Guangdong University of Finance, Guangzhou, China
Abstract:Robust medical Machine Learning (ML) models have the potential to revolutionize healthcare by accelerating clinical research, improving workflows and outcomes, and producing novel insights or capabilities. Developing such ML models from scratch is cost prohibitive and requires substantial compute, data, and time (e.g., expert labeling). To address these challenges, we introduce Health AI Developer Foundations (HAI-DEF), a suite of pre-trained, domain-specific foundation models, tools, and recipes to accelerate building ML for health applications. The models cover various modalities and domains, including radiology (X-rays and computed tomography), histopathology, dermatological imaging, and audio. These models provide domain specific embeddings that facilitate AI development with less labeled data, shorter training times, and reduced computational costs compared to traditional approaches. In addition, we utilize a common interface and style across these models, and prioritize usability to enable developers to integrate HAI-DEF efficiently. We present model evaluations across various tasks and conclude with a discussion of their application and evaluation, covering the importance of ensuring efficacy, fairness, and equity. Finally, while HAI-DEF and specifically the foundation models lower the barrier to entry for ML in healthcare, we emphasize the importance of validation with problem- and population-specific data for each desired usage setting. This technical report will be updated over time as more modalities and features are added.
Abstract:Supporting the health and well-being of dynamic populations around the world requires governmental agencies, organizations and researchers to understand and reason over complex relationships between human behavior and local contexts in order to identify high-risk groups and strategically allocate limited resources. Traditional approaches to these classes of problems often entail developing manually curated, task-specific features and models to represent human behavior and the natural and built environment, which can be challenging to adapt to new, or even, related tasks. To address this, we introduce a Population Dynamics Foundation Model (PDFM) that aims to capture the relationships between diverse data modalities and is applicable to a broad range of geospatial tasks. We first construct a geo-indexed dataset for postal codes and counties across the United States, capturing rich aggregated information on human behavior from maps, busyness, and aggregated search trends, and environmental factors such as weather and air quality. We then model this data and the complex relationships between locations using a graph neural network, producing embeddings that can be adapted to a wide range of downstream tasks using relatively simple models. We evaluate the effectiveness of our approach by benchmarking it on 27 downstream tasks spanning three distinct domains: health indicators, socioeconomic factors, and environmental measurements. The approach achieves state-of-the-art performance on all 27 geospatial interpolation tasks, and on 25 out of the 27 extrapolation and super-resolution tasks. We combined the PDFM with a state-of-the-art forecasting foundation model, TimesFM, to predict unemployment and poverty, achieving performance that surpasses fully supervised forecasting. The full set of embeddings and sample code are publicly available for researchers.
Abstract:The core of self-supervised point cloud learning lies in setting up appropriate pretext tasks, to construct a pre-training framework that enables the encoder to perceive 3D objects effectively. In this paper, we integrate two prevalent methods, masked point modeling (MPM) and 3D-to-2D generation, as pretext tasks within a pre-training framework. We leverage the spatial awareness and precise supervision offered by these two methods to address their respective limitations: ambiguous supervision signals and insensitivity to geometric information. Specifically, the proposed framework, abbreviated as PointCG, consists of a Hidden Point Completion (HPC) module and an Arbitrary-view Image Generation (AIG) module. We first capture visible points from arbitrary views as inputs by removing hidden points. Then, HPC extracts representations of the inputs with an encoder and completes the entire shape with a decoder, while AIG is used to generate rendered images based on the visible points' representations. Extensive experiments demonstrate the superiority of the proposed method over the baselines in various downstream tasks. Our code will be made available upon acceptance.
Abstract:Few-shot 3D point cloud segmentation (FS-PCS) aims at generalizing models to segment novel categories with minimal annotated support samples. While existing FS-PCS methods have shown promise, they primarily focus on unimodal point cloud inputs, overlooking the potential benefits of leveraging multimodal information. In this paper, we address this gap by introducing a cost-free multimodal FS-PCS setup, utilizing textual labels and the potentially available 2D image modality. Under this easy-to-achieve setup, we present the MultiModal Few-Shot SegNet (MM-FSS), a model effectively harnessing complementary information from multiple modalities. MM-FSS employs a shared backbone with two heads to extract intermodal and unimodal visual features, and a pretrained text encoder to generate text embeddings. To fully exploit the multimodal information, we propose a Multimodal Correlation Fusion (MCF) module to generate multimodal correlations, and a Multimodal Semantic Fusion (MSF) module to refine the correlations using text-aware semantic guidance. Additionally, we propose a simple yet effective Test-time Adaptive Cross-modal Calibration (TACC) technique to mitigate training bias, further improving generalization. Experimental results on S3DIS and ScanNet datasets demonstrate significant performance improvements achieved by our method. The efficacy of our approach indicates the benefits of leveraging commonly-ignored free modalities for FS-PCS, providing valuable insights for future research. The code is available at https://github.com/ZhaochongAn/Multimodality-3D-Few-Shot .
Abstract:Wearable sensors have become ubiquitous thanks to a variety of health tracking features. The resulting continuous and longitudinal measurements from everyday life generate large volumes of data; however, making sense of these observations for scientific and actionable insights is non-trivial. Inspired by the empirical success of generative modeling, where large neural networks learn powerful representations from vast amounts of text, image, video, or audio data, we investigate the scaling properties of sensor foundation models across compute, data, and model size. Using a dataset of up to 40 million hours of in-situ heart rate, heart rate variability, electrodermal activity, accelerometer, skin temperature, and altimeter per-minute data from over 165,000 people, we create LSM, a multimodal foundation model built on the largest wearable-signals dataset with the most extensive range of sensor modalities to date. Our results establish the scaling laws of LSM for tasks such as imputation, interpolation and extrapolation, both across time and sensor modalities. Moreover, we highlight how LSM enables sample-efficient downstream learning for tasks like exercise and activity recognition.
