arXiv subjects

Siyan Liu

Publications and source records attributed to Siyan Liu.

17 recordsLinked to original sources

arXiv2026

Semiparametric Receiver Operating Characteristic Analysis in the Presence of an Imperfect Reference Standard via a Box-Cox Density Ratio Model

Receiver operating characteristic (ROC) analysis is commonly used to evaluate the diagnostic accuracy of continuous biomarkers. In practice, the true disease status may be unavailable and only a nominal disease status provided by an imperfect reference standard is observed. Existing nonparametric methods have been developed for ROC analysis in this setting, but may suffer from reduced estimation efficiency, numerical instability, or sensitivity to the choice of biomarker scale. We propose a semiparametric method based on a Box-Cox density ratio model, which links the biomarker distributions of the truly healthy and diseased populations while leaving the baseline distribution unspecified. A key feature of the proposed method is that the transformation parameter is estimated from the data rather than specified in advance, allowing the density-ratio structure to adapt to different transformation scales. We develop an empirical likelihood approach for estimation and an expectation-maximization algorithm for computation. We establish the asymptotic distributions of estimators of the ROC curve, area under the curve, Youden's index, and the sensitivity and specificity at the Youden-optimal cutoff, and develop bootstrap confidence intervals and a goodness-of-fit test. Simulation studies demonstrate that the proposed method provides accurate and numerically stable estimation and inference across a range of distributional settings without requiring the transformation scale to be specified in advance. The proposed method is illustrated using data from a malaria study.

stat.ME↗

arXiv2026

In-Context Positive-Unlabeled Learning

Positive-unlabeled (PU) learning addresses binary classification when only a set of labeled positives is available alongside a pool of unlabeled samples drawn from a mixture of positives and negatives. Existing PU methods typically require dataset-specific training or iterative optimization, which limits their applicability when many tasks must be solved quickly or with little tuning. We introduce PUICL, a pretrained transformer that solves PU classification entirely through in-context learning. PUICL is pretrained on synthetic PU datasets generated from randomly instantiated structural causal models, exposing it to a wide range of feature-label relationships and class-prior configurations. At inference time, PUICL receives the labeled positives and the unlabeled samples as a single input and returns class probabilities for the unlabeled rows in one forward pass, with no gradient updates or per-task fitting. On 20 semi-synthetic PU benchmarks derived from the UCI Machine Learning Repository, OpenML, and scikit-learn, PUICL outperforms four standard PU learning baselines in average AUC and accuracy, and is competitive on F1-score. These results show that the in-context learning paradigm extends naturally beyond fully supervised tabular prediction to the semi-supervised PU setting.

stat.ML↗

arXiv2026

Semiparametric Joint Inference for Sensitivity and Specificity at the Youden-Optimal Cut-Off

Sensitivity and specificity evaluated at an optimal diagnostic cut-off are fundamental measures of classification accuracy when continuous biomarkers are used for disease diagnosis. Joint inference for these quantities is challenging because their estimators are evaluated at a common, data-driven threshold estimated from both diseased and healthy samples, inducing statistical dependence. Existing approaches are largely based on parametric assumptions or fully nonparametric procedures, which may be sensitive to model misspecification or lack efficiency in moderate samples. We propose a semiparametric framework for joint inference on sensitivity and specificity at the Youden-optimal cut-off under the density ratio model. Using maximum empirical likelihood, we derive estimators of the optimal threshold and the corresponding sensitivity and specificity, and establish their joint asymptotic normality. This leads to Wald-type and range-preserving logit-transformed confidence regions. Simulation studies show that the proposed method achieves accurate coverage with improved efficiency relative to existing parametric and nonparametric alternatives across a variety of distributional settings. An analysis of COVID-19 antibody data demonstrates the practical advantages of the proposed approach for diagnostic decision-making.

