadily increasing in the last decades. However, it's hard for users to select suitable one due to great differences between these products, and the accuracy of these GFC products has not been verified on global scale. To provide guidelines for users and producers, it is urgent to produce a validation sample set at the global level. However, this labeling task is time and labor consuming, which has been the main obstacle to the progress of global land cover mapping. In this research, a labor-efficient semi-automatic framework is introduced to build a biggest ever Forest Sample Set (FSS) contained 395280 scattered samples categorized as forest, shrubland, grassland, impervious surface, etc. On the other hand, to provide guidelines for the users, we comprehensively validated the local and global mapping accuracy of all existing 30m GFC products, and analyzed and mapped the agreement of them. Moreover, to provide guidelines for the producers, optimal sampling strategy was proposed to improve the global forest classification. Furthermore, a new global forest cover named GlobeForest2020 has been generated, which proved to improve the previous highest state-of-the-art accuracies (obtained by Gong et al., 2017) by 2.77% in uncertain grids and by 1.11% in certain grids.

cs.CV↗

arXiv2021

Super-resolution-based Change Detection Network with Stacked Attention Module for Images with Different Resolutions

Change detection, which aims to distinguish surface changes based on bi-temporal images, plays a vital role in ecological protection and urban planning. Since high resolution (HR) images cannot be typically acquired continuously over time, bi-temporal images with different resolutions are often adopted for change detection in practical applications. Traditional subpixel-based methods for change detection using images with different resolutions may lead to substantial error accumulation when HR images are employed; this is because of intraclass heterogeneity and interclass similarity. Therefore, it is necessary to develop a novel method for change detection using images with different resolutions, that is more suitable for HR images. To this end, we propose a super-resolution-based change detection network (SRCDNet) with a stacked attention module. The SRCDNet employs a super resolution (SR) module containing a generator and a discriminator to directly learn SR images through adversarial learning and overcome the resolution difference between bi-temporal images. To enhance the useful information in multi-scale features, a stacked attention module consisting of five convolutional block attention modules (CBAMs) is integrated to the feature extractor. The final change map is obtained through a metric learning-based change decision module, wherein a distance map between bi-temporal features is calculated. The experimental results demonstrate the superiority of the proposed method, which not only outperforms all baselines -with the highest F1 scores of 87.40% on the building change detection dataset and 92.94% on the change detection dataset -but also obtains the best accuracies on experiments performed with images having a 4x and 8x resolution difference. The source code of SRCDNet will be available at https://github.com/liumency/SRCDNet.

eess.IV↗

arXiv2021

EC-SAGINs: Edge Computing-enhanced Space-Air-Ground Integrated Networks for Internet of Vehicles

Edge computing-enhanced Internet of Vehicles (EC-IoV) enables ubiquitous data processing and content sharing among vehicles and terrestrial edge computing (TEC) infrastructures (e.g., 5G base stations and roadside units) with little or no human intervention, plays a key role in the intelligent transportation systems. However, EC-IoV is heavily dependent on the connections and interactions between vehicles and TEC infrastructures, thus will break down in some remote areas where TEC infrastructures are unavailable (e.g., desert, isolated islands and disaster-stricken areas). Driven by the ubiquitous connections and global-area coverage, space-air-ground integrated networks (SAGINs) efficiently support seamless coverage and efficient resource management, represent the next frontier for edge computing. In light of this, we first review the state-of-the-art edge computing research for SAGINs in this article. After discussing several existing orbital and aerial edge computing architectures, we propose a framework of edge computing-enabled space-air-ground integrated networks (EC-SAGINs) to support various IoV services for the vehicles in remote areas. The main objective of the framework is to minimize the task completion time and satellite resource usage. To this end, a pre-classification scheme is presented to reduce the size of action space, and a deep imitation learning (DIL) driven offloading and caching algorithm is proposed to achieve real-time decision making. Simulation results show the effectiveness of our proposed scheme. At last, we also discuss some technology challenges and future directions.

cs.NI↗

arXiv2020

Few-Shot Hyperspectral Image Classification With Unknown Classes Using Multitask Deep Learning

Current hyperspectral image classification assumes that a predefined classification system is closed and complete, and there are no unknown or novel classes in the unseen data. However, this assumption may be too strict for the real world. Often, novel classes are overlooked when the classification system is constructed. The closed nature forces a model to assign a label given a new sample and may lead to overestimation of known land covers (e.g., crop area). To tackle this issue, we propose a multitask deep learning method that simultaneously conducts classification and reconstruction in the open world (named MDL4OW) where unknown classes may exist. The reconstructed data are compared with the original data; those failing to be reconstructed are considered unknown, based on the assumption that they are not well represented in the latent features due to the lack of labels. A threshold needs to be defined to separate the unknown and known classes; we propose two strategies based on the extreme value theory for few-shot and many-shot scenarios. The proposed method was tested on real-world hyperspectral images; state-of-the-art results were achieved, e.g., improving the overall accuracy by 4.94% for the Salinas data. By considering the existence of unknown classes in the open world, our method achieved more accurate hyperspectral image classification, especially under the few-shot context.

