TrialEnroll: Predicting Clinical Trial Enrollment Success with Deep & Cross Network and Large Language Models

Clinical trials need to recruit a sufficient number of volunteer patients to demonstrate the statistical power of the treatment (e.g., a new drug) in curing a certain disease. Clinical trial recruitment has a significant impact on trial success. Forecasting whether the recruitment process would be successful before we run the trial would save many resources and time. This paper develops a novel deep & cross network with large language model (LLM)-augmented text feature that learns semantic information from trial eligibility criteria and predicts enrollment success. The proposed method enables interpretability by understanding which sentence/word in eligibility criteria contributes heavily to prediction. We also demonstrate the empirical superiority of the proposed method (0.7002 PR-AUC) over a bunch of well-established machine learning methods. The code and curated dataset are publicly available at https://anonymous.4open.science/r/TrialEnroll-7E12.

Team up GBDTs and DNNs: Advancing Efficient and Effective Tabular Prediction with Tree-hybrid MLPs

Tabular datasets play a crucial role in various applications. Thus, developing efficient, effective, and widely compatible prediction algorithms for tabular data is important. Currently, two prominent model types, Gradient Boosted Decision Trees (GBDTs) and Deep Neural Networks (DNNs), have demonstrated performance advantages on distinct tabular prediction tasks. However, selecting an effective model for a specific tabular dataset is challenging, often demanding time-consuming hyperparameter tuning. To address this model selection dilemma, this paper proposes a new framework that amalgamates the advantages of both GBDTs and DNNs, resulting in a DNN algorithm that is as efficient as GBDTs and is competitively effective regardless of dataset preferences for GBDTs or DNNs. Our idea is rooted in an observation that deep learning (DL) offers a larger parameter space that can represent a well-performing GBDT model, yet the current back-propagation optimizer struggles to efficiently discover such optimal functionality. On the other hand, during GBDT development, hard tree pruning, entropy-driven feature gate, and model ensemble have proved to be more adaptable to tabular data. By combining these key components, we present a Tree-hybrid simple MLP (T-MLP). In our framework, a tensorized, rapidly trained GBDT feature gate, a DNN architecture pruning approach, as well as a vanilla back-propagation optimizer collaboratively train a randomly initialized MLP model. Comprehensive experiments show that T-MLP is competitive with extensively tuned DNNs and GBDTs in their dominating tabular benchmarks (88 datasets) respectively, all achieved with compact model storage and significantly reduced training duration.

TrialBench: Multi-Modal Artificial Intelligence-Ready Clinical Trial Datasets

Clinical trials are pivotal for developing new medical treatments, yet they typically pose some risks such as patient mortality, adverse events, and enrollment failure that waste immense efforts spanning over a decade. Applying artificial intelligence (AI) to forecast or simulate key events in clinical trials holds great potential for providing insights to guide trial designs. However, complex data collection and question definition requiring medical expertise and a deep understanding of trial designs have hindered the involvement of AI thus far. This paper tackles these challenges by presenting a comprehensive suite of meticulously curated AIready datasets covering multi-modal data (e.g., drug molecule, disease code, text, categorical/numerical features) and 8 crucial prediction challenges in clinical trial design, encompassing prediction of trial duration, patient dropout rate, serious adverse event, mortality rate, trial approval outcome, trial failure reason, drug dose finding, design of eligibility criteria. Furthermore, we provide basic validation methods for each task to ensure the datasets' usability and reliability. We anticipate that the availability of such open-access datasets will catalyze the development of advanced AI approaches for clinical trial design, ultimately advancing clinical trial research and accelerating medical solution development. The curated dataset, metrics, and basic models are publicly available at https://github.com/ML2Health/ML2ClinicalTrials/tree/main/AI4Trial.

What is the Visual Cognition Gap between Humans and Multimodal LLMs?

