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Rethinking Retrieval-Augmented Generation for Medicine: A Large-Scale, Systematic Expert Evaluation and Practical Insights

Kim, Hyunjae, Sohn, Jiwoong, Gilson, Aidan, Cochran-Caggiano, Nicholas, Applebaum, Serina, Jin, Heeju, Park, Seihee, Park, Yujin, Park, Jiyeong, Choi, Seoyoung, Contreras, Brittany Alexandra Herrera, Huang, Thomas, Yun, Jaehoon, Wei, Ethan F., Jiang, Roy, Colucci, Leah, Lai, Eric, Dave, Amisha, Guo, Tuo, Singer, Maxwell B., Koo, Yonghoe, Adelman, Ron A., Zou, James, Taylor, Andrew, Cohan, Arman, Xu, Hua, Chen, Qingyu

arXiv.org Artificial Intelligence

Large language models (LLMs) are transforming the landscape of medicine, yet two fundamental challenges persist: keeping up with rapidly evolving medical knowledge and providing verifiable, evidence-grounded reasoning. Retrieval-augmented generation (RAG) has been widely adopted to address these limitations by supplementing model outputs with retrieved evidence. However, whether RAG reliably achieves these goals remains unclear. Here, we present the most comprehensive expert evaluation of RAG in medicine to date. Eighteen medical experts contributed a total of 80,502 annotations, assessing 800 model outputs generated by GPT-4o and Llama-3.1-8B across 200 real-world patient and USMLE-style queries. We systematically decomposed the RAG pipeline into three components: (i) evidence retrieval (relevance of retrieved passages), (ii) evidence selection (accuracy of evidence usage), and (iii) response generation (factuality and completeness of outputs). Contrary to expectation, standard RAG often degraded performance: only 22% of top-16 passages were relevant, evidence selection remained weak (precision 41-43%, recall 27-49%), and factuality and completeness dropped by up to 6% and 5%, respectively, compared with non-RAG variants. Retrieval and evidence selection remain key failure points for the model, contributing to the overall performance drop. We further show that simple yet effective strategies, including evidence filtering and query reformulation, substantially mitigate these issues, improving performance on MedMCQA and MedXpertQA by up to 12% and 8.2%, respectively. These findings call for re-examining RAG's role in medicine and highlight the importance of stage-aware evaluation and deliberate system design for reliable medical LLM applications.


Evaluating the Limitations of Local LLMs in Solving Complex Programming Challenges

Matotek, Kadin, Cassel, Heather, Amiruzzaman, Md, Ngo, Linh B.

arXiv.org Artificial Intelligence

This study examines the performance of today's open-source, locally hosted large-language models (LLMs) in handling complex competitive programming tasks with extended problem descriptions and contexts. Building on the original Framework for AI-driven Code Generation Evaluation (FACE), the authors retrofit the pipeline to work entirely offline through the Ollama runtime, collapsing FACE's sprawling per-problem directory tree into a handful of consolidated JSON files, and adding robust checkpointing so multi-day runs can resume after failures. The enhanced framework generates, submits, and records solutions for the full Kattis corpus of 3,589 problems across eight code-oriented models ranging from 6.7-9 billion parameters. The submission results show that the overall pass@1 accuracy is modest for the local models, with the best models performing at approximately half the acceptance rate of the proprietary models, Gemini 1.5 and ChatGPT-4. These findings expose a persistent gap between private, cost-controlled LLM deployments and state-of-the-art proprietary services, yet also highlight the rapid progress of open models and the practical benefits of an evaluation workflow that organizations can replicate on in-house hardware.


Aligning LLMs for the Classroom with Knowledge-Based Retrieval -- A Comparative RAG Study

