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Jie Gao

Publications and source records attributed to Jie Gao.

At least 91 records · Page 5Linked to original sources
arXiv2025

HelixDesign-Binder: A Scalable Production-Grade Platform for Binder Design Built on HelixFold3

Protein binder design is central to therapeutics, diagnostics, and synthetic biology, yet practical deployment remains challenging due to fragmented workflows, high computational costs, and complex tool integration. We present HelixDesign-Binder, a production-grade, high-throughput platform built on HelixFold3 that automates the full binder design pipeline, from backbone generation and sequence design to structural evaluation and multi-dimensional scoring. By unifying these stages into a scalable and user-friendly system, HelixDesign-Binder enables efficient exploration of binder candidates with favorable structural, energetic, and physicochemical properties. The platform leverages Baidu Cloud's high-performance infrastructure to support large-scale design and incorporates advanced scoring metrics, including ipTM, predicted binding free energy, and interface hydrophobicity. Benchmarking across six protein targets demonstrates that HelixDesign-Binder reliably produces diverse and high-quality binders, some of which match or exceed validated designs in predicted binding affinity. HelixDesign-Binder is accessible via an interactive web interface in PaddleHelix platform, supporting both academic research and industrial applications in antibody and protein binder development.

q-bio.BM↗
arXiv2025

SSRLBot: Designing and Developing a Large Language Model-based Agent using Socially Shared Regulated Learning

Large language model (LLM)--based agents have emerged as pivotal tools in assisting human experts across various fields by transforming complex tasks into more efficient workflows and providing actionable stakeholder insights. Despite their potential, the application of LLM-based agents for medical education remains underexplored. The study aims to assist in evaluating the students' process and outcomes on medical case diagnosis and discussion while incorporating the theoretical framework of Socially Shared Regulation of Learning (SSRL) to assess student performance. SSRL emphasizes metacognitive, cognitive, motivational, and emotional interactions, highlighting the collaborative management of learning processes to improve decision-making outcomes. Grounded in SSRL theory, this tool paper introduces SSRLBot, an LLM-based agent designed to enable team members to reflect on their diagnostic performance and the key SSRL skills that foster team success. SSRLBot's core functions include summarizing dialogue content, analyzing participants' SSRL skills, and evaluating students' diagnostic results. Meanwhile, we evaluated SSRLBot through diagnostic conversation data collected from six groups (12 participants, 1926 conversational turns). Results showed that SSRLBot can deliver detailed, theory-aligned evaluations, link specific behaviors to SSRL dimensions, and offer actionable recommendations for improving teamwork. The findings address a critical gap in medical education, advancing the application of LLM agents to enhance team-based decision-making and collaboration in high-stakes environments.

cs.HC↗
arXiv2025

BEPCII and CEPC

In this paper BEPC, BEPCII and BEPCII-U have been briefly reviewed, which lay a good foundation of CEPC as a Higgs factory. BEPCII reached the designed luminos-ity goal of 10^33cm^-2s^-1 @1.89GeV on April 5, 2016. As an upgrade program of BEPCII, BEPCII-U has been com-pleted and started commissioning in March of 2025 with the luminosity goal as 3.7*10^32cm^-2s^-1 @2.8GeV. CEPC as Higgs factory has been reviewed on Engineering De-sign Report (EDR) status and plan for construction proposal to Chinese government in 2025.

physics.acc-ph↗
arXiv2025

On the Price of Differential Privacy for Hierarchical Clustering

Hierarchical clustering is a fundamental unsupervised machine learning task with the aim of organizing data into a hierarchy of clusters. Many applications of hierarchical clustering involve sensitive user information, therefore motivating recent studies on differentially private hierarchical clustering under the rigorous framework of Dasgupta's objective. However, it has been shown that any privacy-preserving algorithm under edge-level differential privacy necessarily suffers a large error. To capture practical applications of this problem, we focus on the weight privacy model, where each edge of the input graph is at least unit weight. We present a novel algorithm in the weight privacy model that shows significantly better approximation than known impossibility results in the edge-level DP setting. In particular, our algorithm achieves $O(\log^{1.5}n/\varepsilon)$ multiplicative error for $\varepsilon$-DP and runs in polynomial time, where $n$ is the size of the input graph, and the cost is never worse than the optimal additive error in existing work. We complement our algorithm by showing if the unit-weight constraint does not apply, the lower bound for weight-level DP hierarchical clustering is essentially the same as the edge-level DP, i.e. $Ω(n^2/\varepsilon)$ additive error. As a result, we also obtain a new lower bound of $\tildeΩ(1/\varepsilon)$ additive error for balanced sparsest cuts in the weight-level DP model, which may be of independent interest. Finally, we evaluate our algorithm on synthetic and real-world datasets. Our experimental results show that our algorithm performs well in terms of extra cost and has good scalability to large graphs.

