TWIN-GPT: Digital Twins for Clinical Trials via Large Language Model

Recently, there has been a burgeoning interest in virtual clinical trials, which simulate real-world scenarios and hold the potential to significantly enhance patient safety, expedite development, reduce costs, and contribute to the broader scientific knowledge in healthcare. Existing research often focuses on leveraging electronic health records (EHRs) to support clinical trial outcome prediction. Yet, trained with limited clinical trial outcome data, existing approaches frequently struggle to perform accurate predictions. Some research has attempted to generate EHRs to augment model development but has fallen short in personalizing the generation for individual patient profiles. Recently, the emergence of large language models has illuminated new possibilities, as their embedded comprehensive clinical knowledge has proven beneficial in addressing medical issues. In this paper, we propose a large language model-based digital twin creation approach, called TWIN-GPT. TWIN-GPT can establish cross-dataset associations of medical information given limited data, generating unique personalized digital twins for different patients, thereby preserving individual patient characteristics. Comprehensive experiments show that using digital twins created by TWIN-GPT can boost clinical trial outcome prediction, exceeding various previous prediction approaches. Besides, we also demonstrate that TWIN-GPT can generate high-fidelity trial data that closely approximate specific patients, aiding in more accurate result predictions in data-scarce situations. Moreover, our study provides practical evidence for the application of digital twins in healthcare, highlighting its potential significance.

Uncertainty Quantification on Clinical Trial Outcome Prediction

The importance of uncertainty quantification is increasingly recognized in the diverse field of machine learning. Accurately assessing model prediction uncertainty can help provide deeper understanding and confidence for researchers and practitioners. This is especially critical in medical diagnosis and drug discovery areas, where reliable predictions directly impact research quality and patient health. In this paper, we proposed incorporating uncertainty quantification into clinical trial outcome predictions. Our main goal is to enhance the model's ability to discern nuanced differences, thereby significantly improving its overall performance. We have adopted a selective classification approach to fulfill our objective, integrating it seamlessly with the Hierarchical Interaction Network (HINT), which is at the forefront of clinical trial prediction modeling. Selective classification, encompassing a spectrum of methods for uncertainty quantification, empowers the model to withhold decision-making in the face of samples marked by ambiguity or low confidence, thereby amplifying the accuracy of predictions for the instances it chooses to classify. A series of comprehensive experiments demonstrate that incorporating selective classification into clinical trial predictions markedly enhances the model's performance, as evidenced by significant upticks in pivotal metrics such as PR-AUC, F1, ROC-AUC, and overall accuracy. Specifically, the proposed method achieved 32.37\%, 21.43\%, and 13.27\% relative improvement on PR-AUC over the base model (HINT) in phase I, II, and III trial outcome prediction, respectively. When predicting phase III, our method reaches 0.9022 PR-AUC scores. These findings illustrate the robustness and prospective utility of this strategy within the area of clinical trial predictions, potentially setting a new benchmark in the field.

GenoCraft: A Comprehensive, User-Friendly Web-Based Platform for High-Throughput Omics Data Analysis and Visualization

The surge in high-throughput omics data has reshaped the landscape of biological research, underlining the need for powerful, user-friendly data analysis and interpretation tools. This paper presents GenoCraft, a web-based comprehensive software solution designed to handle the entire pipeline of omics data processing. GenoCraft offers a unified platform featuring advanced bioinformatics tools, covering all aspects of omics data analysis. It encompasses a range of functionalities, such as normalization, quality control, differential analysis, network analysis, pathway analysis, and diverse visualization techniques. This software makes state-of-the-art omics data analysis more accessible to a wider range of users. With GenoCraft, researchers and data scientists have access to an array of cutting-edge bioinformatics tools under a user-friendly interface, making it a valuable resource for managing and analyzing large-scale omics data. The API with an interactive web interface is publicly available at https://genocraft.stanford. edu/. We also release all the codes in https://github.com/futianfan/GenoCraft.

Machine Learning for Synthetic Data Generation: a Review

Data plays a crucial role in machine learning. However, in real-world applications, there are several problems with data, e.g., data are of low quality; a limited number of data points lead to under-fitting of the machine learning model; it is hard to access the data due to privacy, safety and regulatory concerns. \textit{Synthetic data generation} offers a promising new avenue, as it can be shared and used in ways that real-world data cannot. This paper systematically reviews the existing works that leverage machine learning models for synthetic data generation. Specifically, we discuss the synthetic data generation works from several perspectives: (i) applications, including computer vision, speech, natural language, healthcare, and business; (ii) machine learning methods, particularly neural network architectures and deep generative models; (iii) privacy and fairness issue. In addition, we identify the challenges and opportunities in this emerging field and suggest future research directions.

Deep Learning based Multi-Label Image Classification of Protest Activities

With the rise of internet technology amidst increasing rates of urbanization, sharing information has never been easier thanks to globally-adopted platforms for digital communication. The resulting output of massive amounts of user-generated data can be used to enhance our understanding of significant societal issues particularly for urbanizing areas. In order to better analyze protest behavior, we enhanced the GSR dataset and manually labeled all the images. We used deep learning techniques to analyze social media data to detect social unrest through image classification, which performed good in predict multi-attributes, then also used map visualization to display protest behaviors across the country.