stat.ME↗

arXiv2025

Semiparametric Learning from Open-Set Label Shift Data

We study the open-set label shift problem, where the test data may include a novel class absent from training. This setting is challenging because both the class proportions and the distribution of the novel class are not identifiable without extra assumptions. Existing approaches often rely on restrictive separability conditions, prior knowledge, or computationally infeasible procedures, and some may lack theoretical guarantees. We propose a semiparametric density ratio model framework that ensures identifiability while allowing overlap between novel and known classes. Within this framework, we develop maximum empirical likelihood estimators and confidence intervals for class proportions, establish their asymptotic validity, and design a stable Expectation-Maximization algorithm for computation. We further construct an approximately optimal classifier based on posterior probabilities with theoretical guarantees. Simulations and a real data application confirm that our methods improve both estimation accuracy and classification performance compared with existing approaches.

stat.ME↗

arXiv2025

A Smart Multimodal Healthcare Copilot with Powerful LLM Reasoning

Misdiagnosis causes significant harm to healthcare systems worldwide, leading to increased costs and patient risks. MedRAG is a smart multimodal healthcare copilot equipped with powerful large language model (LLM) reasoning, designed to enhance medical decision-making. It supports multiple input modalities, including non-intrusive voice monitoring, general medical queries, and electronic health records. MedRAG provides recommendations on diagnosis, treatment, medication, and follow-up questioning. Leveraging retrieval-augmented generation enhanced by knowledge graph-elicited reasoning, MedRAG retrieves and integrates critical diagnostic insights, reducing the risk of misdiagnosis. It has been evaluated on both public and private datasets, outperforming existing models and offering more specific and accurate healthcare assistance. A demonstration video of MedRAG is available at: https://www.youtube.com/watch?v=PNIBDMYRfDM. The source code is available at: https://github.com/SNOWTEAM2023/MedRAG.

cs.AI↗

arXiv2025

MedRAG: Enhancing Retrieval-augmented Generation with Knowledge Graph-Elicited Reasoning for Healthcare Copilot

Retrieval-augmented generation (RAG) is a well-suited technique for retrieving privacy-sensitive Electronic Health Records (EHR). It can serve as a key module of the healthcare copilot, helping reduce misdiagnosis for healthcare practitioners and patients. However, the diagnostic accuracy and specificity of existing heuristic-based RAG models used in the medical domain are inadequate, particularly for diseases with similar manifestations. This paper proposes MedRAG, a RAG model enhanced by knowledge graph (KG)-elicited reasoning for the medical domain that retrieves diagnosis and treatment recommendations based on manifestations. MedRAG systematically constructs a comprehensive four-tier hierarchical diagnostic KG encompassing critical diagnostic differences of various diseases. These differences are dynamically integrated with similar EHRs retrieved from an EHR database, and reasoned within a large language model. This process enables more accurate and specific decision support, while also proactively providing follow-up questions to enhance personalized medical decision-making. MedRAG is evaluated on both a public dataset DDXPlus and a private chronic pain diagnostic dataset (CPDD) collected from Tan Tock Seng Hospital, and its performance is compared against various existing RAG methods. Experimental results show that, leveraging the information integration and relational abilities of the KG, our MedRAG provides more specific diagnostic insights and outperforms state-of-the-art models in reducing misdiagnosis rates. Our code will be available at https://github.com/SNOWTEAM2023/MedRAG

cs.CL↗

arXiv2024

IntellectSeeker: A Personalized Literature Management System with the Probabilistic Model and Large Language Model

