arXiv subjects

Wenqi Shi

Publications and source records attributed to Wenqi Shi.

49 records · Page 3Linked to original sources

arXiv2024

BMRetriever: Tuning Large Language Models as Better Biomedical Text Retrievers

Developing effective biomedical retrieval models is important for excelling at knowledge-intensive biomedical tasks but still challenging due to the deficiency of sufficient publicly annotated biomedical data and computational resources. We present BMRetriever, a series of dense retrievers for enhancing biomedical retrieval via unsupervised pre-training on large biomedical corpora, followed by instruction fine-tuning on a combination of labeled datasets and synthetic pairs. Experiments on 5 biomedical tasks across 11 datasets verify BMRetriever's efficacy on various biomedical applications. BMRetriever also exhibits strong parameter efficiency, with the 410M variant outperforming baselines up to 11.7 times larger, and the 2B variant matching the performance of models with over 5B parameters. The training data and model checkpoints are released at \url{https://huggingface.co/BMRetriever} to ensure transparency, reproducibility, and application to new domains.

cs.CL↗

arXiv2024

MedAdapter: Efficient Test-Time Adaptation of Large Language Models towards Medical Reasoning

Despite their improved capabilities in generation and reasoning, adapting large language models (LLMs) to the biomedical domain remains challenging due to their immense size and corporate privacy. In this work, we propose MedAdapter, a unified post-hoc adapter for test-time adaptation of LLMs towards biomedical applications. Instead of fine-tuning the entire LLM, MedAdapter effectively adapts the original model by fine-tuning only a small BERT-sized adapter to rank candidate solutions generated by LLMs. Experiments demonstrate that MedAdapter effectively adapts both white-box and black-box LLMs in biomedical reasoning, achieving average performance improvements of 25.48% and 11.31%, respectively, without requiring extensive computational resources or sharing data with third parties. MedAdapter also yields superior performance when combined with train-time adaptation, highlighting a flexible and complementary solution to existing adaptation methods. Faced with the challenges of balancing model performance, computational resources, and data privacy, MedAdapter provides an efficient, privacy-preserving, cost-effective, and transparent solution for adapting LLMs to the biomedical domain.

cs.CL↗

arXiv2024

RAM-EHR: Retrieval Augmentation Meets Clinical Predictions on Electronic Health Records

We present RAM-EHR, a Retrieval AugMentation pipeline to improve clinical predictions on Electronic Health Records (EHRs). RAM-EHR first collects multiple knowledge sources, converts them into text format, and uses dense retrieval to obtain information related to medical concepts. This strategy addresses the difficulties associated with complex names for the concepts. RAM-EHR then augments the local EHR predictive model co-trained with consistency regularization to capture complementary information from patient visits and summarized knowledge. Experiments on two EHR datasets show the efficacy of RAM-EHR over previous knowledge-enhanced baselines (3.4% gain in AUROC and 7.2% gain in AUPR), emphasizing the effectiveness of the summarized knowledge from RAM-EHR for clinical prediction tasks. The code will be published at \url{https://github.com/ritaranx/RAM-EHR}.

cs.CL↗

arXiv2023

Autonomous Soft Tissue Retraction Using Demonstration-Guided Reinforcement Learning

In the context of surgery, robots can provide substantial assistance by performing small, repetitive tasks such as suturing, needle exchange, and tissue retraction, thereby enabling surgeons to concentrate on more complex aspects of the procedure. However, existing surgical task learning mainly pertains to rigid body interactions, whereas the advancement towards more sophisticated surgical robots necessitates the manipulation of soft bodies. Previous work focused on tissue phantoms for soft tissue task learning, which can be expensive and can be an entry barrier to research. Simulation environments present a safe and efficient way to learn surgical tasks before their application to actual tissue. In this study, we create a Robot Operating System (ROS)-compatible physics simulation environment with support for both rigid and soft body interactions within surgical tasks. Furthermore, we investigate the soft tissue interactions facilitated by the patient-side manipulator of the DaVinci surgical robot. Leveraging the pybullet physics engine, we simulate kinematics and establish anchor points to guide the robotic arm when manipulating soft tissue. Using demonstration-guided reinforcement learning (RL) algorithms, we investigate their performance in comparison to traditional reinforcement learning algorithms. Our in silico trials demonstrate a proof-of-concept for autonomous surgical soft tissue retraction. The results corroborate the feasibility of learning soft body manipulation through the application of reinforcement learning agents. This work lays the foundation for future research into the development and refinement of surgical robots capable of managing both rigid and soft tissue interactions. Code is available at https://github.com/amritpal-001/tissue_retract.

