arXiv subjects

Jiang Bian

Publications and source records attributed to Jiang Bian.

At least 271 records · Page 15Linked to original sources

arXiv2022

Joint Application of the Target Trial Causal Framework and Machine Learning Modeling to Optimize Antibiotic Therapy: Use Case on Acute Bacterial Skin and Skin Structure Infections due to Methicillin-resistant Staphylococcus aureus

Bacterial infections are responsible for high mortality worldwide. Antimicrobial resistance underlying the infection, and multifaceted patient's clinical status can hamper the correct choice of antibiotic treatment. Randomized clinical trials provide average treatment effect estimates but are not ideal for risk stratification and optimization of therapeutic choice, i.e., individualized treatment effects (ITE). Here, we leverage large-scale electronic health record data, collected from Southern US academic clinics, to emulate a clinical trial, i.e., 'target trial', and develop a machine learning model of mortality prediction and ITE estimation for patients diagnosed with acute bacterial skin and skin structure infection (ABSSSI) due to methicillin-resistant Staphylococcus aureus (MRSA). ABSSSI-MRSA is a challenging condition with reduced treatment options - vancomycin is the preferred choice, but it has non-negligible side effects. First, we use propensity score matching to emulate the trial and create a treatment randomized (vancomycin vs. other antibiotics) dataset. Next, we use this data to train various machine learning methods (including boosted/LASSO logistic regression, support vector machines, and random forest) and choose the best model in terms of area under the receiver characteristic (AUC) through bootstrap validation. Lastly, we use the models to calculate ITE and identify possible averted deaths by therapy change. The out-of-bag tests indicate that SVM and RF are the most accurate, with AUC of 81% and 78%, respectively, but BLR/LASSO is not far behind (76%). By calculating the counterfactuals using the BLR/LASSO, vancomycin increases the risk of death, but it shows a large variation (odds ratio 1.2, 95% range 0.4-3.8) and the contribution to outcome probability is modest. Instead, the RF exhibits stronger changes in ITE, suggesting more complex treatment heterogeneity.

stat.ML↗

arXiv2022

Less Is More: Fast Multivariate Time Series Forecasting with Light Sampling-oriented MLP Structures

Multivariate time series forecasting has seen widely ranging applications in various domains, including finance, traffic, energy, and healthcare. To capture the sophisticated temporal patterns, plenty of research studies designed complex neural network architectures based on many variants of RNNs, GNNs, and Transformers. However, complex models are often computationally expensive and thus face a severe challenge in training and inference efficiency when applied to large-scale real-world datasets. In this paper, we introduce LightTS, a light deep learning architecture merely based on simple MLP-based structures. The key idea of LightTS is to apply an MLP-based structure on top of two delicate down-sampling strategies, including interval sampling and continuous sampling, inspired by a crucial fact that down-sampling time series often preserves the majority of its information. We conduct extensive experiments on eight widely used benchmark datasets. Compared with the existing state-of-the-art methods, LightTS demonstrates better performance on five of them and comparable performance on the rest. Moreover, LightTS is highly efficient. It uses less than 5% FLOPS compared with previous SOTA methods on the largest benchmark dataset. In addition, LightTS is robust and has a much smaller variance in forecasting accuracy than previous SOTA methods in long sequence forecasting tasks.

cs.LG↗

arXiv2022

DDG-DA: Data Distribution Generation for Predictable Concept Drift Adaptation

In many real-world scenarios, we often deal with streaming data that is sequentially collected over time. Due to the non-stationary nature of the environment, the streaming data distribution may change in unpredictable ways, which is known as concept drift. To handle concept drift, previous methods first detect when/where the concept drift happens and then adapt models to fit the distribution of the latest data. However, there are still many cases that some underlying factors of environment evolution are predictable, making it possible to model the future concept drift trend of the streaming data, while such cases are not fully explored in previous work. In this paper, we propose a novel method DDG-DA, that can effectively forecast the evolution of data distribution and improve the performance of models. Specifically, we first train a predictor to estimate the future data distribution, then leverage it to generate training samples, and finally train models on the generated data. We conduct experiments on three real-world tasks (forecasting on stock price trend, electricity load and solar irradiance) and obtain significant improvement on multiple widely-used models.

cs.LG↗

arXiv2022

Towards Applicable Reinforcement Learning: Improving the Generalization and Sample Efficiency with Policy Ensemble

