BioCLIP: A Vision Foundation Model for the Tree of Life

Images of the natural world, collected by a variety of cameras, from drones to individual phones, are increasingly abundant sources of biological information. There is an explosion of computational methods and tools, particularly computer vision, for extracting biologically relevant information from images for science and conservation. Yet most of these are bespoke approaches designed for a specific task and are not easily adaptable or extendable to new questions, contexts, and datasets. A vision model for general organismal biology questions on images is of timely need. To approach this, we curate and release TreeOfLife-10M, the largest and most diverse ML-ready dataset of biology images. We then develop BioCLIP, a foundation model for the tree of life, leveraging the unique properties of biology captured by TreeOfLife-10M, namely the abundance and variety of images of plants, animals, and fungi, together with the availability of rich structured biological knowledge. We rigorously benchmark our approach on diverse fine-grained biology classification tasks, and find that BioCLIP consistently and substantially outperforms existing baselines (by 17% to 20% absolute). Intrinsic evaluation reveals that BioCLIP has learned a hierarchical representation conforming to the tree of life, shedding light on its strong generalizability. Our code, models and data will be made available at https://github.com/Imageomics/bioclip.

A Simple Interpretable Transformer for Fine-Grained Image Classification and Analysis

We present a novel usage of Transformers to make image classification interpretable. Unlike mainstream classifiers that wait until the last fully-connected layer to incorporate class information to make predictions, we investigate a proactive approach, asking each class to search for itself in an image. We realize this idea via a Transformer encoder-decoder inspired by DEtection TRansformer (DETR). We learn ``class-specific'' queries (one for each class) as input to the decoder, enabling each class to localize its patterns in an image via cross-attention. We name our approach INterpretable TRansformer (INTR), which is fairly easy to implement and exhibits several compelling properties. We show that INTR intrinsically encourages each class to attend distinctively; the cross-attention weights thus provide a faithful interpretation of the prediction. Interestingly, via ``multi-head'' cross-attention, INTR could identify different ``attributes'' of a class, making it particularly suitable for fine-grained classification and analysis, which we demonstrate on eight datasets. Our code and pre-trained model are publicly accessible at https://github.com/Imageomics/INTR.

Holistic Transfer: Towards Non-Disruptive Fine-Tuning with Partial Target Data

We propose a learning problem involving adapting a pre-trained source model to the target domain for classifying all classes that appeared in the source data, using target data that covers only a partial label space. This problem is practical, as it is unrealistic for the target end-users to collect data for all classes prior to adaptation. However, it has received limited attention in the literature. To shed light on this issue, we construct benchmark datasets and conduct extensive experiments to uncover the inherent challenges. We found a dilemma -- on the one hand, adapting to the new target domain is important to claim better performance; on the other hand, we observe that preserving the classification accuracy of classes missing in the target adaptation data is highly challenging, let alone improving them. To tackle this, we identify two key directions: 1) disentangling domain gradients from classification gradients, and 2) preserving class relationships. We present several effective solutions that maintain the accuracy of the missing classes and enhance the overall performance, establishing solid baselines for holistic transfer of pre-trained models with partial target data.

Pre-Training LiDAR-Based 3D Object Detectors Through Colorization

Accurate 3D object detection and understanding for self-driving cars heavily relies on LiDAR point clouds, necessitating large amounts of labeled data to train. In this work, we introduce an innovative pre-training approach, Grounded Point Colorization (GPC), to bridge the gap between data and labels by teaching the model to colorize LiDAR point clouds, equipping it with valuable semantic cues. To tackle challenges arising from color variations and selection bias, we incorporate color as "context" by providing ground-truth colors as hints during colorization. Experimental results on the KITTI and Waymo datasets demonstrate GPC's remarkable effectiveness. Even with limited labeled data, GPC significantly improves fine-tuning performance; notably, on just 20% of the KITTI dataset, GPC outperforms training from scratch with the entire dataset. In sum, we introduce a fresh perspective on pre-training for 3D object detection, aligning the objective with the model's intended role and ultimately advancing the accuracy and efficiency of 3D object detection for autonomous vehicles.