cs.LG↗

arXiv2022

Strategy to select most efficient RCT samples based on observational data

Randomized experiments can provide unbiased estimates of sample average treatment effects. However, estimates of population treatment effects can be biased when the experimental sample and the target population differ. In this case, the population average treatment effect can be identified by combining experimental and observational data. A good experiment design trumps all the analyses that come after. While most of the existing literature centers around improving analyses after RCTs, we instead focus on the design stage, fundamentally improving the efficiency of the combined causal estimator through the selection of experimental samples. We explore how the covariate distribution of RCT samples influences the estimation efficiency and derive the optimal covariate allocation that leads to the lowest variance. Our results show that the optimal allocation does not necessarily follow the exact distribution of the target cohort, but adjusted for the conditional variability of potential outcomes. We formulate a metric to compare and choose from candidate RCT sample compositions. We also develop variations of our main results to cater for practical scenarios with various cost constraints and precision requirements. The ultimate goal of this paper is to provide practitioners with a clear and actionable strategy to select RCT samples that will lead to efficient causal inference.

stat.ME↗

arXiv2022

Nonlinear Causal Discovery via Kernel Anchor Regression

Learning causal relationships is a fundamental problem in science. Anchor regression has been developed to address this problem for a large class of causal graphical models, though the relationships between the variables are assumed to be linear. In this work, we tackle the nonlinear setting by proposing kernel anchor regression (KAR). Beyond the natural formulation using a classic two-stage least square estimator, we also study an improved variant that involves nonparametric regression in three separate stages. We provide convergence results for the proposed KAR estimators and the identifiability conditions for KAR to learn the nonlinear structural equation models (SEM). Experimental results demonstrate the superior performances of the proposed KAR estimators over existing baselines.

stat.ML↗

arXiv2022

Rerandomization and covariate adjustment in split-plot designs

The split-plot design arises from agricultural sciences with experimental units, also known as subplots, nested within groups known as whole plots. It assigns the whole-plot intervention by a cluster randomization at the whole-plot level and assigns the subplot intervention by a stratified randomization at the subplot level. The randomization mechanism guarantees covariate balance on average at both the whole-plot and subplot levels, and ensures consistent inference of the average treatment effects by the Horvitz--Thompson and Hajek estimators. However, covariate imbalance often occurs in finite samples and subjects subsequent inference to possibly large variability and conditional bias. Rerandomization is widely used in the design stage of randomized experiments to improve covariate balance. The existing literature on rerandomization nevertheless focuses on designs with treatments assigned at either the unit or the group level, but not both, leaving the corresponding theory for rerandomization in split-plot designs an open problem. To fill the gap, we propose two strategies for conducting rerandomization in split-plot designs based on the Mahalanobis distance and establish the corresponding design-based theory. We show that rerandomization can improve the asymptotic efficiency of the Horvitz--Thompson and Hajek estimators. Moreover, we propose two covariate adjustment methods in the analysis stage, which can further improve the asymptotic efficiency when combined with rerandomization. The validity and improved efficiency of the proposed methods are demonstrated through numerical studies.

stat.ME↗

arXiv2022

Explainable Artificial Intelligence Methods in Combating Pandemics: A Systematic Review

Despite the myriad peer-reviewed papers demonstrating novel Artificial Intelligence (AI)-based solutions to COVID-19 challenges during the pandemic, few have made significant clinical impact. The impact of artificial intelligence during the COVID-19 pandemic was greatly limited by lack of model transparency. This systematic review examines the use of Explainable Artificial Intelligence (XAI) during the pandemic and how its use could overcome barriers to real-world success. We find that successful use of XAI can improve model performance, instill trust in the end-user, and provide the value needed to affect user decision-making. We introduce the reader to common XAI techniques, their utility, and specific examples of their application. Evaluation of XAI results is also discussed as an important step to maximize the value of AI-based clinical decision support systems. We illustrate the classical, modern, and potential future trends of XAI to elucidate the evolution of novel XAI techniques. Finally, we provide a checklist of suggestions during the experimental design process supported by recent publications. Common challenges during the implementation of AI solutions are also addressed with specific examples of potential solutions. We hope this review may serve as a guide to improve the clinical impact of future AI-based solutions.

cs.AI↗

arXiv2022

Multi-user Co-inference with Batch Processing Capable Edge Server

Graphics processing units (GPUs) can improve deep neural network inference throughput via batch processing, where multiple tasks are concurrently processed. We focus on novel scenarios that the energy-constrained mobile devices offload inference tasks to an edge server with GPU. The inference task is partitioned into sub-tasks for a finer granularity of offloading and scheduling, and the user energy consumption minimization problem under inference latency constraints is investigated. To deal with the coupled offloading and scheduling introduced by concurrent batch processing, we first consider an offline problem with a constant edge inference latency and the same latency constraint. It is proven that optimizing the offloading policy of each user independently and aggregating all the same sub-tasks in one batch is optimal, and thus the independent partitioning and same sub-task aggregating (IP-SSA) algorithm is inspired. Further, the optimal grouping (OG) algorithm is proposed to optimally group tasks when the latency constraints are different. Finally, when future task arrivals cannot be precisely predicted, a deep deterministic policy gradient (DDPG) agent is trained to call OG. Experiments show that IP-SSA reduces up to 94.9\% user energy consumption in the offline setting, while DDPG-OG outperforms DDPG-IP-SSA by up to 8.92\% in the online setting.