Recently, Multimodal Large Language Models (MLLMs) have shown great promise in language-guided perceptual tasks such as recognition, segmentation, and object detection. However, their effectiveness in addressing visual cognition problems that require high-level reasoning is not well-established. One such challenge is abstract visual reasoning (AVR) -- the cognitive ability to discern relationships among patterns in a set of images and extrapolate to predict subsequent patterns. This skill is crucial during the early neurodevelopmental stages of children. Inspired by the AVR tasks in Raven's Progressive Matrices (RPM) and Wechsler Intelligence Scale for Children (WISC), we propose a new dataset MaRs-VQA and a new benchmark VCog-Bench containing three datasets to evaluate the zero-shot AVR capability of MLLMs and compare their performance with existing human intelligent investigation. Our comparative experiments with different open-source and closed-source MLLMs on the VCog-Bench revealed a gap between MLLMs and human intelligence, highlighting the visual cognitive limitations of current MLLMs. We believe that the public release of VCog-Bench, consisting of MaRs-VQA, and the inference pipeline will drive progress toward the next generation of MLLMs with human-like visual cognition abilities.

Cross-Table Pretraining towards a Universal Function Space for Heterogeneous Tabular Data

Tabular data from different tables exhibit significant diversity due to varied definitions and types of features, as well as complex inter-feature and feature-target relationships. Cross-dataset pretraining, which learns reusable patterns from upstream data to support downstream tasks, have shown notable success in various fields. Yet, when applied to tabular data prediction, this paradigm faces challenges due to the limited reusable patterns among diverse tabular datasets (tables) and the general scarcity of tabular data available for fine-tuning. In this study, we fill this gap by introducing a cross-table pretrained Transformer, XTFormer, for versatile downstream tabular prediction tasks. Our methodology insight is pretraining XTFormer to establish a "meta-function" space that encompasses all potential feature-target mappings. In pre-training, a variety of potential mappings are extracted from pre-training tabular datasets and are embedded into the "meta-function" space, and suited mappings are extracted from the "meta-function" space for downstream tasks by a specified coordinate positioning approach. Experiments show that, in 190 downstream tabular prediction tasks, our cross-table pretrained XTFormer wins both XGBoost and Catboost on 137 (72%) tasks, and surpasses representative deep learning models FT-Transformer and the tabular pre-training approach XTab on 144 (76%) and 162 (85%) tasks.

TrialDura: Hierarchical Attention Transformer for Interpretable Clinical Trial Duration Prediction

The clinical trial process, also known as drug development, is an indispensable step toward the development of new treatments. The major objective of interventional clinical trials is to assess the safety and effectiveness of drug-based treatment in treating certain diseases in the human body. However, clinical trials are lengthy, labor-intensive, and costly. The duration of a clinical trial is a crucial factor that influences overall expenses. Therefore, effective management of the timeline of a clinical trial is essential for controlling the budget and maximizing the economic viability of the research. To address this issue, We propose TrialDura, a machine learning-based method that estimates the duration of clinical trials using multimodal data, including disease names, drug molecules, trial phases, and eligibility criteria. Then, we encode them into Bio-BERT embeddings specifically tuned for biomedical contexts to provide a deeper and more relevant semantic understanding of clinical trial data. Finally, the model's hierarchical attention mechanism connects all of the embeddings to capture their interactions and predict clinical trial duration. Our proposed model demonstrated superior performance with a mean absolute error (MAE) of 1.04 years and a root mean square error (RMSE) of 1.39 years compared to the other models, indicating more accurate clinical trial duration prediction. Publicly available code can be found at https://anonymous.4open.science/r/TrialDura-F196