cs.DS↗
arXiv2025

HALHF: a hybrid, asymmetric, linear Higgs factory using plasma- and RF-based acceleration

HALHF is a hybrid linear collider that uses electron-driven plasma-wakefield acceleration to accelerate electrons to high energy while using radio-frequency cavity technology to accelerate positrons. The most cost-effective solution collides low-energy positrons with high-energy electrons, producing a boost to the final state in the electron direction with $γ= 1.67$. The current HALHF baseline design produces a luminosity comparable to that of the baseline ILC but with a greatly reduced construction and carbon footprint and hence much lower cost than the mature linear-collider designs ILC and CLIC. Costs for HALHF are evaluated, together with that for the approximate 15-year R\&D programme necessary to realise HALHF. Time scales and cost for the R\&D are estimated. Upgrade paths for HALHF technology from a 250~GeV Higgs factory, through 380 and 550~GeV, up to 10~TeV are sketched.

physics.acc-ph↗
arXiv2025

Timing the Match: A Deep Reinforcement Learning Approach for Ride-Hailing and Ride-Pooling Services

Efficient timing in ride-matching is crucial for improving the performance of ride-hailing and ride-pooling services, as it determines the number of drivers and passengers considered in each matching process. Traditional batched matching methods often use fixed time intervals to accumulate ride requests before assigning matches. While this approach increases the number of available drivers and passengers for matching, it fails to adapt to real-time supply-demand fluctuations, often leading to longer passenger wait times and driver idle periods. To address this limitation, we propose an adaptive ride-matching strategy using deep reinforcement learning (RL) to dynamically determine when to perform matches based on real-time system conditions. Unlike fixed-interval approaches, our method continuously evaluates system states and executes matching at moments that minimize total passenger wait time. Additionally, we incorporate a potential-based reward shaping (PBRS) mechanism to mitigate sparse rewards, accelerating RL training and improving decision quality. Extensive empirical evaluations using a realistic simulator trained on real-world data demonstrate that our approach outperforms fixed-interval matching strategies, significantly reducing passenger waiting times and detour delays, thereby enhancing the overall efficiency of ride-hailing and ride-pooling systems.

cs.LG↗
arXiv2025

Minute-cadence observations on Galactic plane with Wide Field Survey Telescope (WFST): Overview, methodology and early results

As the time-domain survey telescope of the highest survey power in the northern hemisphere currently, Wide Field Survey Telescope (WFST) is scheduled to hourly/daily/semi-weekly scan northern sky up to ~23 mag in four optical (ugri) bands. Unlike the observation cadences in the forthcoming regular survey missions, WFST performed "staring" observations toward Galactic plane in a cadence of $\approx$1 minute for a total on-source time of about 13 hours, during the commissioning and pilot observation phases. Such an observation cadence is well applied in producing densely sampling light curves and hunting for stars exhibiting fast stellar variabilities. Here we introduce the primary methodologies in detecting variability, periodicity, and stellar flares among a half million sources from the minute-cadence observations, and present the WFST g-/r-band light curves generated from periodic variable stars and flaring stars. Benefit from high photometric precisions and deep detection limits of WFST, the observations have captured several rare variable stars, such as a variable hot white dwarf (WD) and an ellipsoidal WD binary candidate. By surveying the almost unexplored parameter spaces for variables, WFST will lead to new opportunities in discovering unique variable stars in the northern sky.

astro-ph.SR↗
arXiv2025

User-centric Immersive Communications in 6G: A Data-oriented Framework via Digital Twin

In this article, we present a novel user-centric service provision for immersive communications (IC) in 6G to deal with the uncertainty of individual user behaviors while satisfying unique requirements on the quality of multi-sensory experience. To this end, we propose a data-oriented framework for network resource management, featuring personalized data management that can support network modeling tailored to different user demands. Our framework leverages the digital twin (DT) technique as a key enabler. Particularly, a DT is established for each user, and the data attributes in the DT are customized based on the characteristics of the user. The DT functions, corresponding to various data operations, are customized in the development, evaluation, and update of network models to meet unique user demands. A trace-driven case study demonstrates the effectiveness of our framework in achieving user-centric IC and the significance of personalized data management in 6G.