cs.CV↗

arXiv2020

Active Ensemble Deep Learning for Polarimetric Synthetic Aperture Radar Image Classification

Although deep learning has achieved great success in image classification tasks, its performance is subject to the quantity and quality of training samples. For classification of polarimetric synthetic aperture radar (PolSAR) images, it is nearly impossible to annotate the images from visual interpretation. Therefore, it is urgent for remote sensing scientists to develop new techniques for PolSAR image classification under the condition of very few training samples. In this letter, we take the advantage of active learning and propose active ensemble deep learning (AEDL) for PolSAR image classification. We first show that only 35\% of the predicted labels of a deep learning model's snapshots near its convergence were exactly the same. The disagreement between snapshots is non-negligible. From the perspective of multiview learning, the snapshots together serve as a good committee to evaluate the importance of unlabeled instances. Using the snapshots committee to give out the informativeness of unlabeled data, the proposed AEDL achieved better performance on two real PolSAR images compared with standard active learning strategies. It achieved the same classification accuracy with only 86% and 55% of the training samples compared with breaking ties active learning and random selection for the Flevoland dataset.

cs.CV↗

arXiv2020

Diverse electronic and magnetic properties of CrS2 enabling novel strain-controlled 2D lateral heterostructure spintronic devices

Lateral heterostructures of two-dimensional (2D) materials, integrating different phases or materials into a single piece of nanosheet, have attracted intensive research interests in the past few years for high-performance electronic and optoelectronic devices. It also holds promises to significantly improve the performance and enable new functions of spintronic devices. It is imperative to have a 2D material possessing diverse electronic and magnetic properties that are required in spintronics. In this work, using density functional theory calculations, we surveyed all IV, V and VI group transition metal dichalcogenides (TMDs) and discovered that CrS2 has the most diverse electronic and magnetic properties: antiferromagnetic (AFM) metallic 1T phase, nonmagnetic (NM) semiconductor 2H phase, and ferromagnetic (FM) semiconductor 1T_prime phase with a Curie temperature of ~1000 K. More interestingly, we found that a tensile or compressive strain could turn 1T_prime phase into a spin-up or spin-down half metal. Such a unique feature enables designing strain-controlled spintronic devices using a single piece of CrS2 crystal with improved energy efficiency, which remains a challenge in miniaturization of spintronic devices. In-depth analysis attributed the unique strain tunability to the interplay between strain-induced lattice deformation and different spatial orientation of the spin-up/spin-down electronic orbitals. A prototypical design of a simple spin-valve logic device operated by strain is also presented.

cond-mat.mtrl-sci↗

arXiv2019

Multitask Deep Learning with Spectral Knowledge for Hyperspectral Image Classification

In this letter, we propose a multitask deep learning method for classification of multiple hyperspectral data in a single training. Deep learning models have achieved promising results on hyperspectral image classification, but their performance highly rely on sufficient labeled samples, which are scarce on hyperspectral images. However, samples from multiple data sets might be sufficient to train one deep learning model, thereby improving its performance. To do so, we trained an identical feature extractor for all data, and the extracted features were fed into corresponding Softmax classifiers. Spectral knowledge was introduced to ensure that the shared features were similar across domains. Four hyperspectral data sets were used in the experiments. We achieved higher classification accuracies on three data sets (Pavia University, Pavia Center, and Indian Pines) and competitive results on the Salinas Valley data compared with the baseline. Spectral knowledge was useful to prevent the deep network from overfitting when the data shared similar spectral response. The proposed method tested on two deep CNNs successfully shows its ability to utilize samples from multiple data sets and enhance networks' performance.

cs.CV↗

arXiv2019

Modulating Peierls distortion of 1T_prime MoS2 via charge doping: a new charge density wave phase, reversible phase transition, and excellent electromechanical properties

The 1T_prime phase of transition metal dichalcogenides (TMDs) is a low symmetry charge density wave (CDW) phase, which can be regarded as a periodically distorted structure (Peierls distortion) of the high symmetry 1T phase. In this paper, using density functional theory (DFT) calculations, we report that the positive charge (hole) injection is an effective method to modulate the Peierls distortion of MoS2 1T_prime for new CDW phase and superior electromechanical properties. A new stable CDW phase is discovered at hole doping level of ~ 0.10h+/atom, named as 1Tt_prime. The hole charging and discharging can induce a reversible phase transition of MoS2 among the three phases, 1T, 1T_prime and 1Tt_prime. Such reversible phase transition leads to superior electromechanical properties including a strain output as high as -5.8% with a small hysteresis loop, multi-step super-elasticity, and multi-shape memory effect, which are valuable in active electromechanical device designs at nanoscale. In-depth analysis on the change of electronic structure under hole doping was performed to understand the new CDW phase and the observed phase transition. Using charge doping to modulate the Peierls distortion in two-dimensional materials can serve as a general concept for nano-active material designs.

cond-mat.mtrl-sci↗