arXiv subjects

Wei-Lun Chao

Publications and source records attributed to Wei-Lun Chao.

At least 55 records · Page 3Linked to original sources

arXiv2025

Finer-CAM: Spotting the Difference Reveals Finer Details for Visual Explanation

Class activation map (CAM) has been widely used to highlight image regions that contribute to class predictions. Despite its simplicity and computational efficiency, CAM often struggles to identify discriminative regions that distinguish visually similar fine-grained classes. Prior efforts address this limitation by introducing more sophisticated explanation processes, but at the cost of extra complexity. In this paper, we propose Finer-CAM, a method that retains CAM's efficiency while achieving precise localization of discriminative regions. Our key insight is that the deficiency of CAM lies not in "how" it explains, but in "what" it explains. Specifically, previous methods attempt to identify all cues contributing to the target class's logit value, which inadvertently also activates regions predictive of visually similar classes. By explicitly comparing the target class with similar classes and spotting their differences, Finer-CAM suppresses features shared with other classes and emphasizes the unique, discriminative details of the target class. Finer-CAM is easy to implement, compatible with various CAM methods, and can be extended to multi-modal models for accurate localization of specific concepts. Additionally, Finer-CAM allows adjustable comparison strength, enabling users to selectively highlight coarse object contours or fine discriminative details. Quantitatively, we show that masking out the top 5% of activated pixels by Finer-CAM results in a larger relative confidence drop compared to baselines. The source code and demo are available at https://github.com/Imageomics/Finer-CAM.

cs.CV↗

arXiv2025

Building Machine Learning Challenges for Anomaly Detection in Science

Scientific discoveries are often made by finding a pattern or object that was not predicted by the known rules of science. Oftentimes, these anomalous events or objects that do not conform to the norms are an indication that the rules of science governing the data are incomplete, and something new needs to be present to explain these unexpected outliers. The challenge of finding anomalies can be confounding since it requires codifying a complete knowledge of the known scientific behaviors and then projecting these known behaviors on the data to look for deviations. When utilizing machine learning, this presents a particular challenge since we require that the model not only understands scientific data perfectly but also recognizes when the data is inconsistent and out of the scope of its trained behavior. In this paper, we present three datasets aimed at developing machine learning-based anomaly detection for disparate scientific domains covering astrophysics, genomics, and polar science. We present the different datasets along with a scheme to make machine learning challenges around the three datasets findable, accessible, interoperable, and reusable (FAIR). Furthermore, we present an approach that generalizes to future machine learning challenges, enabling the possibility of large, more compute-intensive challenges that can ultimately lead to scientific discovery.

cs.LG↗

arXiv2025

Learning 3D Perception from Others' Predictions

Accurate 3D object detection in real-world environments requires a huge amount of annotated data with high quality. Acquiring such data is tedious and expensive, and often needs repeated effort when a new sensor is adopted or when the detector is deployed in a new environment. We investigate a new scenario to construct 3D object detectors: learning from the predictions of a nearby unit that is equipped with an accurate detector. For example, when a self-driving car enters a new area, it may learn from other traffic participants whose detectors have been optimized for that area. This setting is label-efficient, sensor-agnostic, and communication-efficient: nearby units only need to share the predictions with the ego agent (e.g., car). Naively using the received predictions as ground-truths to train the detector for the ego car, however, leads to inferior performance. We systematically study the problem and identify viewpoint mismatches and mislocalization (due to synchronization and GPS errors) as the main causes, which unavoidably result in false positives, false negatives, and inaccurate pseudo labels. We propose a distance-based curriculum, first learning from closer units with similar viewpoints and subsequently improving the quality of other units' predictions via self-training. We further demonstrate that an effective pseudo label refinement module can be trained with a handful of annotated data, largely reducing the data quantity necessary to train an object detector. We validate our approach on the recently released real-world collaborative driving dataset, using reference cars' predictions as pseudo labels for the ego car. Extensive experiments including several scenarios (e.g., different sensors, detectors, and domains) demonstrate the effectiveness of our approach toward label-efficient learning of 3D perception from other units' predictions.

