Multimodal Learning for Embryo Viability Prediction in Clinical IVF

In clinical In-Vitro Fertilization (IVF), identifying the most viable embryo for transfer is important to increasing the likelihood of a successful pregnancy. Traditionally, this process involves embryologists manually assessing embryos' static morphological features at specific intervals using light microscopy. This manual evaluation is not only time-intensive and costly, due to the need for expert analysis, but also inherently subjective, leading to variability in the selection process. To address these challenges, we develop a multimodal model that leverages both time-lapse video data and Electronic Health Records (EHRs) to predict embryo viability. One of the primary challenges of our research is to effectively combine time-lapse video and EHR data, owing to their inherent differences in modality. We comprehensively analyze our multimodal model with various modality inputs and integration approaches. Our approach will enable fast and automated embryo viability predictions in scale for clinical IVF.

Unleashing the Power of Task-Specific Directions in Parameter Efficient Fine-tuning

Large language models demonstrate impressive performance on downstream tasks, yet requiring extensive resource consumption when fully fine-tuning all parameters. To mitigate this, Parameter Efficient Fine-Tuning (PEFT) strategies, such as LoRA, have been developed. In this paper, we delve into the concept of task-specific directions--critical for transitioning large models from pre-trained states to task-specific enhancements in PEFT. We propose a framework to clearly define these directions and explore their properties, and practical utilization challenges. We then introduce a novel approach, LoRA-Dash, which aims to maximize the impact of task-specific directions during the fine-tuning process, thereby enhancing model performance on targeted tasks. Extensive experiments have conclusively demonstrated the effectiveness of LoRA-Dash, and in-depth analyses further reveal the underlying mechanisms of LoRA-Dash. The code is available at https://github.com/Chongjie-Si/Subspace-Tuning.

MoRA: LoRA Guided Multi-Modal Disease Diagnosis with Missing Modality

Multi-modal pre-trained models efficiently extract and fuse features from different modalities with low memory requirements for fine-tuning. Despite this efficiency, their application in disease diagnosis is under-explored. A significant challenge is the frequent occurrence of missing modalities, which impairs performance. Additionally, fine-tuning the entire pre-trained model demands substantial computational resources. To address these issues, we introduce Modality-aware Low-Rank Adaptation (MoRA), a computationally efficient method. MoRA projects each input to a low intrinsic dimension but uses different modality-aware up-projections for modality-specific adaptation in cases of missing modalities. Practically, MoRA integrates into the first block of the model, significantly improving performance when a modality is missing. It requires minimal computational resources, with less than 1.6% of the trainable parameters needed compared to training the entire model. Experimental results show that MoRA outperforms existing techniques in disease diagnosis, demonstrating superior performance, robustness, and training efficiency.

BeyondCT: A deep learning model for predicting pulmonary function from chest CT scans

Abstract Background: Pulmonary function tests (PFTs) and computed tomography (CT) imaging are vital in diagnosing, managing, and monitoring lung diseases. A common issue in practice is the lack of access to recorded pulmonary functions despite available chest CT scans. Purpose: To develop and validate a deep learning algorithm for predicting pulmonary function directly from chest CT scans. Methods: The development cohort came from the Pittsburgh Lung Screening Study (PLuSS) (n=3619). The validation cohort came from the Specialized Centers of Clinically Oriented Research (SCCOR) in COPD (n=662). A deep learning model called BeyondCT, combining a three-dimensional (3D) convolutional neural network (CNN) and Vision Transformer (ViT) architecture, was used to predict forced vital capacity (FVC) and forced expiratory volume in one second (FEV1) from non-contrasted inspiratory chest CT scans. A 3D CNN model without ViT was used for comparison. Subject demographics (age, gender, smoking status) were also incorporated into the model. Performance was compared to actual PFTs using mean absolute error (MAE, L), percentage error, and R square. Results: The 3D-CNN model achieved MAEs of 0.395 L and 0.383 L, percentage errors of 13.84% and 18.85%, and R square of 0.665 and 0.679 for FVC and FEV1, respectively. The BeyondCT model without demographics had MAEs of 0.362 L and 0.371 L, percentage errors of 10.89% and 14.96%, and R square of 0.719 and 0.727, respectively. Including demographics improved performance (p<0.05), with MAEs of 0.356 L and 0.353 L, percentage errors of 10.79% and 14.82%, and R square of 0.77 and 0.739 for FVC and FEV1 in the test set. Conclusion: The BeyondCT model showed robust performance in predicting lung function from non-contrast inspiratory chest CT scans.