Abstract:Target speaker extraction (TSE) aims to isolate individual speaker voices from complex speech environments. The effectiveness of TSE systems is often compromised when the speaker characteristics are similar to each other. Recent research has introduced curriculum learning (CL), in which TSE models are trained incrementally on speech samples of increasing complexity. In CL training, the model is first trained on samples with low speaker similarity between the target and interference speakers, and then on samples with high speaker similarity. To further improve CL, this paper uses a $k$-nearest neighbor-based voice conversion method to simulate and generate speech of diverse interference speakers, and then uses the generated data as part of the CL. Experiments demonstrate that training data based on synthetic speakers can effectively enhance the model's capabilities and significantly improve the performance of multiple TSE systems.
Abstract:In recent years, orthogonal chirp division modulation (OCDM) has gained attention as a robust communication waveform due to its strong resistance to both time-domain and frequency-domain interference. However, similar to orthogonal frequency division multiplexing (OFDM), OCDM suffers from a high peak-to-average power ratio (PAPR), resulting in increased hardware costs and reduced energy efficiency of the transmitter's power amplifiers. In this work, we introduce a novel unitary transform called the Generalized Discrete Fresnel Transform (GDFnT) and propose a new waveform based on this transform, named Generalized Orthogonal Chirp Division Modulation (GOCDM). In GOCDM, data symbols from the constellation diagram are independently placed in the Generalized Fresnel (GF) domain. We derive the GF-domain channel matrix for the GOCDM system under time-frequency doubly selective channels and leverages the sparsity of the GF-domain channel matrix to design an iterative receiver based on the message-passing algorithm. Simulation results demonstrate that GOCDM achieves better PAPR performance than OCDM without compromising bit error rate (BER) performance.
Abstract:T-cell receptors (TCRs) play a crucial role in the immune system by recognizing and binding to specific antigens presented by infected or cancerous cells. Understanding the sequence patterns of TCRs is essential for developing targeted immune therapies and designing effective vaccines. Language models, such as auto-regressive transformers, offer a powerful solution to this problem by learning the probability distributions of TCR repertoires, enabling the generation of new TCR sequences that inherit the underlying patterns of the repertoire. We introduce TCR-GPT, a probabilistic model built on a decoder-only transformer architecture, designed to uncover and replicate sequence patterns in TCR repertoires. TCR-GPT demonstrates an accuracy of 0.953 in inferring sequence probability distributions measured by Pearson correlation coefficient. Furthermore, by leveraging Reinforcement Learning(RL), we adapted the distribution of TCR sequences to generate TCRs capable of recognizing specific peptides, offering significant potential for advancing targeted immune therapies and vaccine development. With the efficacy of RL, fine-tuned pretrained TCR-GPT models demonstrated the ability to produce TCR repertoires likely to bind specific peptides, illustrating RL's efficiency in enhancing the model's adaptability to the probability distributions of biologically relevant TCR sequences.
Abstract:Single-image dehazing is a pivotal challenge in computer vision that seeks to remove haze from images and restore clean background details. Recognizing the limitations of traditional physical model-based methods and the inefficiencies of current attention-based solutions, we propose a new dehazing network combining an innovative Haze-Aware Attention Module (HAAM) with a Multiscale Frequency Enhancement Module (MFEM). The HAAM is inspired by the atmospheric scattering model, thus skillfully integrating physical principles into high-dimensional features for targeted dehazing. It picks up on latent features during the image restoration process, which gives a significant boost to the metrics, while the MFEM efficiently enhances high-frequency details, thus sidestepping wavelet or Fourier transform complexities. It employs multiscale fields to extract and emphasize key frequency components with minimal parameter overhead. Integrated into a simple U-Net framework, our Haze-Aware Attention Network (HAA-Net) for single-image dehazing significantly outperforms existing attention-based and transformer models in efficiency and effectiveness. Tested across various public datasets, the HAA-Net sets new performance benchmarks. Our work not only advances the field of image dehazing but also offers insights into the design of attention mechanisms for broader applications in computer vision.
Abstract:Microscopic interpretation of histopathology images underlies many important diagnostic and treatment decisions. While advances in vision-language modeling raise new opportunities for analysis of such images, the gigapixel-scale size of whole slide images (WSIs) introduces unique challenges. Additionally, pathology reports simultaneously highlight key findings from small regions while also aggregating interpretation across multiple slides, often making it difficult to create robust image-text pairs. As such, pathology reports remain a largely untapped source of supervision in computational pathology, with most efforts relying on region-of-interest annotations or self-supervision at the patch-level. In this work, we develop a vision-language model based on the BLIP-2 framework using WSIs paired with curated text from pathology reports. This enables applications utilizing a shared image-text embedding space, such as text or image retrieval for finding cases of interest, as well as integration of the WSI encoder with a frozen large language model (LLM) for WSI-based generative text capabilities such as report generation or AI-in-the-loop interactions. We utilize a de-identified dataset of over 350,000 WSIs and diagnostic text pairs, spanning a wide range of diagnoses, procedure types, and tissue types. We present pathologist evaluation of text generation and text retrieval using WSI embeddings, as well as results for WSI classification and workflow prioritization (slide-level triaging). Model-generated text for WSIs was rated by pathologists as accurate, without clinically significant error or omission, for 78% of WSIs on average. This work demonstrates exciting potential capabilities for language-aligned WSI embeddings.