SearchRAG: Can Search Engines Be Helpful for LLM-based Medical Question Answering?

Large Language Models (LLMs) have shown remarkable capabilities in general domains but often struggle with tasks requiring specialized knowledge. Conventional Retrieval-Augmented Generation (RAG) techniques typically retrieve external information from static knowledge bases, which can be outdated or incomplete, missing fine-grained clinical details essential for accurate medical question answering. In this work, we propose SearchRAG, a novel framework that overcomes these limitations by leveraging real-time search engines. Our method employs synthetic query generation to convert complex medical questions into search-engine-friendly queries and utilizes uncertainty-based knowledge selection to filter and incorporate the most relevant and informative medical knowledge into the LLM's input. Experimental results demonstrate that our method significantly improves response accuracy in medical question answering tasks, particularly for complex questions requiring detailed and up-to-date knowledge.

Fine-Tuning Open-Source Large Language Models to Improve Their Performance on Radiation Oncology Tasks: A Feasibility Study to Investigate Their Potential Clinical Applications in Radiation Oncology

Background: The radiation oncology clinical practice involves many steps relying on the dynamic interplay of abundant text data. Large language models have displayed remarkable capabilities in processing complex text information. But their direct applications in specific fields like radiation oncology remain underexplored. Purpose: This study aims to investigate whether fine-tuning LLMs with domain knowledge can improve the performance on Task (1) treatment regimen generation, Task (2) treatment modality selection (photon, proton, electron, or brachytherapy), and Task (3) ICD-10 code prediction in radiation oncology. Methods: Data for 15,724 patient cases were extracted. Cases where patients had a single diagnostic record, and a clearly identifiable primary treatment plan were selected for preprocessing and manual annotation to have 7,903 cases of the patient diagnosis, treatment plan, treatment modality, and ICD-10 code. Each case was used to construct a pair consisting of patient diagnostics details and an answer (treatment regimen, treatment modality, or ICD-10 code respectively) for the supervised fine-tuning of these three tasks. Open source LLaMA2-7B and Mistral-7B models were utilized for the fine-tuning with the Low-Rank Approximations method. Accuracy and ROUGE-1 score were reported for the fine-tuned models and original models. Clinical evaluation was performed on Task (1) by radiation oncologists, while precision, recall, and F-1 score were evaluated for Task (2) and (3). One-sided Wilcoxon signed-rank tests were used to statistically analyze the results. Results: Fine-tuned LLMs outperformed original LLMs across all tasks with p-value <= 0.001. Clinical evaluation demonstrated that over 60% of the fine-tuned LLMs-generated treatment regimens were clinically acceptable. Precision, recall, and F1-score showed improved performance of fine-tuned LLMs.

Large Language Models for Bioinformatics

With the rapid advancements in large language model (LLM) technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and limitations inherent in BioLMs, including data privacy and security concerns, interpretability issues, biases in training data and model outputs, and domain adaptation complexities. Finally, we highlight emerging trends and future directions, offering valuable insights to guide researchers and clinicians toward advancing BioLMs for increasingly sophisticated biological and clinical applications.

End-to-End Deep Learning for Interior Tomography with Low-Dose X-ray CT

Objective: There exist several X-ray computed tomography (CT) scanning strategies to reduce a radiation dose, such as (1) sparse-view CT, (2) low-dose CT, and (3) region-of-interest (ROI) CT (called interior tomography). To further reduce the dose, the sparse-view and/or low-dose CT settings can be applied together with interior tomography. Interior tomography has various advantages in terms of reducing the number of detectors and decreasing the X-ray radiation dose. However, a large patient or small field-of-view (FOV) detector can cause truncated projections, and then the reconstructed images suffer from severe cupping artifacts. In addition, although the low-dose CT can reduce the radiation exposure dose, analytic reconstruction algorithms produce image noise. Recently, many researchers have utilized image-domain deep learning (DL) approaches to remove each artifact and demonstrated impressive performances, and the theory of deep convolutional framelets supports the reason for the performance improvement. Approach: In this paper, we found that the image-domain convolutional neural network (CNN) is difficult to solve coupled artifacts, based on deep convolutional framelets. Significance: To address the coupled problem, we decouple it into two sub-problems: (i) image domain noise reduction inside truncated projection to solve low-dose CT problem and (ii) extrapolation of projection outside truncated projection to solve the ROI CT problem. The decoupled sub-problems are solved directly with a novel proposed end-to-end learning using dual-domain CNNs. Main results: We demonstrate that the proposed method outperforms the conventional image-domain deep learning methods, and a projection-domain CNN shows better performance than the image-domain CNNs which are commonly used by many researchers.