It is challenging for reinforcement learning (RL) algorithms to succeed in real-world applications like financial trading and logistic system due to the noisy observation and environment shifting between training and evaluation. Thus, it requires both high sample efficiency and generalization for resolving real-world tasks. However, directly applying typical RL algorithms can lead to poor performance in such scenarios. Considering the great performance of ensemble methods on both accuracy and generalization in supervised learning (SL), we design a robust and applicable method named Ensemble Proximal Policy Optimization (EPPO), which learns ensemble policies in an end-to-end manner. Notably, EPPO combines each policy and the policy ensemble organically and optimizes both simultaneously. In addition, EPPO adopts a diversity enhancement regularization over the policy space which helps to generalize to unseen states and promotes exploration. We theoretically prove EPPO increases exploration efficacy, and through comprehensive experimental evaluations on various tasks, we demonstrate that EPPO achieves higher efficiency and is robust for real-world applications compared with vanilla policy optimization algorithms and other ensemble methods. Code and supplemental materials are available at https://seqml.github.io/eppo.

cs.LG↗

arXiv2022

DEPTS: Deep Expansion Learning for Periodic Time Series Forecasting

Periodic time series (PTS) forecasting plays a crucial role in a variety of industries to foster critical tasks, such as early warning, pre-planning, resource scheduling, etc. However, the complicated dependencies of the PTS signal on its inherent periodicity as well as the sophisticated composition of various periods hinder the performance of PTS forecasting. In this paper, we introduce a deep expansion learning framework, DEPTS, for PTS forecasting. DEPTS starts with a decoupled formulation by introducing the periodic state as a hidden variable, which stimulates us to make two dedicated modules to tackle the aforementioned two challenges. First, we develop an expansion module on top of residual learning to perform a layer-by-layer expansion of those complicated dependencies. Second, we introduce a periodicity module with a parameterized periodic function that holds sufficient capacity to capture diversified periods. Moreover, our two customized modules also have certain interpretable capabilities, such as attributing the forecasts to either local momenta or global periodicity and characterizing certain core periodic properties, e.g., amplitudes and frequencies. Extensive experiments on both synthetic data and real-world data demonstrate the effectiveness of DEPTS on handling PTS. In most cases, DEPTS achieves significant improvements over the best baseline. Specifically, the error reduction can even reach up to 20% for a few cases. Finally, all codes are publicly available.

cs.LG↗

arXiv2022

Temporal Subtyping of Alzheimer's Disease Using Medical Conditions Preceding Alzheimer's Disease Onset in Electronic Health Records

Subtyping of Alzheimer's disease (AD) can facilitate diagnosis, treatment, prognosis and disease management. It can also support the testing of new prevention and treatment strategies through clinical trials. In this study, we employed spectral clustering to cluster 29,922 AD patients in the OneFlorida Data Trust using their longitudinal EHR data of diagnosis and conditions into four subtypes. These subtypes exhibit different patterns of progression of other conditions prior to the first AD diagnosis. In addition, according to the results of various statistical tests, these subtypes are also significantly different with respect to demographics, mortality, and prescription medications after the AD diagnosis. This study could potentially facilitate early detection and personalized treatment of AD as well as data-driven generalizability assessment of clinical trials for AD.

cs.LG↗

arXiv2022

AF$_2$: Adaptive Focus Framework for Aerial Imagery Segmentation

As a specific semantic segmentation task, aerial imagery segmentation has been widely employed in high spatial resolution (HSR) remote sensing images understanding. Besides common issues (e.g. large scale variation) faced by general semantic segmentation tasks, aerial imagery segmentation has some unique challenges, the most critical one among which lies in foreground-background imbalance. There have been some recent efforts that attempt to address this issue by proposing sophisticated neural network architectures, since they can be used to extract informative multi-scale feature representations and increase the discrimination of object boundaries. Nevertheless, many of them merely utilize those multi-scale representations in ad-hoc measures but disregard the fact that the semantic meaning of objects with various sizes could be better identified via receptive fields of diverse ranges. In this paper, we propose Adaptive Focus Framework (AF$_2$), which adopts a hierarchical segmentation procedure and focuses on adaptively utilizing multi-scale representations generated by widely adopted neural network architectures. Particularly, a learnable module, called Adaptive Confidence Mechanism (ACM), is proposed to determine which scale of representation should be used for the segmentation of different objects. Comprehensive experiments show that AF$_2$ has significantly improved the accuracy on three widely used aerial benchmarks, as fast as the mainstream method.