Personalized Heart Disease Detection via ECG Digital Twin Generation

Heart diseases rank among the leading causes of global mortality, demonstrating a crucial need for early diagnosis and intervention. Most traditional electrocardiogram (ECG) based automated diagnosis methods are trained at population level, neglecting the customization of personalized ECGs to enhance individual healthcare management. A potential solution to address this limitation is to employ digital twins to simulate symptoms of diseases in real patients. In this paper, we present an innovative prospective learning approach for personalized heart disease detection, which generates digital twins of healthy individuals' anomalous ECGs and enhances the model sensitivity to the personalized symptoms. In our approach, a vector quantized feature separator is proposed to locate and isolate the disease symptom and normal segments in ECG signals with ECG report guidance. Thus, the ECG digital twins can simulate specific heart diseases used to train a personalized heart disease detection model. Experiments demonstrate that our approach not only excels in generating high-fidelity ECG signals but also improves personalized heart disease detection. Moreover, our approach ensures robust privacy protection, safeguarding patient data in model development.

Multi-rater Prompting for Ambiguous Medical Image Segmentation

Multi-rater annotations commonly occur when medical images are independently annotated by multiple experts (raters). In this paper, we tackle two challenges arisen in multi-rater annotations for medical image segmentation (called ambiguous medical image segmentation): (1) How to train a deep learning model when a group of raters produces a set of diverse but plausible annotations, and (2) how to fine-tune the model efficiently when computation resources are not available for re-training the entire model on a different dataset domain. We propose a multi-rater prompt-based approach to address these two challenges altogether. Specifically, we introduce a series of rater-aware prompts that can be plugged into the U-Net model for uncertainty estimation to handle multi-annotation cases. During the prompt-based fine-tuning process, only 0.3% of learnable parameters are required to be updated comparing to training the entire model. Further, in order to integrate expert consensus and disagreement, we explore different multi-rater incorporation strategies and design a mix-training strategy for comprehensive insight learning. Extensive experiments verify the effectiveness of our new approach for ambiguous medical image segmentation on two public datasets while alleviating the heavy burden of model re-training.

PoCo: A Self-Supervised Approach via Polar Transformation Based Progressive Contrastive Learning for Ophthalmic Disease Diagnosis

Automatic ophthalmic disease diagnosis on fundus images is important in clinical practice. However, due to complex fundus textures and limited annotated data, developing an effective automatic method for this problem is still challenging. In this paper, we present a self-supervised method via polar transformation based progressive contrastive learning, called PoCo, for ophthalmic disease diagnosis. Specifically, we novelly inject the polar transformation into contrastive learning to 1) promote contrastive learning pre-training to be faster and more stable and 2) naturally capture task-free and rotation-related textures, which provides insights into disease recognition on fundus images. Beneficially, simple normal translation-invariant convolution on transformed images can equivalently replace the complex rotation-invariant and sector convolution on raw images. After that, we develop a progressive contrastive learning method to efficiently utilize large unannotated images and a novel progressive hard negative sampling scheme to gradually reduce the negative sample number for efficient training and performance enhancement. Extensive experiments on three public ophthalmic disease datasets show that our PoCo achieves state-of-the-art performance with good generalization ability, validating that our method can reduce annotation efforts and provide reliable diagnosis. Codes are available at \url{https://github.com/wjh892521292/PoCo}.

Making Pre-trained Language Models Great on Tabular Prediction

The transferability of deep neural networks (DNNs) has made significant progress in image and language processing. However, due to the heterogeneity among tables, such DNN bonus is still far from being well exploited on tabular data prediction (e.g., regression or classification tasks). Condensing knowledge from diverse domains, language models (LMs) possess the capability to comprehend feature names from various tables, potentially serving as versatile learners in transferring knowledge across distinct tables and diverse prediction tasks, but their discrete text representation space is inherently incompatible with numerical feature values in tables. In this paper, we present TP-BERTa, a specifically pre-trained LM for tabular data prediction. Concretely, a novel relative magnitude tokenization converts scalar numerical feature values to finely discrete, high-dimensional tokens, and an intra-feature attention approach integrates feature values with the corresponding feature names. Comprehensive experiments demonstrate that our pre-trained TP-BERTa leads the performance among tabular DNNs and is competitive with Gradient Boosted Decision Tree models in typical tabular data regime.