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arXiv2025

Frequency-Guided Masking for Enhanced Vision Self-Supervised Learning

We present a novel frequency-based Self-Supervised Learning (SSL) approach that significantly enhances its efficacy for pre-training. Prior work in this direction masks out pre-defined frequencies in the input image and employs a reconstruction loss to pre-train the model. While achieving promising results, such an implementation has two fundamental limitations as identified in our paper. First, using pre-defined frequencies overlooks the variability of image frequency responses. Second, pre-trained with frequency-filtered images, the resulting model needs relatively more data to adapt to naturally looking images during fine-tuning. To address these drawbacks, we propose FOurier transform compression with seLf-Knowledge distillation (FOLK), integrating two dedicated ideas. First, inspired by image compression, we adaptively select the masked-out frequencies based on image frequency responses, creating more suitable SSL tasks for pre-training. Second, we employ a two-branch framework empowered by knowledge distillation, enabling the model to take both the filtered and original images as input, largely reducing the burden of downstream tasks. Our experimental results demonstrate the effectiveness of FOLK in achieving competitive performance to many state-of-the-art SSL methods across various downstream tasks, including image classification, few-shot learning, and semantic segmentation.

cs.CV↗

arXiv2025

Lessons and Insights from a Unifying Study of Parameter-Efficient Fine-Tuning (PEFT) in Visual Recognition

Parameter-efficient fine-tuning (PEFT) has attracted significant attention due to the growth of pre-trained model sizes and the need to fine-tune (FT) them for superior downstream performance. Despite a surge in new PEFT methods, a systematic study to understand their performance and suitable application scenarios is lacking, leaving questions like "when to apply PEFT" and "which method to use" largely unanswered, especially in visual recognition. In this paper, we conduct a unifying empirical study of representative PEFT methods with Vision Transformers. We systematically tune their hyperparameters to fairly compare their accuracy on downstream tasks. Our study offers a practical user guide and unveils several new insights. First, if tuned carefully, different PEFT methods achieve similar accuracy in the low-shot benchmark VTAB-1K. This includes simple approaches like FT the bias terms that were reported inferior. Second, despite similar accuracy, we find that PEFT methods make different mistakes and high-confidence predictions, likely due to their different inductive biases. Such an inconsistency (or complementarity) opens up the opportunity for ensemble methods, and we make preliminary attempts at this. Third, going beyond the commonly used low-shot tasks, we find that PEFT is also useful in many-shot regimes, achieving comparable or better accuracy than full FT while using significantly fewer parameters. Lastly, we investigate PEFT's ability to preserve a pre-trained model's robustness to distribution shifts (e.g., CLIP). Perhaps not surprisingly, PEFT approaches outperform full FT alone. However, with weight-space ensembles, full FT can better balance target distribution and distribution shift performance, suggesting a future research direction for robust PEFT.

cs.LG↗

arXiv2025

Federated Inverse Probability Treatment Weighting for Individual Treatment Effect Estimation

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 FED-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 FED-IPTW outperform 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.

cs.LG↗

arXiv2025

Revisiting Nearest Neighbor for Tabular Data: A Deep Tabular Baseline Two Decades Later

The widespread enthusiasm for deep learning has recently expanded into the domain of tabular data. Recognizing that the advancement in deep tabular methods is often inspired by classical methods, e.g., integration of nearest neighbors into neural networks, we investigate whether these classical methods can be revitalized with modern techniques. We revisit a differentiable version of $K$-nearest neighbors (KNN) -- Neighbourhood Components Analysis (NCA) -- originally designed to learn a linear projection to capture semantic similarities between instances, and seek to gradually add modern deep learning techniques on top. Surprisingly, our implementation of NCA using SGD and without dimensionality reduction already achieves decent performance on tabular data, in contrast to the results of using existing toolboxes like scikit-learn. Further equipping NCA with deep representations and additional training stochasticity significantly enhances its capability, being on par with the leading tree-based method CatBoost and outperforming existing deep tabular models in both classification and regression tasks on 300 datasets. We conclude our paper by analyzing the factors behind these improvements, including loss functions, prediction strategies, and deep architectures. The code is available at https://github.com/qile2000/LAMDA-TALENT.

