PathInsight: Instruction Tuning of Multimodal Datasets and Models for Intelligence Assisted Diagnosis in Histopathology

Pathological diagnosis remains the definitive standard for identifying tumors. The rise of multimodal large models has simplified the process of integrating image analysis with textual descriptions. Despite this advancement, the substantial costs associated with training and deploying these complex multimodal models, together with a scarcity of high-quality training datasets, create a significant divide between cutting-edge technology and its application in the clinical setting. We had meticulously compiled a dataset of approximately 45,000 cases, covering over 6 different tasks, including the classification of organ tissues, generating pathology report descriptions, and addressing pathology-related questions and answers. We have fine-tuned multimodal large models, specifically LLaVA, Qwen-VL, InternLM, with this dataset to enhance instruction-based performance. We conducted a qualitative assessment of the capabilities of the base model and the fine-tuned model in performing image captioning and classification tasks on the specific dataset. The evaluation results demonstrate that the fine-tuned model exhibits proficiency in addressing typical pathological questions. We hope that by making both our models and datasets publicly available, they can be valuable to the medical and research communities.

What a Whole Slide Image Can Tell? Subtype-guided Masked Transformer for Pathological Image Captioning

Pathological captioning of Whole Slide Images (WSIs), though is essential in computer-aided pathological diagnosis, has rarely been studied due to the limitations in datasets and model training efficacy. In this paper, we propose a new paradigm Subtype-guided Masked Transformer (SGMT) for pathological captioning based on Transformers, which treats a WSI as a sequence of sparse patches and generates an overall caption sentence from the sequence. An accompanying subtype prediction is introduced into SGMT to guide the training process and enhance the captioning accuracy. We also present an Asymmetric Masked Mechansim approach to tackle the large size constraint of pathological image captioning, where the numbers of sequencing patches in SGMT are sampled differently in the training and inferring phases, respectively. Experiments on the PatchGastricADC22 dataset demonstrate that our approach effectively adapts to the task with a transformer-based model and achieves superior performance than traditional RNN-based methods. Our codes are to be made available for further research and development.

HTEC: Human Transcription Error Correction

High-quality human transcription is essential for training and improving Automatic Speech Recognition (ASR) models. Recent study~\cite{libricrowd} has found that every 1% worse transcription Word Error Rate (WER) increases approximately 2% ASR WER by using the transcriptions to train ASR models. Transcription errors are inevitable for even highly-trained annotators. However, few studies have explored human transcription correction. Error correction methods for other problems, such as ASR error correction and grammatical error correction, do not perform sufficiently for this problem. Therefore, we propose HTEC for Human Transcription Error Correction. HTEC consists of two stages: Trans-Checker, an error detection model that predicts and masks erroneous words, and Trans-Filler, a sequence-to-sequence generative model that fills masked positions. We propose a holistic list of correction operations, including four novel operations handling deletion errors. We further propose a variant of embeddings that incorporates phoneme information into the input of the transformer. HTEC outperforms other methods by a large margin and surpasses human annotators by 2.2% to 4.5% in WER. Finally, we deployed HTEC to assist human annotators and showed HTEC is particularly effective as a co-pilot, which improves transcription quality by 15.1% without sacrificing transcription velocity.