Faced with the burgeoning volume of academic literature, researchers often need help with uncertain article quality and mismatches in term searches using traditional academic engines. We introduce IntellectSeeker, an innovative and personalized intelligent academic literature management platform to address these challenges. This platform integrates a Large Language Model (LLM)--based semantic enhancement bot with a sophisticated probability model to personalize and streamline literature searches. We adopted the GPT-3.5-turbo model to transform everyday language into professional academic terms across various scenarios using multiple rounds of few-shot learning. This adaptation mainly benefits academic newcomers, effectively bridging the gap between general inquiries and academic terminology. The probabilistic model intelligently filters academic articles to align closely with the specific interests of users, which are derived from explicit needs and behavioral patterns. Moreover, IntellectSeeker incorporates an advanced recommendation system and text compression tools. These features enable intelligent article recommendations based on user interactions and present search results through concise one-line summaries and innovative word cloud visualizations, significantly enhancing research efficiency and user experience. IntellectSeeker offers academic researchers a highly customizable literature management solution with exceptional search precision and matching capabilities. The code can be found here: https://github.com/LuckyBian/ISY5001

cs.IR↗

arXiv2024

CogSimulator: A Model for Simulating User Cognition & Behavior with Minimal Data for Tailored Cognitive Enhancement

The interplay between cognition and gaming, notably through educational games enhancing cognitive skills, has garnered significant attention in recent years. This research introduces the CogSimulator, a novel algorithm for simulating user cognition in small-group settings with minimal data, as the educational game Wordle exemplifies. The CogSimulator employs Wasserstein-1 distance and coordinates search optimization for hyperparameter tuning, enabling precise few-shot predictions in new game scenarios. Comparative experiments with the Wordle dataset illustrate that our model surpasses most conventional machine learning models in mean Wasserstein-1 distance, mean squared error, and mean accuracy, showcasing its efficacy in cognitive enhancement through tailored game design.

cs.HC↗

arXiv2024

A Scalable Real-Time Data Assimilation Framework for Predicting Turbulent Atmosphere Dynamics

The weather and climate domains are undergoing a significant transformation thanks to advances in AI-based foundation models such as FourCastNet, GraphCast, ClimaX and Pangu-Weather. While these models show considerable potential, they are not ready yet for operational use in weather forecasting or climate prediction. This is due to the lack of a data assimilation method as part of their workflow to enable the assimilation of incoming Earth system observations in real time. This limitation affects their effectiveness in predicting complex atmospheric phenomena such as tropical cyclones and atmospheric rivers. To overcome these obstacles, we introduce a generic real-time data assimilation framework and demonstrate its end-to-end performance on the Frontier supercomputer. This framework comprises two primary modules: an ensemble score filter (EnSF), which significantly outperforms the state-of-the-art data assimilation method, namely, the Local Ensemble Transform Kalman Filter (LETKF); and a vision transformer-based surrogate capable of real-time adaptation through the integration of observational data. The ViT surrogate can represent either physics-based models or AI-based foundation models. We demonstrate both the strong and weak scaling of our framework up to 1024 GPUs on the Exascale supercomputer, Frontier. Our results not only illustrate the framework's exceptional scalability on high-performance computing systems, but also demonstrate the importance of supercomputers in real-time data assimilation for weather and climate predictions. Even though the proposed framework is tested only on a benchmark surface quasi-geostrophic (SQG) turbulence system, it has the potential to be combined with existing AI-based foundation models, making it suitable for future operational implementations.

cs.LG↗

arXiv2024

Positive and Unlabeled Data: Model, Estimation, Inference, and Classification

This study introduces a new approach to addressing positive and unlabeled (PU) data through the double exponential tilting model (DETM). Traditional methods often fall short because they only apply to selected completely at random (SCAR) PU data, where the labeled positive and unlabeled positive data are assumed to be from the same distribution. In contrast, our DETM's dual structure effectively accommodates the more complex and underexplored selected at random PU data, where the labeled and unlabeled positive data can be from different distributions. We rigorously establish the theoretical foundations of DETM, including identifiability, parameter estimation, and asymptotic properties. Additionally, we move forward to statistical inference by developing a goodness-of-fit test for the SCAR condition and constructing confidence intervals for the proportion of positive instances in the target domain. We leverage an approximated Bayes classifier for classification tasks, demonstrating DETM's robust performance in prediction. Through theoretical insights and practical applications, this study highlights DETM as a comprehensive framework for addressing the challenges of PU data.

