Mia K. Markey

Mengkun Chen, Yen-Tung Liu, Fadeel Sher Khan et al.

Virtual staining streamlines traditional staining procedures by digitally generating stained images from unstained or differently stained images. While conventional staining methods involve time-consuming chemical processes, virtual staining offers an efficient and low infrastructure alternative. Leveraging microscopy-based techniques, such as confocal microscopy, researchers can expedite tissue analysis without the need for physical sectioning. However, interpreting grayscale or pseudo-color microscopic images remains a challenge for pathologists and surgeons accustomed to traditional histologically stained images. To fill this gap, various studies explore digitally simulating staining to mimic targeted histological stains. This paper introduces a novel network, In-and-Out Net, specifically designed for virtual staining tasks. Based on Generative Adversarial Networks (GAN), our model efficiently transforms Reflectance Confocal Microscopy (RCM) images into Hematoxylin and Eosin (H&E) stained images. We enhance nuclei contrast in RCM images using aluminum chloride preprocessing for skin tissues. Training the model with virtual H\&E labels featuring two fluorescence channels eliminates the need for image registration and provides pixel-level ground truth. Our contributions include proposing an optimal training strategy, conducting a comparative analysis demonstrating state-of-the-art performance, validating the model through an ablation study, and collecting perfectly matched input and ground truth images without registration. In-and-Out Net showcases promising results, offering a valuable tool for virtual staining tasks and advancing the field of histological image analysis.

Seungjun Yi, Joakim Nguyen, Huimin Xu et al.

Congenital heart disease (CHD) presents complex, lifelong challenges often underrepresented in traditional clinical metrics. While unstructured narratives offer rich insights into patient and caregiver experiences, manual thematic analysis (TA) remains labor-intensive and unscalable. We propose a fully automated large language model (LLM) pipeline that performs end-to-end TA on clinical narratives, which eliminates the need for manual coding or full transcript review. Our system employs a novel multi-agent framework, where specialized LLM agents assume roles to enhance theme quality and alignment with human analysis. To further improve thematic relevance, we optionally integrate reinforcement learning from human feedback (RLHF). This supports scalable, patient-centered analysis of large qualitative datasets and allows LLMs to be fine-tuned for specific clinical contexts.

Seungjun Yi, Joakim Nguyen, Terence Lim et al.

This position paper examines how large language models (LLMs) can support thematic analysis of unstructured clinical transcripts, a widely used but resource-intensive method for uncovering patterns in patient and provider narratives. We conducted a systematic review of recent studies applying LLMs to thematic analysis, complemented by an interview with a practicing clinician. Our findings reveal that current approaches remain fragmented across multiple dimensions including types of thematic analysis, datasets, prompting strategies and models used, most notably in evaluation. Existing evaluation methods vary widely (from qualitative expert review to automatic similarity metrics), hindering progress and preventing meaningful benchmarking across studies. We argue that establishing standardized evaluation practices is critical for advancing the field. To this end, we propose an evaluation framework centered on three dimensions: validity, reliability, and interpretability.

Seungjun Yi, Joakim Nguyen, Huimin Xu et al.

Thematic Analysis (TA) is a widely used qualitative method that provides a structured yet flexible framework for identifying and reporting patterns in clinical interview transcripts. However, manual thematic analysis is time-consuming and limits scalability. Recent advances in LLMs offer a pathway to automate thematic analysis, but alignment with human results remains limited. To address these limitations, we propose SFT-TA, an automated thematic analysis framework that embeds supervised fine-tuned (SFT) agents within a multi-agent system. Our framework outperforms existing frameworks and the gpt-4o baseline in alignment with human reference themes. We observed that SFT agents alone may underperform, but achieve better results than the baseline when embedded within a multi-agent system. Our results highlight that embedding SFT agents in specific roles within a multi-agent system is a promising pathway to improve alignment with desired outputs for thematic analysis.

Sungsoo Kim, Jin Soo Park, Christos G. Bampis et al.

We propose a video compression framework using conditional Generative Adversarial Networks (GANs). We rely on two encoders: one that deploys a standard video codec and another which generates low-level maps via a pipeline of down-sampling, a newly devised soft edge detector, and a novel lossless compression scheme. For decoding, we use a standard video decoder as well as a neural network based one, which is trained using a conditional GAN. Recent "deep" approaches to video compression require multiple videos to pre-train generative networks to conduct interpolation. In contrast to this prior work, our scheme trains a generative decoder on pairs of a very limited number of key frames taken from a single video and corresponding low-level maps. The trained decoder produces reconstructed frames relying on a guidance of low-level maps, without any interpolation. Experiments on a diverse set of 131 videos demonstrate that our proposed GAN-based compression engine achieves much higher quality reconstructions at very low bitrates than prevailing standard codecs such as H.264 or HEVC.

Tejaswini Ganapathi, David Vining, Roland Bassett et al.

The purpose of this research is to evaluate the human and technical factors required to create a human-computer interface (HCI) for a structured reporting solution based on eye-gaze and speech signals. Gaze and speech signals from radiologists acquired during simulated image interpretation and dictation sessions were analyzed to determine a) variation of temporal relationship between eye gaze and speech in a dictation environment, and b) variation in eye movements for a particular image interpretation task among radiologists. Knowledge of these factors provides information regarding the complexity of the image interpretation or dictation task, and provides information that can be used to design a HCI for use in diagnostic radiology. Our ultimate goal is to use these data to create an HCI to automate the generation of a particular type of structured radiology report. Our data indicate that the a) temporal relationships between eye gaze and speech and b) scan paths substantially vary among radiologists, thus implying that an HCI system based on eye gaze and speech for automating the capture of data for structured reporting processes should be customized for each user. The image resolution and layout, image content, and order of targets during an image interpretation session are not relevant factors to consider when designing an HCI. Our findings can be applied to the design of other HCI solutions for radiological applications that involve visual inspection and verbal descriptions of image findings.