cs.CV↗

arXiv2022

Dynamic Relation Discovery and Utilization in Multi-Entity Time Series Forecasting

Time series forecasting plays a key role in a variety of domains. In a lot of real-world scenarios, there exist multiple forecasting entities (e.g. power station in the solar system, stations in the traffic system). A straightforward forecasting solution is to mine the temporal dependency for each individual entity through 1d-CNN, RNN, transformer, etc. This approach overlooks the relations between these entities and, in consequence, loses the opportunity to improve performance using spatial-temporal relation. However, in many real-world scenarios, beside explicit relation, there could exist crucial yet implicit relation between entities. How to discover the useful implicit relation between entities and effectively utilize the relations for each entity under various circumstances is crucial. In order to mine the implicit relation between entities as much as possible and dynamically utilize the relation to improve the forecasting performance, we propose an attentional multi-graph neural network with automatic graph learning (A2GNN) in this work. Particularly, a Gumbel-softmax based auto graph learner is designed to automatically capture the implicit relation among forecasting entities. We further propose an attentional relation learner that enables every entity to dynamically pay attention to its preferred relations. Extensive experiments are conducted on five real-world datasets from three different domains. The results demonstrate the effectiveness of A2GNN beyond several state-of-the-art methods.

cs.LG↗

arXiv2022

HIST: A Graph-based Framework for Stock Trend Forecasting via Mining Concept-Oriented Shared Information

Stock trend forecasting, which forecasts stock prices' future trends, plays an essential role in investment. The stocks in a market can share information so that their stock prices are highly correlated. Several methods were recently proposed to mine the shared information through stock concepts (e.g., technology, Internet Retail) extracted from the Web to improve the forecasting results. However, previous work assumes the connections between stocks and concepts are stationary, and neglects the dynamic relevance between stocks and concepts, limiting the forecasting results. Moreover, existing methods overlook the invaluable shared information carried by hidden concepts, which measure stocks' commonness beyond the manually defined stock concepts. To overcome the shortcomings of previous work, we proposed a novel stock trend forecasting framework that can adequately mine the concept-oriented shared information from predefined concepts and hidden concepts. The proposed framework simultaneously utilize the stock's shared information and individual information to improve the stock trend forecasting performance. Experimental results on the real-world tasks demonstrate the efficiency of our framework on stock trend forecasting. The investment simulation shows that our framework can achieve a higher investment return than the baselines.

q-fin.ST↗

arXiv2021

SHGNN: Structure-Aware Heterogeneous Graph Neural Network

Many real-world graphs (networks) are heterogeneous with different types of nodes and edges. Heterogeneous graph embedding, aiming at learning the low-dimensional node representations of a heterogeneous graph, is vital for various downstream applications. Many meta-path based embedding methods have been proposed to learn the semantic information of heterogeneous graphs in recent years. However, most of the existing techniques overlook the graph structure information when learning the heterogeneous graph embeddings. This paper proposes a novel Structure-Aware Heterogeneous Graph Neural Network (SHGNN) to address the above limitations. In detail, we first utilize a feature propagation module to capture the local structure information of intermediate nodes in the meta-path. Next, we use a tree-attention aggregator to incorporate the graph structure information into the aggregation module on the meta-path. Finally, we leverage a meta-path aggregator to fuse the information aggregated from different meta-paths. We conducted experiments on node classification and clustering tasks and achieved state-of-the-art results on the benchmark datasets, which shows the effectiveness of our proposed method.

cs.SI↗

arXiv2021

Deep Risk Model: A Deep Learning Solution for Mining Latent Risk Factors to Improve Covariance Matrix Estimation

Modeling and managing portfolio risk is perhaps the most important step to achieve growing and preserving investment performance. Within the modern portfolio construction framework that built on Markowitz's theory, the covariance matrix of stock returns is a required input to calculate portfolio risk. Traditional approaches to estimate the covariance matrix are based on human-designed risk factors, which often require tremendous time and effort to design better risk factors to improve the covariance estimation. In this work, we formulate the quest of mining risk factors as a learning problem and propose a deep learning solution to effectively ``design'' risk factors with neural networks. The learning objective is also carefully set to ensure the learned risk factors are effective in explaining the variance of stock returns as well as having desired orthogonality and stability. Our experiments on the stock market data demonstrate the effectiveness of the proposed solution: our method can obtain $1.9\%$ higher explained variance measured by $R^2$ and also reduce the risk of a global minimum variance portfolio. The incremental analysis further supports our design of both the architecture and the learning objective.

