Wei-Lun Chao

Individual Treatment Effect (ITE) estimation is to evaluate the causal effects of treatment strategies on some important outcomes, which is a crucial problem in healthcare. Most existing ITE estimation methods are designed for centralized settings. However, in real-world clinical scenarios, the raw data are usually not shareable among hospitals due to the potential privacy and security risks, which makes the methods not applicable. In this work, we study the ITE estimation task in a federated setting, which allows us to harness the decentralized data from multiple hospitals. Due to the unavoidable confounding bias in the collected data, a model directly learned from it would be inaccurate. One well-known solution is Inverse Probability Treatment Weighting (IPTW), which uses the conditional probability of treatment given the covariates to re-weight each training example. Applying IPTW in a federated setting, however, is non-trivial. We found that even with a well-estimated conditional probability, the local model training step using each hospital’s data alone would still suffer from confounding bias. To address this, we propose F ED -IPTW, a novel algorithm to extend IPTW into a federated setting that enforces both global (over all the data) and local (within each hospital) decorrelation between covariates and treatments. We validated our approach on the task of comparing the treatment effects of mechanical ventilation on improving survival probability for patients with breadth difficulties in the Intensive Care Unit (ICU). We conducted experiments on both synthetic and real-world eICU datasets, and the results show that F ED -IPTW outperforms state-of-the-art methods on all the metrics on factual prediction and ITE estimation tasks, paving the way for personalized treatment strategy design in mechanical ventilation usage.

We present a data-domain sampling regime for quantifying CNNs' graphic perception behaviors. This regime lets us evaluate CNNs' ratio estimation ability in bar charts from three perspectives: sensitivity to training-test distribution discrepancies, stability to limited samples, and relative expertise to human observers. After analyzing 16 million trials from 800 CNN models and 6,825 trials from 113 human participants, we arrived at a simple and actionable conclusion: CNNs can outperform humans and their biases simply depend on the training-test distance. We show evidence of this simple, elegant behavior of the machines when they interpret visualization images. osf.io/gfqc3 provides registration, the code for our sampling regime, and experimental results.

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution. (Model and code can be found at imageomics.github.io/phylo-diffusion)

Camera traps are important tools in animal ecology for biodiversity monitoring and conservation. However, their practical application is limited by issues such as poor generalization to new and unseen locations. Images are typically associated with diverse forms of context, which may exist in different modalities. In this work, we exploit the structured context linked to camera trap images to boost out-of-distribution generalization for species classification tasks in camera traps. For instance, a picture of a wild animal could be linked to details about the time and place it was captured, as well as structured biological knowledge about the animal species. While often overlooked by existing studies, incorporating such context offers several potential benefits for better image understanding, such as addressing data scarcity and enhancing generalization. However, effectively incorporating such heterogeneous context into the visual domain is a challenging problem. To address this, we propose a novel framework that transforms species classification as link prediction in a multimodal knowledge graph (KG). This framework enables the seamless integration of diverse multimodal contexts for visual recognition. We apply this framework for out-of-distribution species classification on the iWildCam2020-WILDS and Snapshot Mountain Zebra datasets and achieve competitive performance with state-of-the-art approaches. Furthermore, our framework enhances sample efficiency for recognizing under-represented species.

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution.

Understanding and measuring the resilience of food supply networks is a global imperative to tackle increasing food insecurity. However, the complexity of these networks, with their multidimensional interactions and decisions, presents significant challenges. This paper proposes FLEE-GNN, a novel Federated Learning System for Edge-Enhanced Graph Neural Network, designed to overcome these challenges and enhance the analysis of geospatial resilience of multicommodity food flow network, which is one type of spatial networks. FLEE-GNN addresses the limitations of current methodologies, such as entropy-based methods, in terms of generalizability, scalability, and data privacy. It combines the robustness and adaptability of graph neural networks with the privacy-conscious and decentralized aspects of federated learning on food supply network resilience analysis across geographical regions. This paper also discusses FLEE-GNN's innovative data generation techniques, experimental designs, and future directions for improvement. The results show the advancements of this approach to quantifying the resilience of multicommodity food flow networks, contributing to efforts towards ensuring global food security using AI methods. The developed FLEE-GNN has the potential to be applied in other spatial networks with spatially heterogeneous sub-network distributions.

The rapid development of 3D object detection systems for self-driving cars has significantly improved accuracy. However, these systems struggle to generalize across diverse driving environments, which can lead to safety-critical failures in detecting traffic participants. To address this, we propose a method that utilizes unlabeled repeated traversals of multiple locations to adapt object detectors to new driving environments. By incorporating statistics computed from repeated LiDAR scans, we guide the adaptation process effectively. Our approach enhances LiDAR-based detection models using spatial quantized historical features and introduces a lightweight regression head to leverage the statistics for feature regularization. Additionally, we leverage the statistics for a novel self-training process to stabilize the training. The framework is detector model-agnostic and experiments on real-world datasets demonstrate significant improvements, achieving up to a 20-point performance gain, especially in detecting pedestrians and distant objects. Code is available at https://github.com/zhangtravis/Hist-DA.

Out-of-distribution (OOD) detection aims to identify test examples that do not belong to the training distribution and are thus unlikely to be predicted reliably. Despite a plethora of existing works, most of them focused only on the scenario where OOD examples come from semantic shift (e.g., unseen categories), ignoring other possible causes (e.g., covariate shift). In this paper, we present a novel, unifying framework to study OOD detection in a broader scope. Instead of detecting OOD examples from a particular cause, we propose to detect examples that a deployed machine learning model (e.g., an image classifier) is unable to predict correctly. That is, whether a test example should be detected and rejected or not is "model-specific". We show that this framework unifies the detection of OOD examples caused by semantic shift and covariate shift, and closely addresses the concern of applying a machine learning model to uncontrolled environments. We provide an extensive analysis that involves a variety of models (e.g., different architectures and training strategies), sources of OOD examples, and OOD detection approaches, and reveal several insights into improving and understanding OOD detection in uncontrolled environments.

The ability to recognize and reason about text embedded in visual inputs is often lacking in vision-and-language (V&L) models, perhaps because V&L pre-training methods have often failed to include such an ability in their training objective. In this paper, we propose PreSTU, a novel pre-training recipe dedicated to scene-text understanding (STU). PreSTU introduces OCR-aware pre-training objectives that encourage the model to recognize text from an image and connect it to the rest of the image content. We implement PreSTU using a simple transformer-based encoder-decoder architecture, combined with large-scale image-text datasets with scene text obtained from an off-the-shelf OCR system. We empirically demonstrate the effectiveness of this pre-training approach on eight visual question answering and four image captioning benchmarks.