Jain, Amay, Cui, Liu, Chen, Si

arXiv.org Artificial Intelligence

Large language models like ChatGPT are increasingly used in classrooms, but they often provide outdated or fabricated information that can mislead students. Retrieval Augmented Generation (RAG) improves reliability of LLMs by grounding responses in external resources. We investigate two accessible RAG paradigms, vector-based retrieval and graph-based retrieval to identify best practices for classroom question answering (QA). Existing comparative studies fail to account for pedagogical factors such as educational disciplines, question types, and practical deployment costs. Using a novel dataset, EduScopeQA, of 3,176 questions across academic subjects, we measure performance on various educational query types, from specific facts to broad thematic discussions. We also evaluate system alignment with a dataset of systematically altered textbooks that contradict the LLM's latent knowledge. We find that OpenAI Vector Search RAG (representing vector-based RAG) performs well as a low-cost generalist, especially for quick fact retrieval. On the other hand, GraphRAG Global excels at providing pedagogically rich answers to thematic queries, and GraphRAG Local achieves the highest accuracy with the dense, altered textbooks when corpus integrity is critical. Accounting for the 10-20x higher resource usage of GraphRAG (representing graph-based RAG), we show that a dynamic branching framework that routes queries to the optimal retrieval method boosts fidelity and efficiency. These insights provide actionable guidelines for educators and system designers to integrate RAG-augmented LLMs into learning environments effectively.


AirRAG: Activating Intrinsic Reasoning for Retrieval Augmented Generation using Tree-based Search

Feng, Wenfeng, Hao, Chuzhan, Zhang, Yuewei, Song, Jingyi, Wang, Hao

arXiv.org Artificial Intelligence

Leveraging the autonomous decision-making capabilities of large language models (LLMs) has demonstrated superior performance in reasoning tasks. However, despite the success of iterative or recursive retrieval-augmented generation (RAG) techniques, these methods are often constrained to a single solution space when confronted with complex problems. In this paper, we propose a novel thinking pattern in RAG that integrates system analysis with efficient reasoning actions, significantly activating intrinsic reasoning capabilities and expanding the solution space of specific tasks via Monte Carlo Tree Search (MCTS), which we refer to as AirRAG. Specifically, our approach designs five fundamental reasoning actions, which are expanded to a broad tree-based reasoning space using MCTS. The approach also incorporates self-consistency verification to explore potential reasoning paths and inference scaling law. Additionally, computationally optimal strategies are employed to allocate more inference resources to key actions, thereby enhancing overall performance. Experimental results demonstrate the effectiveness of AirRAG, showing significant performance gains on complex question-answering datasets. Furthermore, AirRAG is flexible and lightweight, making it easy to integrate with other advanced technologies.


Neural network interpretability with layer-wise relevance propagation: novel techniques for neuron selection and visualization

Bhati, Deepshikha, Neha, Fnu, Amiruzzaman, Md, Guercio, Angela, Shukla, Deepak Kumar, Ward, Ben

arXiv.org Artificial Intelligence

Interpreting complex neural networks is crucial for understanding their decision-making processes, particularly in applications where transparency and accountability are essential. This proposed method addresses this need by focusing on layer-wise Relevance Propagation (LRP), a technique used in explainable artificial intelligence (XAI) to attribute neural network outputs to input features through backpropagated relevance scores. Existing LRP methods often struggle with precision in evaluating individual neuron contributions. To overcome this limitation, we present a novel approach that improves the parsing of selected neurons during LRP backward propagation, using the Visual Geometry Group 16 (VGG16) architecture as a case study. Our method creates neural network graphs to highlight critical paths and visualizes these paths with heatmaps, optimizing neuron selection through accuracy metrics like Mean Squared Error (MSE) and Symmetric Mean Absolute Percentage Error (SMAPE). Additionally, we utilize a deconvolutional visualization technique to reconstruct feature maps, offering a comprehensive view of the network's inner workings. Extensive experiments demonstrate that our approach enhances interpretability and supports the development of more transparent artificial intelligence (AI) systems for computer vision applications. This advancement has the potential to improve the trustworthiness of AI models in real-world machine vision applications, thereby increasing their reliability and effectiveness.


A Tiered GAN Approach for Monet-Style Image Generation

Neha, FNU, Bhati, Deepshikha, Shukla, Deepak Kumar, Amiruzzaman, Md

arXiv.org Artificial Intelligence

Generative Adversarial Networks (GANs) have proven to be a powerful tool in generating artistic images, capable of mimicking the styles of renowned painters, such as Claude Monet. This paper introduces a tiered GAN model to progressively refine image quality through a multi-stage process, enhancing the generated images at each step. The model transforms random noise into detailed artistic representations, addressing common challenges such as instability in training, mode collapse, and output quality. This approach combines downsampling and convolutional techniques, enabling the generation of high-quality Monet-style artwork while optimizing computational efficiency. Experimental results demonstrate the architecture's ability to produce foundational artistic structures, though further refinements are necessary for achieving higher levels of realism and fidelity to Monet's style. Future work focuses on improving training methodologies and model complexity to bridge the gap between generated and true artistic images. Additionally, the limitations of traditional GANs in artistic generation are analyzed, and strategies to overcome these shortcomings are proposed.