q-fin.RM↗

arXiv2021

Instance-wise Graph-based Framework for Multivariate Time Series Forecasting

The multivariate time series forecasting has attracted more and more attention because of its vital role in different fields in the real world, such as finance, traffic, and weather. In recent years, many research efforts have been proposed for forecasting multivariate time series. Although some previous work considers the interdependencies among different variables in the same timestamp, existing work overlooks the inter-connections between different variables at different time stamps. In this paper, we propose a simple yet efficient instance-wise graph-based framework to utilize the inter-dependencies of different variables at different time stamps for multivariate time series forecasting. The key idea of our framework is aggregating information from the historical time series of different variables to the current time series that we need to forecast. We conduct experiments on the Traffic, Electricity, and Exchange-Rate multivariate time series datasets. The results show that our proposed model outperforms the state-of-the-art baseline methods.

cs.LG↗

arXiv2021

Clinical Relation Extraction Using Transformer-based Models

The newly emerged transformer technology has a tremendous impact on NLP research. In the general English domain, transformer-based models have achieved state-of-the-art performances on various NLP benchmarks. In the clinical domain, researchers also have investigated transformer models for clinical applications. The goal of this study is to systematically explore three widely used transformer-based models (i.e., BERT, RoBERTa, and XLNet) for clinical relation extraction and develop an open-source package with clinical pre-trained transformer-based models to facilitate information extraction in the clinical domain. We developed a series of clinical RE models based on three transformer architectures, namely BERT, RoBERTa, and XLNet. We evaluated these models using 2 publicly available datasets from 2018 MADE1.0 and 2018 n2c2 challenges. We compared two classification strategies (binary vs. multi-class classification) and investigated two approaches to generate candidate relations in different experimental settings. In this study, we compared three transformer-based (BERT, RoBERTa, and XLNet) models for relation extraction. We demonstrated that the RoBERTa-clinical RE model achieved the best performance on the 2018 MADE1.0 dataset with an F1-score of 0.8958. On the 2018 n2c2 dataset, the XLNet-clinical model achieved the best F1-score of 0.9610. Our results indicated that the binary classification strategy consistently outperformed the multi-class classification strategy for clinical relation extraction. Our methods and models are publicly available at https://github.com/uf-hobi-informatics-lab/ClinicalTransformerRelationExtraction. We believe this work will improve current practice on clinical relation extraction and other related NLP tasks in the biomedical domain.

cs.CL↗

arXiv2021

Explaining Algorithmic Fairness Through Fairness-Aware Causal Path Decomposition

Algorithmic fairness has aroused considerable interests in data mining and machine learning communities recently. So far the existing research has been mostly focusing on the development of quantitative metrics to measure algorithm disparities across different protected groups, and approaches for adjusting the algorithm output to reduce such disparities. In this paper, we propose to study the problem of identification of the source of model disparities. Unlike existing interpretation methods which typically learn feature importance, we consider the causal relationships among feature variables and propose a novel framework to decompose the disparity into the sum of contributions from fairness-aware causal paths, which are paths linking the sensitive attribute and the final predictions, on the graph. We also consider the scenario when the directions on certain edges within those paths cannot be determined. Our framework is also model agnostic and applicable to a variety of quantitative disparity measures. Empirical evaluations on both synthetic and real-world data sets are provided to show that our method can provide precise and comprehensive explanations to the model disparities.

cs.LG↗

arXiv2021

A Study of Social and Behavioral Determinants of Health in Lung Cancer Patients Using Transformers-based Natural Language Processing Models