stat.ME↗

arXiv2024

ORBIT: Oak Ridge Base Foundation Model for Earth System Predictability

Earth system predictability is challenged by the complexity of environmental dynamics and the multitude of variables involved. Current AI foundation models, although advanced by leveraging large and heterogeneous data, are often constrained by their size and data integration, limiting their effectiveness in addressing the full range of Earth system prediction challenges. To overcome these limitations, we introduce the Oak Ridge Base Foundation Model for Earth System Predictability (ORBIT), an advanced vision transformer model that scales up to 113 billion parameters using a novel hybrid tensor-data orthogonal parallelism technique. As the largest model of its kind, ORBIT surpasses the current climate AI foundation model size by a thousandfold. Performance scaling tests conducted on the Frontier supercomputer have demonstrated that ORBIT achieves 684 petaFLOPS to 1.6 exaFLOPS sustained throughput, with scaling efficiency maintained at 41% to 85% across 49,152 AMD GPUs. These breakthroughs establish new advances in AI-driven climate modeling and demonstrate promise to significantly improve the Earth system predictability.

physics.ao-ph↗

arXiv2024

Sequence Length Scaling in Vision Transformers for Scientific Images on Frontier

Vision Transformers (ViTs) are pivotal for foundational models in scientific imagery, including Earth science applications, due to their capability to process large sequence lengths. While transformers for text has inspired scaling sequence lengths in ViTs, yet adapting these for ViTs introduces unique challenges. We develop distributed sequence parallelism for ViTs, enabling them to handle up to 1M tokens. Our approach, leveraging DeepSpeed-Ulysses and Long-Sequence-Segmentation with model sharding, is the first to apply sequence parallelism in ViT training, achieving a 94% batch scaling efficiency on 2,048 AMD-MI250X GPUs. Evaluating sequence parallelism in ViTs, particularly in models up to 10B parameters, highlighted substantial bottlenecks. We countered these with hybrid sequence, pipeline, tensor parallelism, and flash attention strategies, to scale beyond single GPU memory limits. Our method significantly enhances climate modeling accuracy by 20% in temperature predictions, marking the first training of a transformer model on a full-attention matrix over 188K sequence length.

cs.CV↗

arXiv2024

Hierarchical Bayesian approach for adaptive integration of Bragg peaks in time-of-flight neutron scattering data

The Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL) operates in the event mode. Time-of-flight (TOF) information about each detected neutron is collected separately and saved as a descriptive entry in a database enabling unprecedented accuracy of the collected experimental data. Nevertheless, the common data processing pipeline still involves the binning of data to perform analysis and feature extraction. For weak reflections, improper binning leads to sparse histograms with low signal-to-noise ratios, rendering them uninformative. In this study, we propose the Bayesian approach for the identification of Bragg peaks in TOF diffraction data. The method is capable of adaptively handling the varying sampling rates found in different regions of the reciprocal space. Unlike histogram fitting methods, our approach focuses on estimating the true neutron flux function. We accomplish this by employing a profile fitting algorithm based on the event-level likelihood, along with a multiresolution histogram-level prior. By using this approach, we ensure that there is no loss of information due to data reduction in strong reflections and that the search space is appropriately restricted for weak reflections. To demonstrate the effectiveness of our proposed model, we apply it to real experimental data collected at the TOPAZ single crystal diffractometer at SNS.

cond-mat.mtrl-sci↗

arXiv2023

DeepSpeed4Science Initiative: Enabling Large-Scale Scientific Discovery through Sophisticated AI System Technologies