cs.NI↗
arXiv2025

Label-free Prediction of Vascular Connectivity in Perfused Microvascular Networks in vitro

Continuous monitoring and in-situ assessment of microvascular connectivity have significant implications for culturing vascularized organoids and optimizing the therapeutic strategies. However, commonly used methods for vascular connectivity assessment heavily rely on fluorescent labels that may either raise biocompatibility concerns or interrupt the normal cell growth process. To address this issue, a Vessel Connectivity Network (VC-Net) was developed for label-free assessment of vascular connectivity. To validate the VC-Net, microvascular networks (MVNs) were cultured in vitro and their microscopic images were acquired at different culturing conditions as a training dataset. The VC-Net employs a Vessel Queue Contrastive Learning (VQCL) method and a class imbalance algorithm to address the issues of limited sample size, indistinctive class features and imbalanced class distribution in the dataset. The VC-Net successfully evaluated the vascular connectivity with no significant deviation from that by fluorescence imaging. In addition, the proposed VC-Net successfully differentiated the connectivity characteristics between normal and tumor-related MVNs. In comparison with those cultured in the regular microenvironment, the averaged connectivity of MVNs cultured in the tumor-related microenvironment decreased by 30.8%, whereas the non-connected area increased by 37.3%. This study provides a new avenue for label-free and continuous assessment of organoid or tumor vascularization in vitro.

eess.IV↗
arXiv2025

Maximizing Truth Learning in a Social Network is NP-hard

Sequential learning models situations where agents predict a ground truth in sequence, by using their private, noisy measurements, and the predictions of agents who came earlier in the sequence. We study sequential learning in a social network, where agents only see the actions of the previous agents in their own neighborhood. The fraction of agents who predict the ground truth correctly depends heavily on both the network topology and the ordering in which the predictions are made. A natural question is to find an ordering, with a given network, to maximize the (expected) number of agents who predict the ground truth correctly. In this paper, we show that it is in fact NP-hard to answer this question for a general network, with both the Bayesian learning model and a simple majority rule model. Finally, we show that even approximating the answer is hard.

cs.SI↗
arXiv2024

Neuc-MDS: Non-Euclidean Multidimensional Scaling Through Bilinear Forms

We introduce Non-Euclidean-MDS (Neuc-MDS), an extension of classical Multidimensional Scaling (MDS) that accommodates non-Euclidean and non-metric inputs. The main idea is to generalize the standard inner product to symmetric bilinear forms to utilize the negative eigenvalues of dissimilarity Gram matrices. Neuc-MDS efficiently optimizes the choice of (both positive and negative) eigenvalues of the dissimilarity Gram matrix to reduce STRESS, the sum of squared pairwise error. We provide an in-depth error analysis and proofs of the optimality in minimizing lower bounds of STRESS. We demonstrate Neuc-MDS's ability to address limitations of classical MDS raised by prior research, and test it on various synthetic and real-world datasets in comparison with both linear and non-linear dimension reduction methods.

cs.LG↗
arXiv2024

Focusing Image Generation to Mitigate Spurious Correlations

Instance features in images exhibit spurious correlations with background features, affecting the training process of deep neural classifiers. This leads to insufficient attention to instance features by the classifier, resulting in erroneous classification outcomes. In this paper, we propose a data augmentation method called Spurious Correlations Guided Synthesis (SCGS) that mitigates spurious correlations through image generation model. This approach does not require expensive spurious attribute (group) labels for the training data and can be widely applied to other debiasing methods. Specifically, SCGS first identifies the incorrect attention regions of a pre-trained classifier on the training images, and then uses an image generation model to generate new training data based on these incorrect attended regions. SCGS increases the diversity and scale of the dataset to reduce the impact of spurious correlations on classifiers. Changes in the classifier's attention regions and experimental results on three different domain datasets demonstrate that this method is effective in reducing the classifier's reliance on spurious correlations.

