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Shikai Jin

dblp:185/0655 · DBLP profile ↗
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4ranked-venue papers
0as first author
3since 2021 · last 2026
0000-0001-9525-4166ORCID · corroborated

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 2 · 1 since 2021Computer networks · 1 · 1 since 2021Graphics, computer vision, multimedia, augmented reality and games · 1 · 1 since 2021Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Artificial intelligence
1 paper
Representation and self-supervised learning · 87% Generative modeling · 13%
Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 4 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Machine learning › Representation and self-supervised learning › transferable representation › transferable representation learning
cross-domain representation learning
0.912025
Learning Cross-Domain Representations for Transferable Drug Perturbations on Single-Cell Transcriptional Responses · AAAI 2025
Machine learning › Representation and self-supervised learning
feature decoupling
0.912025
Learning Cross-Domain Representations for Transferable Drug Perturbations on Single-Cell Transcriptional Responses · AAAI 2025
Bioinformatics and computational biology › drug discovery
computational drug discovery
0.912025
Learning Cross-Domain Representations for Transferable Drug Perturbations on Single-Cell Transcriptional Responses · AAAI 2025
Machine learning › Generative modeling
variational autoencoder
0.312025
Learning Cross-Domain Representations for Transferable Drug Perturbations on Single-Cell Transcriptional Responses · AAAI 2025

Methods — techniques the papers use, named apart from their topics

shared decoder · 1.7domain separation encoders · 1.7cross-transfer constraint · 1.7
YearPublicationVenuePosition
2026 Pedestrian and Router Colocalization Framework Using Distributed-IMU-Based VDR and Wi-Fi RTT
abstract
Inertial navigation and WiFi are two common approaches for pedestrian localization. However, conventional pedestrian dead reckoning (PDR) and WiFi fingerprinting suffer from limited adaptability to different users and poor robustness to environmental changes, respectively. Recent deep-learning-based methods address pedestrian localization by modeling sequential dependencies in inertial data, but they typically rely on a single inertial measurement unit (IMU), which is insufficient to capture the spatial correlations of human skeletal motion. In parallel, the Fine Time Measurement (FTM) procedure in IEEE 802.11mc enables round-trip time (RTT)–based ranging and localization, yet the coordinates of WiFi routers still require labor-intensive prior surveying, limiting deployment flexibility. This paper presents a pedestrian and router colocalization framework that jointly estimates pedestrian trajectories and WiFi router positions. The proposed framework employs multiple body-worn IMUs and a long short-term memory (LSTM) network to learn both spatial and temporal dependencies in human motion, thereby enabling velocity dead reckoning (VDR). The VDR-estimated pedestrian velocity is then fused with WiFi RTT measurements through factor graph optimization (FGO), in which both pedestrian and router coordinates are treated as unknown variables. Experimental results demonstrate that the multi-IMU-based VDR effectively models pedestrian velocity, while WiFi RTT ranging constrains the long-term drift of VDR. The combined VDR/WiFi RTT framework achieves meter-level positioning accuracy in both indoor and outdoor environments, without requiring pre-surveyed router coordinates, and thus provides a promising solution for pedestrian localization in the Internet of Things (IoT) era.
Mingxi Wang, Fuqiang Gu, Liang Chen 0007, Ruizhi Chen, Shikai Jin
IEEE Internet Things J.8
2025 Learning Cross-Domain Representations for Transferable Drug Perturbations on Single-Cell Transcriptional Responses
abstract
Phenotypic drug discovery has attracted widespread attention because of its potential to identify bioactive molecules. Transcriptomic profiling provides a comprehensive reflection of phenotypic changes in cellular responses to external perturbations. In this paper, we propose XTransferCDR, a novel generative framework designed for feature decoupling and transferable representation learning across domains. Given a pair of perturbed expression profiles, our approach decouples the perturbation representations from basal states through domain separation encoders and then cross-transfers them in the latent space. The transferred representations are then used to reconstruct the corresponding perturbed expression profiles via a shared decoder. This cross-transfer constraint effectively promotes the learning of transferable drug perturbation representations. We conducted extensive evaluations of our model on multiple datasets, including single-cell transcriptional responses to drugs and single- and combinatorial genetic perturbations. The experimental results show that XTransferCDR achieved better performance than current state-of-the-art methods, showcasing its potential to advance phenotypic drug discovery.
Hui Liu 0026, Shikai Jin
AAAI2
2021 OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations
abstract
We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM's Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM's Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen's early Nobel prize winning experiments by using OpenMM's Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.
Carlos Bueno, Nicholas P. Schafer, Joshua Moller, Shikai Jin, Mingchen Chen, Aram Davtyan, Juan de Pablo, Peter G. Wolynes
PLoS Comput. Biol.5
2017 Risk Assessment and Online Forewarning of Oil & Gas Storage and Transportation Facilities Based on Data Mining
abstract
In this paper, we focus on oil & gas storage and transportations facilities (OSTF), and research on the risk assessment and the hysteretic nature of contingency plans. First, with principal component analysis to select forewarning indicators, we structure a risk assessment model based on logistic regression, and the model has strong robustness. What’s more, we link multidimensional data with different contingency plans by K-means Cluster Analysis. In conclusion, we realize the accuracy of assessment of OSTF from the view of data mining, and come up with a new management mode including “Big data monitoring---Intelligent assessment---Automatically forewarning---The advance of emergency measures” with the help of MIS to realize the timeliness of contingency management.
Tianteng Wang, Yingzhi Xia, Zexi Zhang, Shikai Jin
KES5