In the upcoming decade, deep learning may revolutionize the natural sciences, enhancing our capacity to model and predict natural occurrences. This could herald a new era of scientific exploration, bringing significant advancements across sectors from drug development to renewable energy. To answer this call, we present DeepSpeed4Science initiative (deepspeed4science.ai) which aims to build unique capabilities through AI system technology innovations to help domain experts to unlock today's biggest science mysteries. By leveraging DeepSpeed's current technology pillars (training, inference and compression) as base technology enablers, DeepSpeed4Science will create a new set of AI system technologies tailored for accelerating scientific discoveries by addressing their unique complexity beyond the common technical approaches used for accelerating generic large language models (LLMs). In this paper, we showcase the early progress we made with DeepSpeed4Science in addressing two of the critical system challenges in structural biology research.

cs.AI↗

arXiv2022

PI3NN: Out-of-distribution-aware prediction intervals from three neural networks

We propose a novel prediction interval (PI) method for uncertainty quantification, which addresses three major issues with the state-of-the-art PI methods. First, existing PI methods require retraining of neural networks (NNs) for every given confidence level and suffer from the crossing issue in calculating multiple PIs. Second, they usually rely on customized loss functions with extra sensitive hyperparameters for which fine tuning is required to achieve a well-calibrated PI. Third, they usually underestimate uncertainties of out-of-distribution (OOD) samples leading to over-confident PIs. Our PI3NN method calculates PIs from linear combinations of three NNs, each of which is independently trained using the standard mean squared error loss. The coefficients of the linear combinations are computed using root-finding algorithms to ensure tight PIs for a given confidence level. We theoretically prove that PI3NN can calculate PIs for a series of confidence levels without retraining NNs and it completely avoids the crossing issue. Additionally, PI3NN does not introduce any unusual hyperparameters resulting in a stable performance. Furthermore, we address OOD identification challenge by introducing an initialization scheme which provides reasonably larger PIs of the OOD samples than those of the in-distribution samples. Benchmark and real-world experiments show that our method outperforms several state-of-the-art approaches with respect to predictive uncertainty quality, robustness, and OOD samples identification.

cs.LG↗

arXiv2020

Application of variational policy gradient to atomic-scale materials synthesis

Atomic-scale materials synthesis via layer deposition techniques present a unique opportunity to control material structures and yield systems that display unique functional properties that cannot be stabilized using traditional bulk synthetic routes. However, the deposition process itself presents a large, multidimensional space that is traditionally optimized via intuition and trial and error, slowing down progress. Here, we present an application of deep reinforcement learning to a simulated materials synthesis problem, utilizing the Stein variational policy gradient (SVPG) approach to train multiple agents to optimize a stochastic policy to yield desired functional properties. Our contributions are (1) A fully open source simulation environment for layered materials synthesis problems, utilizing a kinetic Monte-Carlo engine and implemented in the OpenAI Gym framework, (2) Extension of the Stein variational policy gradient approach to deal with both image and tabular input, and (3) Developing a parallel (synchronous) implementation of SVPG using Horovod, distributing multiple agents across GPUs and individual simulation environments on CPUs. We demonstrate the utility of this approach in optimizing for a material surface characteristic, surface roughness, and explore the strategies used by the agents as compared with a traditional actor-critic (A2C) baseline. Further, we find that SVPG stabilizes the training process over traditional A2C. Such trained agents can be useful to a variety of atomic-scale deposition techniques, including pulsed laser deposition and molecular beam epitaxy, if the implementation challenges are addressed.

physics.comp-ph↗

arXiv2018

Bounds on the edge-Wiener index of cacti with $n$ vertices and $t$ cycles

The edge-Wiener index $W_e(G)$ of a connected graph $G$ is the sum of distances between all pairs of edges of $G$. A connected graph $G$ is said to be a cactus if each of its blocks is either a cycle or an edge. Let $\mathcal{G}_{n,t}$ denote the class of all cacti with $n$ vertices and $t$ cycles. In this paper, the upper bound and lower bound on the edge-Wiener index of graphs in $\mathcal{G}_{n,t}$ are identified and the corresponding extremal graphs are characterized.

math.CO↗