cs.CV↗
arXiv2024

Technical Report of HelixFold3 for Biomolecular Structure Prediction

The AlphaFold series has transformed protein structure prediction with remarkable accuracy, often matching experimental methods. AlphaFold2, AlphaFold-Multimer, and the latest AlphaFold3 represent significant strides in predicting single protein chains, protein complexes, and biomolecular structures. While AlphaFold2 and AlphaFold-Multimer are open-sourced, facilitating rapid and reliable predictions, AlphaFold3 remains partially accessible through a limited online server and has not been open-sourced, restricting further development. To address these challenges, the PaddleHelix team is developing HelixFold3, aiming to replicate AlphaFold3's capabilities. Leveraging insights from previous models and extensive datasets, HelixFold3 achieves accuracy comparable to AlphaFold3 in predicting the structures of the conventional ligands, nucleic acids, and proteins. The initial release of HelixFold3 is available as open source on GitHub for academic research, promising to advance biomolecular research and accelerate discoveries. The latest version will be continuously updated on the HelixFold3 web server, providing both interactive visualization and API access.

q-bio.BM↗
arXiv2024

BearLLM: A Prior Knowledge-Enhanced Bearing Health Management Framework with Unified Vibration Signal Representation

We propose a bearing health management framework leveraging large language models (BearLLM), a novel multimodal model that unifies multiple bearing-related tasks by processing user prompts and vibration signals. Specifically, we introduce a prior knowledge-enhanced unified vibration signal representation to handle various working conditions across multiple datasets. This involves adaptively sampling the vibration signals based on the sampling rate of the sensor, incorporating the frequency domain to unify input dimensions, and using a fault-free reference signal as an auxiliary input. To extract features from vibration signals, we first train a fault classification network, then convert and align the extracted features into word embedding, and finally concatenate these with text embedding as input to an LLM. To evaluate the performance of the proposed method, we constructed the first large-scale multimodal bearing health management (MBHM) dataset, including paired vibration signals and textual descriptions. With our unified vibration signal representation, BearLLM using one set of pre-trained weights achieves state-of-the-art performance on nine publicly available fault diagnosis benchmarks, outperforming specific methods designed for individual datasets. We provide a dataset, our model, and code to inspire future research on building more capable industrial multimodal models https://github.com/SIA-IDE/BearLLM.

cs.AI↗
arXiv2024

Precise Antigen-Antibody Structure Predictions Enhance Antibody Development with HelixFold-Multimer

The accurate prediction of antigen-antibody structures is essential for advancing immunology and therapeutic development, as it helps elucidate molecular interactions that underlie immune responses. Despite recent progress with deep learning models like AlphaFold and RoseTTAFold, accurately modeling antigen-antibody complexes remains a challenge due to their unique evolutionary characteristics. HelixFold-Multimer, a specialized model developed for this purpose, builds on the framework of AlphaFold-Multimer and demonstrates improved precision for antigen-antibody structures. HelixFold-Multimer not only surpasses other models in accuracy but also provides essential insights into antibody development, enabling more precise identification of binding sites, improved interaction prediction, and enhanced design of therapeutic antibodies. These advances underscore HelixFold-Multimer's potential in supporting antibody research and therapeutic innovation.

q-bio.BM↗
arXiv2024

PAC Privacy Preserving Diffusion Models

Data privacy protection is garnering increased attention among researchers. Diffusion models (DMs), particularly with strict differential privacy, can potentially produce images with both high privacy and visual quality. However, challenges arise such as in ensuring robust protection in privatizing specific data attributes, areas where current models often fall short. To address these challenges, we introduce the PAC Privacy Preserving Diffusion Model, a model leverages diffusion principles and ensure Probably Approximately Correct (PAC) privacy. We enhance privacy protection by integrating a private classifier guidance into the Langevin Sampling Process. Additionally, recognizing the gap in measuring the privacy of models, we have developed a novel metric to gauge privacy levels. Our model, assessed with this new metric and supported by Gaussian matrix computations for the PAC bound, has shown superior performance in privacy protection over existing leading private generative models according to benchmark tests.

cs.LG↗
arXiv2024

CP-UNet: Contour-based Probabilistic Model for Medical Ultrasound Images Segmentation

Deep learning-based segmentation methods are widely utilized for detecting lesions in ultrasound images. Throughout the imaging procedure, the attenuation and scattering of ultrasound waves cause contour blurring and the formation of artifacts, limiting the clarity of the acquired ultrasound images. To overcome this challenge, we propose a contour-based probabilistic segmentation model CP-UNet, which guides the segmentation network to enhance its focus on contour during decoding. We design a novel down-sampling module to enable the contour probability distribution modeling and encoding stages to acquire global-local features. Furthermore, the Gaussian Mixture Model utilizes optimized features to model the contour distribution, capturing the uncertainty of lesion boundaries. Extensive experiments with several state-of-the-art deep learning segmentation methods on three ultrasound image datasets show that our method performs better on breast and thyroid lesions segmentation.

eess.IV↗