Semi-supervised learning (SSL) leverages abundant unlabeled data alongside limited labeled data to enhance learning. As vision foundation models (VFMs) increasingly serve as the backbone of vision applications, it remains unclear how SSL interacts with these pre-trained models. To address this gap, we develop new SSL benchmark datasets where frozen VFMs underperform and systematically evaluate representative SSL methods. We make a surprising observation: parameter-efficient fine-tuning (PEFT) using only labeled data often matches SSL performance, even without leveraging unlabeled data. This motivates us to revisit self-training, a conceptually simple SSL baseline, where we use the supervised PEFT model to pseudo-label unlabeled data for further training. To overcome the notorious issue of noisy pseudo-labels, we propose ensembling multiple PEFT approaches and VFM backbones to produce more robust pseudo-labels. Empirical results validate the effectiveness of this simple yet powerful approach, providing actionable insights into SSL with VFMs and paving the way for more scalable and practical semi-supervised learning in the era of foundation models.

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.

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.

Tabular datasets are inherently heterogeneous, posing significant challenges for developing pre-trained foundation models. The recently introduced transformer-based Tabular Prior-data Fitted Network v2 (TabPFN v2) achieves unprecedented in-context learning accuracy across multiple tabular datasets, marking a pivotal advancement in tabular foundation models. In this paper, we comprehensively evaluate TabPFN v2 on over 300 datasets, confirming its exceptional generalization capabilities on small- to medium-scale tasks. Our analysis identifies randomized feature tokens as a key factor behind TabPFN v2's success, as they unify heterogeneous datasets into a fixed-dimensional representation, enabling more effective training and inference. To further understand TabPFN v2's predictions, we propose a leave-one-fold-out approach, transforming TabPFN v2 into a feature extractor and revealing its capability to simplify data distributions and boost accuracy. Lastly, to address TabPFN v2's limitations in high-dimensional, large-scale, and many-category tasks, we introduce a divide-and-conquer mechanism inspired by Chain-of-Thought prompting, enabling scalable inference. By uncovering the mechanisms behind TabPFN v2's success and introducing strategies to expand its applicability, this study provides key insights into the future of tabular foundation models.

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.

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.

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.

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.

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.

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 them for superior downstream performance. This community-wide enthusiasm has sparked a plethora of approaches. Nevertheless, a systematic study to understand their performance and suitable application scenarios is lacking, leaving questions like "when to apply PETL" and "which approach to use" largely unanswered, especially in visual recognition. In this paper, we conduct a unifying empirical study of representative PETL approaches in the context of Vision Transformers (ViT). 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 approaches can obtain quite similar accuracy in the low-shot benchmark VTAB-1K. This includes simple approaches like fine-tuning the bias terms that were reported inferior. Second, though with similar accuracy, we find that PETL approaches 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 finetuning, 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 approaches outperform full fine-tuning alone. However, with weight-space ensembles, the fully fine-tuned model can better balance target (i.e., downstream) distribution and distribution shift performance, suggesting a future research direction for PETL Pre-training and then fine-tuning has become the standard practice to tackle visual recognition problems (Bommasani et al., 2021). The community-wide enthusiasm for open-sourcing has made it possible to access large, powerful pre-trained models learned from a gigantic amount of data, e.g., ImageNet-21K (Ridnik et al., 2021) or LAION-5B (Schuhmann et al., 2022). More research focus has thus been on how to fine-tune such large models (Yu et al., 2023a). Among existing efforts, parameter-efficient transfer learning (PETL), a.k.a parameter-efficient fine-tuning (PEFT), has attracted increasing attention lately (Han et al., 2024; Ding et al., 2023). Instead of fine-tuning the whole model (i.e., full fine-tuning) or the last fully connected layer (i.e., linear probing), PETL approaches seek to update or insert a relatively small number of parameters to the pre-trained model (Xin et al., 2024).