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arXiv2025

Fish-Vista: A Multi-Purpose Dataset for Understanding & Identification of Traits from Images

We introduce Fish-Visual Trait Analysis (Fish-Vista), the first organismal image dataset designed for the analysis of visual traits of aquatic species directly from images using problem formulations in computer vision. Fish-Vista contains 69,126 annotated images spanning 4,154 fish species, curated and organized to serve three downstream tasks of species classification, trait identification, and trait segmentation. Our work makes two key contributions. First, we perform a fully reproducible data processing pipeline to process images sourced from various museum collections. We annotate these images with carefully curated labels from biological databases and manual annotations to create an AI-ready dataset of visual traits, contributing to the advancement of AI in biodiversity science. Second, our proposed downstream tasks offer fertile grounds for novel computer vision research in addressing a variety of challenges such as long-tailed distributions, out-of-distribution generalization, learning with weak labels, explainable AI, and segmenting small objects. We benchmark the performance of several existing methods for our proposed tasks to expose future research opportunities in AI for biodiversity science problems involving visual traits.

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arXiv2025

Rethinking Pre-Training in Tabular Data: A Neighborhood Embedding Perspective

Pre-training is prevalent in deep learning for vision and text data, leveraging knowledge from other datasets to enhance downstream tasks. However, for tabular data, the inherent heterogeneity in attribute and label spaces across datasets complicates the learning of shareable knowledge. We propose Tabular data Pre-Training via Meta-representation (TabPTM), aiming to pre-train a general tabular model over diverse datasets. The core idea is to embed data instances into a shared feature space, where each instance is represented by its distance to a fixed number of nearest neighbors and their labels. This ''meta-representation'' transforms heterogeneous tasks into homogeneous local prediction problems, enabling the model to infer labels (or scores for each label) based on neighborhood information. As a result, the pre-trained TabPTM can be applied directly to new datasets, regardless of their diverse attributes and labels, without further fine-tuning. Extensive experiments on 101 datasets confirm TabPTM's effectiveness in both classification and regression tasks, with and without fine-tuning.

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arXiv2025

MLLM-CompBench: A Comparative Reasoning Benchmark for Multimodal LLMs

The ability to compare objects, scenes, or situations is crucial for effective decision-making and problem-solving in everyday life. For instance, comparing the freshness of apples enables better choices during grocery shopping while comparing sofa designs helps optimize the aesthetics of our living space. Despite its significance, the comparative capability is largely unexplored in artificial general intelligence (AGI). In this paper, we introduce MLLM-CompBench, a benchmark designed to evaluate the comparative reasoning capability of multimodal large language models (MLLMs). MLLM-CompBench mines and pairs images through visually oriented questions covering eight dimensions of relative comparison: visual attribute, existence, state, emotion, temporality, spatiality, quantity, and quality. We curate a collection of around 40K image pairs using metadata from diverse vision datasets and CLIP similarity scores. These image pairs span a broad array of visual domains, including animals, fashion, sports, and both outdoor and indoor scenes. The questions are carefully crafted to discern relative characteristics between two images and are labeled by human annotators for accuracy and relevance. We use MLLM-CompBench to evaluate recent MLLMs, including GPT-4V(ision), Gemini-Pro, and LLaVA-1.6. Our results reveal notable shortcomings in their comparative abilities. We believe MLLM-COMPBENCH not only sheds light on these limitations but also establishes a solid foundation for future enhancements in the comparative capability of MLLMs.

cs.CV↗

arXiv2024

DiffuBox: Refining 3D Object Detection with Point Diffusion

Ensuring robust 3D object detection and localization is crucial for many applications in robotics and autonomous driving. Recent models, however, face difficulties in maintaining high performance when applied to domains with differing sensor setups or geographic locations, often resulting in poor localization accuracy due to domain shift. To overcome this challenge, we introduce a novel diffusion-based box refinement approach. This method employs a domain-agnostic diffusion model, conditioned on the LiDAR points surrounding a coarse bounding box, to simultaneously refine the box's location, size, and orientation. We evaluate this approach under various domain adaptation settings, and our results reveal significant improvements across different datasets, object classes and detectors. Our PyTorch implementation is available at \href{https://github.com/cxy1997/DiffuBox}{https://github.com/cxy1997/DiffuBox}.

cs.CV↗

arXiv2024

FedNE: Surrogate-Assisted Federated Neighbor Embedding for Dimensionality Reduction