Social and behavioral determinants of health (SBDoH) have important roles in shaping people's health. In clinical research studies, especially comparative effectiveness studies, failure to adjust for SBDoH factors will potentially cause confounding issues and misclassification errors in either statistical analyses and machine learning-based models. However, there are limited studies to examine SBDoH factors in clinical outcomes due to the lack of structured SBDoH information in current electronic health record (EHR) systems, while much of the SBDoH information is documented in clinical narratives. Natural language processing (NLP) is thus the key technology to extract such information from unstructured clinical text. However, there is not a mature clinical NLP system focusing on SBDoH. In this study, we examined two state-of-the-art transformer-based NLP models, including BERT and RoBERTa, to extract SBDoH concepts from clinical narratives, applied the best performing model to extract SBDoH concepts on a lung cancer screening patient cohort, and examined the difference of SBDoH information between NLP extracted results and structured EHRs (SBDoH information captured in standard vocabularies such as the International Classification of Diseases codes). The experimental results show that the BERT-based NLP model achieved the best strict/lenient F1-score of 0.8791 and 0.8999, respectively. The comparison between NLP extracted SBDoH information and structured EHRs in the lung cancer patient cohort of 864 patients with 161,933 various types of clinical notes showed that much more detailed information about smoking, education, and employment were only captured in clinical narratives and that it is necessary to use both clinical narratives and structured EHRs to construct a more complete picture of patients' SBDoH factors.

cs.CL↗

arXiv2021

Model Complexity of Deep Learning: A Survey

Model complexity is a fundamental problem in deep learning. In this paper we conduct a systematic overview of the latest studies on model complexity in deep learning. Model complexity of deep learning can be categorized into expressive capacity and effective model complexity. We review the existing studies on those two categories along four important factors, including model framework, model size, optimization process and data complexity. We also discuss the applications of deep learning model complexity including understanding model generalization, model optimization, and model selection and design. We conclude by proposing several interesting future directions.

cs.LG↗

arXiv2021

Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions

Whole genome sequencing (WGS) is quickly becoming the customary means for identification of antimicrobial resistance (AMR) due to its ability to obtain high resolution information about the genes and mechanisms that are causing resistance and driving pathogen mobility. By contrast, traditional phenotypic (antibiogram) testing cannot easily elucidate such information. Yet development of AMR prediction tools from genotype-phenotype data can be biased, since sampling is non-randomized. Sample provenience, period of collection, and species representation can confound the association of genetic traits with AMR. Thus, prediction models can perform poorly on new data with sampling distribution shifts. In this work -- under an explicit set of causal assumptions -- we evaluate the effectiveness of propensity-based rebalancing and confounding adjustment on AMR prediction using genotype-phenotype AMR data from the Pathosystems Resource Integration Center (PATRIC). We select bacterial genotypes (encoded as k-mer signatures, i.e. DNA fragments of length k), country, year, species, and AMR phenotypes for the tetracycline drug class, preparing test data with recent genomes coming from a single country. We test boosted logistic regression (BLR) and random forests (RF) with/without bias-handling. On 10,936 instances, we find evidence of species, location and year imbalance with respect to the AMR phenotype. The crude versus bias-adjusted change in effect of genetic signatures on AMR varies but only moderately (selecting the top 20,000 out of 40+ million k-mers). The area under the receiver operating characteristic (AUROC) of the RF (0.95) is comparable to that of BLR (0.94) on both out-of-bag samples from bootstrap and the external test (n=1,085), where AUROCs do not decrease. We observe a 1%-5% gain in AUROC with bias-handling compared to the sole use of genetic signatures. ...

q-bio.GN↗

arXiv2021

Learning Multiple Stock Trading Patterns with Temporal Routing Adaptor and Optimal Transport

Successful quantitative investment usually relies on precise predictions of the future movement of the stock price. Recently, machine learning based solutions have shown their capacity to give more accurate stock prediction and become indispensable components in modern quantitative investment systems. However, the i.i.d. assumption behind existing methods is inconsistent with the existence of diverse trading patterns in the stock market, which inevitably limits their ability to achieve better stock prediction performance. In this paper, we propose a novel architecture, Temporal Routing Adaptor (TRA), to empower existing stock prediction models with the ability to model multiple stock trading patterns. Essentially, TRA is a lightweight module that consists of a set of independent predictors for learning multiple patterns as well as a router to dispatch samples to different predictors. Nevertheless, the lack of explicit pattern identifiers makes it quite challenging to train an effective TRA-based model. To tackle this challenge, we further design a learning algorithm based on Optimal Transport (OT) to obtain the optimal sample to predictor assignment and effectively optimize the router with such assignment through an auxiliary loss term. Experiments on the real-world stock ranking task show that compared to the state-of-the-art baselines, e.g., Attention LSTM and Transformer, the proposed method can improve information coefficient (IC) from 0.053 to 0.059 and 0.051 to 0.056 respectively. Our dataset and code used in this work are publicly available: https://github.com/microsoft/qlib/tree/main/examples/benchmarks/TRA.

cs.LG↗