cs.DC↗

arXiv2020

Edge Learning with Timeliness Constraints: Challenges and Solutions

Future machine learning (ML) powered applications, such as autonomous driving and augmented reality, involve training and inference tasks with timeliness requirements and are communication and computation intensive, which demands for the edge learning framework. The real-time requirements drive us to go beyond accuracy for ML. In this article, we introduce the concept of timely edge learning, aiming to achieve accurate training and inference while minimizing the communication and computation delay. We discuss key challenges and propose corresponding solutions from data, model and resource management perspectives to meet the timeliness requirements. Particularly, for edge training, we argue that the total training delay rather than rounds should be considered, and propose data or model compression, and joint device scheduling and resource management schemes for both centralized training and federated learning systems. For edge inference, we explore the dependency between accuracy and delay for communication and computation, and propose dynamic data compression and flexible pruning schemes. Two case studies show that the timeliness performances, including the training accuracy under a given delay budget and the completion ratio of inference tasks within deadline, are highly improved with the proposed solutions.

cs.NI↗

arXiv2020

Joint Device Scheduling and Resource Allocation for Latency Constrained Wireless Federated Learning

In federated learning (FL), devices contribute to the global training by uploading their local model updates via wireless channels. Due to limited computation and communication resources, device scheduling is crucial to the convergence rate of FL. In this paper, we propose a joint device scheduling and resource allocation policy to maximize the model accuracy within a given total training time budget for latency constrained wireless FL. A lower bound on the reciprocal of the training performance loss, in terms of the number of training rounds and the number of scheduled devices per round, is derived. Based on the bound, the accuracy maximization problem is solved by decoupling it into two sub-problems. First, given the scheduled devices, the optimal bandwidth allocation suggests allocating more bandwidth to the devices with worse channel conditions or weaker computation capabilities. Then, a greedy device scheduling algorithm is introduced, which in each step selects the device consuming the least updating time obtained by the optimal bandwidth allocation, until the lower bound begins to increase, meaning that scheduling more devices will degrade the model accuracy. Experiments show that the proposed policy outperforms state-of-the-art scheduling policies under extensive settings of data distributions and cell radius.

cs.IT↗

arXiv2019

Device Scheduling with Fast Convergence for Wireless Federated Learning

Owing to the increasing need for massive data analysis and model training at the network edge, as well as the rising concerns about the data privacy, a new distributed training framework called federated learning (FL) has emerged. In each iteration of FL (called round), the edge devices update local models based on their own data and contribute to the global training by uploading the model updates via wireless channels. Due to the limited spectrum resources, only a portion of the devices can be scheduled in each round. While most of the existing work on scheduling focuses on the convergence of FL w.r.t. rounds, the convergence performance under a total training time budget is not yet explored. In this paper, a joint bandwidth allocation and scheduling problem is formulated to capture the long-term convergence performance of FL, and is solved by being decoupled into two sub-problems. For the bandwidth allocation sub-problem, the derived optimal solution suggests to allocate more bandwidth to the devices with worse channel conditions or weaker computation capabilities. For the device scheduling sub-problem, by revealing the trade-off between the number of rounds required to attain a certain model accuracy and the latency per round, a greedy policy is inspired, that continuously selects the device that consumes the least time in model updating until achieving a good trade-off between the learning efficiency and latency per round. The experiments show that the proposed policy outperforms other state-of-the-art scheduling policies, with the best achievable model accuracy under training time budgets.

cs.NI↗

arXiv2019

Improving Device-Edge Cooperative Inference of Deep Learning via 2-Step Pruning

Deep neural networks (DNNs) are state-of-the-art solutions for many machine learning applications, and have been widely used on mobile devices. Running DNNs on resource-constrained mobile devices often requires the help from edge servers via computation offloading. However, offloading through a bandwidth-limited wireless link is non-trivial due to the tight interplay between the computation resources on mobile devices and wireless resources. Existing studies have focused on cooperative inference where DNN models are partitioned at different neural network layers, and the two parts are executed at the mobile device and the edge server, respectively. Since the output data size of a DNN layer can be larger than that of the raw data, offloading intermediate data between layers can suffer from high transmission latency under limited wireless bandwidth. In this paper, we propose an efficient and flexible 2-step pruning framework for DNN partition between mobile devices and edge servers. In our framework, the DNN model only needs to be pruned once in the training phase where unimportant convolutional filters are removed iteratively. By limiting the pruning region, our framework can greatly reduce either the wireless transmission workload of the device or the total computation workload. A series of pruned models are generated in the training phase, from which the framework can automatically select to satisfy varying latency and accuracy requirements. Furthermore, coding for the intermediate data is added to provide extra transmission workload reduction. Our experiments show that the proposed framework can achieve up to 25.6$\times$ reduction on transmission workload, 6.01$\times$ acceleration on total computation and 4.81$\times$ reduction on end-to-end latency as compared to partitioning the original DNN model without pruning.

cs.NI↗