Federated learning (FL) has rapidly evolved as a promising paradigm that enables collaborative model training across distributed participants without exchanging their local data. Despite its broad applications in fields such as computer vision, graph learning, and natural language processing, the development of a data projection model that can be effectively used to visualize data in the context of FL is crucial yet remains heavily under-explored. Neighbor embedding (NE) is an essential technique for visualizing complex high-dimensional data, but collaboratively learning a joint NE model is difficult. The key challenge lies in the objective function, as effective visualization algorithms like NE require computing loss functions among pairs of data. In this paper, we introduce \textsc{FedNE}, a novel approach that integrates the \textsc{FedAvg} framework with the contrastive NE technique, without any requirements of shareable data. To address the lack of inter-client repulsion which is crucial for the alignment in the global embedding space, we develop a surrogate loss function that each client learns and shares with each other. Additionally, we propose a data-mixing strategy to augment the local data, aiming to relax the problems of invisible neighbors and false neighbors constructed by the local $k$NN graphs. We conduct comprehensive experiments on both synthetic and real-world datasets. The results demonstrate that our \textsc{FedNE} can effectively preserve the neighborhood data structures and enhance the alignment in the global embedding space compared to several baseline methods.

cs.LG↗

arXiv2024

Fine-Tuning is Fine, if Calibrated

Fine-tuning is arguably the most straightforward way to tailor a pre-trained model (e.g., a foundation model) to downstream applications, but it also comes with the risk of losing valuable knowledge the model had learned in pre-training. For example, fine-tuning a pre-trained classifier capable of recognizing a large number of classes to master a subset of classes at hand is shown to drastically degrade the model's accuracy in the other classes it had previously learned. As such, it is hard to further use the fine-tuned model when it encounters classes beyond the fine-tuning data. In this paper, we systematically dissect the issue, aiming to answer the fundamental question, "What has been damaged in the fine-tuned model?" To our surprise, we find that the fine-tuned model neither forgets the relationship among the other classes nor degrades the features to recognize these classes. Instead, the fine-tuned model often produces more discriminative features for these other classes, even if they were missing during fine-tuning! {What really hurts the accuracy is the discrepant logit scales between the fine-tuning classes and the other classes}, implying that a simple post-processing calibration would bring back the pre-trained model's capability and at the same time unveil the feature improvement over all classes. We conduct an extensive empirical study to demonstrate the robustness of our findings and provide preliminary explanations underlying them, suggesting new directions for future theoretical analysis. Our code is available at https://github.com/OSU-MLB/Fine-Tuning-Is-Fine-If-Calibrated.

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arXiv2024

VLM4Bio: A Benchmark Dataset to Evaluate Pretrained Vision-Language Models for Trait Discovery from Biological Images

Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of 12 state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of 469K question-answer pairs involving 30K images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images. The code and datasets for running all the analyses reported in this paper can be found at https://github.com/sammarfy/VLM4Bio.

cs.CV↗

arXiv2024

Reviving the Context: Camera Trap Species Classification as Link Prediction on Multimodal Knowledge Graphs

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.

cs.CV↗

arXiv2024

Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution

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.

q-bio.PE↗

arXiv2024

Jigsaw Game: Federated Clustering

Federated learning has recently garnered significant attention, especially within the domain of supervised learning. However, despite the abundance of unlabeled data on end-users, unsupervised learning problems such as clustering in the federated setting remain underexplored. In this paper, we investigate the federated clustering problem, with a focus on federated k-means. We outline the challenge posed by its non-convex objective and data heterogeneity in the federated framework. To tackle these challenges, we adopt a new perspective by studying the structures of local solutions in k-means and propose a one-shot algorithm called FeCA (Federated Centroid Aggregation). FeCA adaptively refines local solutions on clients, then aggregates these refined solutions to recover the global solution of the entire dataset in a single round. We empirically demonstrate the robustness of FeCA under various federated scenarios on both synthetic and real-world data. Additionally, we extend FeCA to representation learning and present DeepFeCA, which combines DeepCluster and FeCA for unsupervised feature learning in the federated setting.

cs.LG↗

arXiv2024

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 models are publicly accessible at the Imageomics Institute GitHub site: https://github.com/Imageomics/INTR.

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