Prompt-CAM: A Simpler Interpretable Transformer for Fine-Grained Analysis

We present a simple usage of pre-trained Vision Transformers (ViTs) for fine-grained analysis, aiming to identify and localize the traits that distinguish visually similar categories, such as different bird species or dog breeds. Pre-trained ViTs such as DINO have shown remarkable capabilities to extract localized, informative features. However, using saliency maps like Grad-CAM can hardly point out the traits: they often locate the whole object by a blurred, coarse heatmap, not traits. We propose a novel approach Prompt Class Attention Map (Prompt-CAM) to the rescue. Prompt-CAM learns class-specific prompts to a pre-trained ViT and uses the corresponding outputs for classification. To classify an image correctly, the true-class prompt must attend to the unique image patches not seen in other classes' images, i.e., traits. As such, the true class's multi-head attention maps reveal traits and their locations. Implementation-wise, Prompt-CAM is almost a free lunch by simply modifying the prediction head of Visual Prompt Tuning (VPT). This makes Prompt-CAM fairly easy to train and apply, sharply contrasting other interpretable methods that design specific models and training processes. It is even simpler than the recently published INterpretable TRansformer (INTR), whose encoder-decoder architecture prevents it from leveraging pre-trained ViTs. Extensive empirical studies on a dozen datasets from various domains (e.g., birds, fishes, insects, fungi, flowers, food, and cars) validate Prompt-CAM superior interpretation capability.

Static Segmentation by Tracking: A Frustratingly Label-Efficient Approach to Fine-Grained Segmentation

We study image segmentation in the biological domain, particularly trait and part segmentation from specimen images (e.g., butterfly wing stripes or beetle body parts). This is a crucial, fine-grained task that aids in understanding the biology of organisms. The conventional approach involves hand-labeling masks, often for hundreds of images per species, and training a segmentation model to generalize these labels to other images, which can be exceedingly laborious. We present a label-efficient method named Static Segmentation by Tracking (SST). SST is built upon the insight: while specimens of the same species have inherent variations, the traits and parts we aim to segment show up consistently. This motivates us to concatenate specimen images into a ``pseudo-video'' and reframe trait and part segmentation as a tracking problem. Concretely, SST generates masks for unlabeled images by propagating annotated or predicted masks from the ``pseudo-preceding'' images. Powered by Segment Anything Model 2 (SAM~2) initially developed for video segmentation, we show that SST can achieve high-quality trait and part segmentation with merely one labeled image per species -- a breakthrough for analyzing specimen images. We further develop a cycle-consistent loss to fine-tune the model, again using one labeled image. Additionally, we highlight the broader potential of SST, including one-shot instance segmentation on images taken in the wild and trait-based image retrieval.

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.

KnobGen: Controlling the Sophistication of Artwork in Sketch-Based Diffusion Models

Recent advances in diffusion models have significantly improved text-to-image (T2I) generation, but they often struggle to balance fine-grained precision with high-level control. Methods like ControlNet and T2I-Adapter excel at following sketches by seasoned artists but tend to be overly rigid, replicating unintentional flaws in sketches from novice users. Meanwhile, coarse-grained methods, such as sketch-based abstraction frameworks, offer more accessible input handling but lack the precise control needed for detailed, professional use. To address these limitations, we propose KnobGen, a dual-pathway framework that democratizes sketch-based image generation by seamlessly adapting to varying levels of sketch complexity and user skill. KnobGen uses a Coarse-Grained Controller (CGC) module for high-level semantics and a Fine-Grained Controller (FGC) module for detailed refinement. The relative strength of these two modules can be adjusted through our knob inference mechanism to align with the user's specific needs. These mechanisms ensure that KnobGen can flexibly generate images from both novice sketches and those drawn by seasoned artists. This maintains control over the final output while preserving the natural appearance of the image, as evidenced on the MultiGen-20M dataset and a newly collected sketch dataset.

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.

Lessons Learned from a Unifying Empirical Study of Parameter-Efficient Transfer Learning (PETL) in Visual Recognition

Parameter-efficient transfer learning (PETL) has attracted significant attention lately, due to the increasing size of pre-trained models and the need to fine-tune (FT) them for superior downstream performance. This community-wide enthusiasm has sparked a plethora of new methods. Nevertheless, a systematic study to understand their performance and suitable application scenarios is lacking, leaving questions like when to apply PETL and which method to use largely unanswered. In this paper, we conduct a unifying empirical study of representative PETL methods in the context of Vision Transformers. We systematically tune their hyper-parameters to fairly compare their accuracy on downstream tasks. Our study not only offers a valuable user guide but also unveils several new insights. First, if tuned carefully, different PETL methods can obtain quite similar accuracy in the low-shot benchmark VTAB-1K. This includes simple methods like FT the bias terms that were reported inferior. Second, though with similar accuracy, we find that PETL methods make different mistakes and high-confidence predictions, likely due to their different inductive biases. Such an inconsistency (or complementariness) 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 PETL is also useful in many-shot regimes -- it achieves comparable and sometimes better accuracy than full FT, using much fewer learnable parameters. Last but not least, we investigate PETL's ability to preserve a pre-trained model's robustness to distribution shifts (e.g., a CLIP backbone). Perhaps not surprisingly, PETL methods outperform full FT alone. However, with weight-space ensembles, the fully FT model can achieve a better balance between downstream and out-of-distribution performance, suggesting a future research direction for PETL.

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.

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.

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.

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.