From classical techniques to convolution-based models: A review of object detection algorithms

Neha, Fnu, Bhati, Deepshikha, Shukla, Deepak Kumar, Amiruzzaman, Md

arXiv.org Artificial Intelligence

Object detection is a fundamental task in computer vision and image understanding, with the goal of identifying and localizing objects of interest within an image while assigning them corresponding class labels. Traditional methods, which relied on handcrafted features and shallow models, struggled with complex visual data and showed limited performance. These methods combined low-level features with contextual information and lacked the ability to capture high-level semantics. Deep learning, especially Convolutional Neural Networks (CNNs), addressed these limitations by automatically learning rich, hierarchical features directly from data. These features include both semantic and high-level representations essential for accurate object detection. This paper reviews object detection frameworks, starting with classical computer vision methods. We categorize object detection approaches into two groups: (1) classical computer vision techniques and (2) CNN-based detectors. We compare major CNN models, discussing their strengths and limitations. In conclusion, this review highlights the significant advancements in object detection through deep learning and identifies key areas for further research to improve performance.


Distributed Swarm Intelligence

Kanjula, Karthik Reddy, Kolla, Sai Meghana

arXiv.org Artificial Intelligence

This paper presents the development of a distributed application that facilitates the understanding and application of swarm intelligence in solving optimization problems. The platform comprises a search space of customizable random particles, allowing users to tailor the solution to their specific needs. By leveraging the power of Ray distributed computing, the application can support multiple users simultaneously, offering a flexible and scalable solution. The primary objective of this project is to provide a user-friendly platform that enhances the understanding and practical use of swarm intelligence in problem-solving.


Light in the Larynx: a Miniaturized Robotic Optical Fiber for In-office Laser Surgery of the Vocal Folds

Chiluisa, Alex J., Pacheco, Nicholas E., Do, Hoang S., Tougas, Ryan M., Minch, Emily V., Mihaleva, Rositsa, Shen, Yao, Liu, Yuxiang, Carroll, Thomas L., Fichera, Loris

arXiv.org Artificial Intelligence

This letter reports the design, construction, and experimental validation of a novel hand-held robot for in-office laser surgery of the vocal folds. In-office endoscopic laser surgery is an emerging trend in Laryngology: It promises to deliver the same patient outcomes of traditional surgical treatment (i.e., in the operating room), at a fraction of the cost. Unfortunately, office procedures can be challenging to perform; the optical fibers used for laser delivery can only emit light forward in a line-of-sight fashion, which severely limits anatomical access. The robot we present in this letter aims to overcome these challenges. The end effector of the robot is a steerable laser fiber, created through the combination of a thin optical fiber (0.225 mm) with a tendon-actuated Nickel-Titanium notched sheath that provides bending. This device can be seamlessly used with most commercially available endoscopes, as it is sufficiently small (1.1 mm) to pass through a working channel. To control the fiber, we propose a compact actuation unit that can be mounted on top of the endoscope handle, so that, during a procedure, the operating physician can operate both the endoscope and the steerable fiber with a single hand. We report simulation and phantom experiments demonstrating that the proposed device substantially enhances surgical access compared to current clinical fibers.


Deep Graph Random Process for Relational-Thinking-Based Speech Recognition

Huang, Hengguan, Xue, Fuzhao, Wang, Hao, Wang, Ye

arXiv.org Machine Learning

Lying at the core of human intelligence, relational thinking is characterized by initially relying on innumerable unconscious percepts pertaining to relations between new sensory signals and prior knowledge, consequently becoming a recognizable concept or object through coupling and transformation of these percepts. Such mental processes are difficult to model in real-world problems such as in conversational automatic speech recognition (ASR), as the percepts (if they are modelled as graphs indicating relationships among utterances) are supposed to be innumerable and not directly observable. In this paper, we present a Bayesian nonparametric deep learning method called deep graph random process (DGP) that can generate an infinite number of probabilistic graphs representing percepts. We further provide a closed-form solution for coupling and transformation of these percept graphs for acoustic modeling. Our approach is able to successfully infer relations among utterances without using any relational data during training. Experimental evaluations on ASR tasks including CHiME-2 and CHiME-5 demonstrate the effectiveness and benefits of our method.