An Ordinary Differential Equation Sampler with Stochastic Start for Diffusion Bridge Models

Diffusion bridge models have demonstrated promising performance in conditional image generation tasks, such as image restoration and translation, by initializing the generative process from corrupted images instead of pure Gaussian noise. However, existing diffusion bridge models often rely on Stochastic Differential Equation (SDE) samplers, which result in slower inference speed compared to diffusion models that employ high-order Ordinary Differential Equation (ODE) solvers for acceleration. To mitigate this gap, we propose a high-order ODE sampler with a stochastic start for diffusion bridge models. To overcome the singular behavior of the probability flow ODE (PF-ODE) at the beginning of the reverse process, a posterior sampling approach was introduced at the first reverse step. The sampling was designed to ensure a smooth transition from corrupted images to the generative trajectory while reducing discretization errors. Following this stochastic start, Heun's second-order solver is applied to solve the PF-ODE, achieving high perceptual quality with significantly reduced neural function evaluations (NFEs). Our method is fully compatible with pretrained diffusion bridge models and requires no additional training. Extensive experiments on image restoration and translation tasks, including super-resolution, JPEG restoration, Edges-to-Handbags, and DIODE-Outdoor, demonstrated that our sampler outperforms state-of-the-art methods in both visual quality and Frechet Inception Distance (FID).

Enhancing LLMs for Impression Generation in Radiology Reports through a Multi-Agent System

This study introduces "RadCouncil," a multi-agent Large Language Model (LLM) framework designed to enhance the generation of impressions in radiology reports from the finding section. RadCouncil comprises three specialized agents: 1) a "Retrieval" Agent that identifies and retrieves similar reports from a vector database, 2) a "Radiologist" Agent that generates impressions based on the finding section of the given report plus the exemplar reports retrieved by the Retrieval Agent, and 3) a "Reviewer" Agent that evaluates the generated impressions and provides feedback. The performance of RadCouncil was evaluated using both quantitative metrics (BLEU, ROUGE, BERTScore) and qualitative criteria assessed by GPT-4, using chest X-ray as a case study. Experiment results show improvements in RadCouncil over the single-agent approach across multiple dimensions, including diagnostic accuracy, stylistic concordance, and clarity. This study highlights the potential of utilizing multiple interacting LLM agents, each with a dedicated task, to enhance performance in specialized medical tasks and the development of more robust and adaptable healthcare AI solutions.

Towards Next-Generation Medical Agent: How o1 is Reshaping Decision-Making in Medical Scenarios

Artificial Intelligence (AI) has become essential in modern healthcare, with large language models (LLMs) offering promising advances in clinical decision-making. Traditional model-based approaches, including those leveraging in-context demonstrations and those with specialized medical fine-tuning, have demonstrated strong performance in medical language processing but struggle with real-time adaptability, multi-step reasoning, and handling complex medical tasks. Agent-based AI systems address these limitations by incorporating reasoning traces, tool selection based on context, knowledge retrieval, and both short- and long-term memory. These additional features enable the medical AI agent to handle complex medical scenarios where decision-making should be built on real-time interaction with the environment. Therefore, unlike conventional model-based approaches that treat medical queries as isolated questions, medical AI agents approach them as complex tasks and behave more like human doctors. In this paper, we study the choice of the backbone LLM for medical AI agents, which is the foundation for the agent's overall reasoning and action generation. In particular, we consider the emergent o1 model and examine its impact on agents' reasoning, tool-use adaptability, and real-time information retrieval across diverse clinical scenarios, including high-stakes settings such as intensive care units (ICUs). Our findings demonstrate o1's ability to enhance diagnostic accuracy and consistency, paving the way for smarter, more responsive AI tools that support better patient outcomes and decision-making efficacy in clinical practice.