FLEE-GNN: A Federated Learning System for Edge-Enhanced Graph Neural Network in Analyzing Geospatial Resilience of Multicommodity Food Flows

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.

Unsupervised Domain Adaptation for Self-Driving from Past Traversal Features

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.

Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often a subjective and labor-intensive process, making trait discovery a highly label-scarce problem. We present a novel approach for discovering evolutionary traits directly from images without relying on trait labels. Our proposed approach, Phylo-NN, encodes the image of an organism into a sequence of quantized feature vectors -- or codes -- where different segments of the sequence capture evolutionary signals at varying ancestry levels in the phylogeny. We demonstrate the effectiveness of our approach in producing biologically meaningful results in a number of downstream tasks including species image generation and species-to-species image translation, using fish species as a target example.

Probabilistic Uncertainty Quantification of Prediction Models with Application to Visual Localization

The uncertainty quantification of prediction models (e.g., neural networks) is crucial for their adoption in many robotics applications. This is arguably as important as making accurate predictions, especially for safety-critical applications such as self-driving cars. This paper proposes our approach to uncertainty quantification in the context of visual localization for autonomous driving, where we predict locations from images. Our proposed framework estimates probabilistic uncertainty by creating a sensor error model that maps an internal output of the prediction model to the uncertainty. The sensor error model is created using multiple image databases of visual localization, each with ground-truth location. We demonstrate the accuracy of our uncertainty prediction framework using the Ithaca365 dataset, which includes variations in lighting, weather (sunny, snowy, night), and alignment errors between databases. We analyze both the predicted uncertainty and its incorporation into a Kalman-based localization filter. Our results show that prediction error variations increase with poor weather and lighting condition, leading to greater uncertainty and outliers, which can be predicted by our proposed uncertainty model. Additionally, our probabilistic error model enables the filter to remove ad hoc sensor gating, as the uncertainty automatically adjusts the model to the input data

Towards Open-World Segmentation of Parts

Segmenting object parts such as cup handles and animal bodies is important in many real-world applications but requires more annotation effort. The largest dataset nowadays contains merely two hundred object categories, implying the difficulty to scale up part segmentation to an unconstrained setting. To address this, we propose to explore a seemingly simplified but empirically useful and scalable task, class-agnostic part segmentation. In this problem, we disregard the part class labels in training and instead treat all of them as a single part class. We argue and demonstrate that models trained without part classes can better localize parts and segment them on objects unseen in training. We then present two further improvements. First, we propose to make the model object-aware, leveraging the fact that parts are "compositions", whose extents are bounded by the corresponding objects and whose appearances are by nature not independent but bundled. Second, we introduce a novel approach to improve part segmentation on unseen objects, inspired by an interesting finding -- for unseen objects, the pixel-wise features extracted by the model often reveal high-quality part segments. To this end, we propose a novel self-supervised procedure that iterates between pixel clustering and supervised contrastive learning that pulls pixels closer or pushes them away. Via extensive experiments on PartImageNet and Pascal-Part, we show notable and consistent gains by our approach, essentially a critical step towards open-world part segmentation.

Federated Learning of Shareable Bases for Personalization-Friendly Image Classification

Personalized federated learning (PFL) aims to harness the collective wisdom of clients' data to build customized models tailored to individual clients' data distributions. Existing works offer personalization primarily to clients who participate in the FL process, making it hard to encompass new clients who were absent or newly show up. In this paper, we propose FedBasis, a novel PFL framework to tackle such a deficiency. FedBasis learns a set of few, shareable ``basis'' models, which can be linearly combined to form personalized models for clients. Specifically for a new client, only a small set of combination coefficients, not the models, needs to be learned. This notion makes FedBasis more parameter-efficient, robust, and accurate compared to other competitive PFL baselines, especially in the low data regime, without increasing the inference cost. To demonstrate its applicability, we also present a more practical PFL testbed for image classification, featuring larger data discrepancies across clients in both the image and label spaces as well as more faithful training and test splits.