EchoFM: Foundation Model for Generalizable Echocardiogram Analysis

Foundation models have recently gained significant attention because of their generalizability and adaptability across multiple tasks and data distributions. Although medical foundation models have emerged, solutions for cardiac imaging, especially echocardiography videos, are still unexplored. In this paper, we introduce EchoFM, a foundation model specifically designed to represent and analyze echocardiography videos. In EchoFM, we propose a self-supervised learning framework that captures both spatial and temporal variability patterns through a spatio-temporal consistent masking strategy and periodic-driven contrastive learning. This framework can effectively capture the spatio-temporal dynamics of echocardiography and learn the representative video features without any labels. We pre-train our model on an extensive dataset comprising over 290,000 echocardiography videos covering 26 scan views across different imaging modes, with up to 20 million frames of images. The pre-trained EchoFM can then be easily adapted and fine-tuned for a variety of downstream tasks, serving as a robust backbone model. Our evaluation was systemically designed for four downstream tasks after the echocardiography examination routine. Experiment results show that EchoFM surpasses state-of-the-art methods, including specialized echocardiography methods, self-supervised pre-training models, and general-purposed pre-trained foundation models, across all downstream tasks.

Retrieval Instead of Fine-tuning: A Retrieval-based Parameter Ensemble for Zero-shot Learning

Foundation models have become a cornerstone in deep learning, with techniques like Low-Rank Adaptation (LoRA) offering efficient fine-tuning of large models. Similarly, methods such as Retrieval-Augmented Generation (RAG), which leverage vectorized databases, have further improved model performance by grounding outputs in external information. While these approaches have demonstrated notable success, they often require extensive training or labeled data, which can limit their adaptability in resource-constrained environments. To address these challenges, we introduce Retrieval-based Parameter Ensemble (RPE), a new method that creates a vectorized database of LoRAs, enabling efficient retrieval and application of model adaptations to new tasks. RPE minimizes the need for extensive training and eliminates the requirement for labeled data, making it particularly effective for zero-shot learning. Additionally, RPE is well-suited for privacy-sensitive domains like healthcare, as it modifies model parameters without accessing raw data. When applied to tasks such as medical report generation and image segmentation, RPE not only proved effective but also surpassed supervised fine-tuning methods in certain cases, highlighting its potential to enhance both computational efficiency and privacy in deep learning applications.

ECHOPulse: ECG controlled echocardio-grams video generation

Echocardiography (ECHO) is essential for cardiac assessments, but its video quality and interpretation heavily relies on manual expertise, leading to inconsistent results from clinical and portable devices. ECHO video generation offers a solution by improving automated monitoring through synthetic data and generating high-quality videos from routine health data. However, existing models often face high computational costs, slow inference, and rely on complex conditional prompts that require experts' annotations. To address these challenges, we propose ECHOPULSE, an ECG-conditioned ECHO video generation model. ECHOPULSE introduces two key advancements: (1) it accelerates ECHO video generation by leveraging VQ-VAE tokenization and masked visual token modeling for fast decoding, and (2) it conditions on readily accessible ECG signals, which are highly coherent with ECHO videos, bypassing complex conditional prompts. To the best of our knowledge, this is the first work to use time-series prompts like ECG signals for ECHO video generation. ECHOPULSE not only enables controllable synthetic ECHO data generation but also provides updated cardiac function information for disease monitoring and prediction beyond ECG alone. Evaluations on three public and private datasets demonstrate state-of-the-art performance in ECHO video generation across both qualitative and quantitative measures. Additionally, ECHOPULSE can be easily generalized to other modality generation tasks, such as cardiac MRI, fMRI, and 3D CT generation. Demo can seen from \url{https://github.com/levyisthebest/ECHOPulse_Prelease}.