We present a simple approach to make pre-trained Vision Transformers (ViTs) interpretable for fine-grained analysis, aiming to identify and localize the traits that distinguish visually similar categories, such as bird species. Pretrained ViTs, such as DINO, have demonstrated remarkable capabilities in extracting localized, discriminative features. However, saliency maps like Grad-CAM often fail to identify these traits, producing blurred, coarse heatmaps that highlight entire objects instead. We propose a novel approach, Prompt Class Attention Map (Prompt-CAM), to address this limitation. Prompt-CAM learns class-specific prompts for a pre-trained ViT and uses the corresponding outputs for classification. To correctly classify an image, the true-class prompt must attend to unique image patches not present in other classes’ images (i.e., traits). As a result, the true class’s multi-head attention maps reveal traits and their locations. Implementation-wise, Prompt-CAM is almost a "free lunch," requiring only a modification to the prediction head of Visual Prompt Tuning (VPT). This makes Prompt-CAM easy to train and apply, in stark contrast to other interpretable methods that require designing specific models and training processes. Extensive empirical studies on a dozen datasets from various domains (e.g., birds, fishes, insects, fungi, flowers, food, and cars) validate the superior interpretation capability of Prompt-CAM. The source code and demo are available at https://github.com/Imageomics/Prompt_CAM.

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 PEFT1.

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.

Causal discovery in non-stationary time series data is crucial for understanding complex systems but remains challenging due to evolving relationships over time. This paper presents a novel two-stage approach for causal discovery in non-stationary multivariate time series data. The first stage employs a Temporal Attention Forecasting Network (TAFNet), a modified Transformer architecture, to capture complex temporal dependencies and generate informative attention matrices. The second stage utilizes these matrices in an iterative process for Granger causality discovery, refining the predicted causal graph while improving forecasting accuracy. The proposed method addresses the limitations of existing approaches and provides a more complete understanding of causal relationships in non-stationary systems. Extensive experiments demonstrate the method’s superior performance compared to state-of-the-art approaches, particularly in handling non-linear relationships and scaling to high-dimensional data.

Zhongwei Wan, Hui Shen, Xin Wang, Che Liu, Zheda Mai, Mi Zhang. Proceedings of the 2025 Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 1: Long Papers). 2025.

Foundation models trained at scale exhibit remarkable emergent behaviors, learning new capabilities beyond their initial training objectives. We find such emergent behaviors in biological vision models via large-scale contrastive vision-language training. To achieve this, we first curate TreeOfLife-200M, comprising 214 million images of living organisms, the largest and most diverse biological organism image dataset to date. We then train BioCLIP 2 on TreeOfLife-200M to distinguish different species. Despite the narrow training objective, BioCLIP 2 yields extraordinary accuracy when applied to various biological visual tasks such as habitat classification and trait prediction. We identify emergent properties in the learned embedding space of BioCLIP 2. At the inter-species level, the embedding distribution of different species aligns closely with functional and ecological meanings (e.g., beak sizes and habitats). At the intra-species level, instead of being diminished, the intra-species variations (e.g., life stages and sexes) are preserved and better separated in subspaces orthogonal to inter-species distinctions. We provide formal proof and analyses to explain why hierarchical supervision and contrastive objectives encourage these emergent properties. Crucially, our results reveal that these properties become increasingly significant with larger-scale training data, leading to a biologically meaningful embedding space.

Semi-supervised learning (SSL) enhances model performance by leveraging abundant unlabeled data alongside limited labeled data. As vision foundation models (VFMs) become central to modern vision applications, this paper revisits SSL in the context of these powerful pre-trained models. We conduct a systematic study on tasks where frozen VFMs underperform and reveal several key insights when fine-tuning them. First, parameter-efficient fine-tuning (PEFT) using only labeled data often surpasses traditional SSL methods---even without access to unlabeled data. Second, pseudo-labels generated by PEFT models offer valuable supervisory signals for unlabeled data, and different PEFT techniques yield complementary pseudo-labels. These findings motivate a simple yet effective SSL baseline for the VFM era: \emph{ensemble pseudo-labeling across diverse PEFT methods and VFM backbones}. Extensive experiments validate the effectiveness of this approach, offering actionable insights into SSL with VFMs and paving the way for more scalable and robust semi-supervised learning in the foundation model era.

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.

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.

Intermediate features of a pretrained model have been shown informative for making accurate predictions on downstream tasks, even if the model backbone is kept frozen. The key challenge is how to utilize these intermediate features given their gigantic amount. We propose visual query tuning (VQT), a simple yet effective approach to aggregate intermediate features of Vision Transformers. Through introducing a handful of learnable “query” tokens to each layer, VQT leverages the inner workings of Transformers to “summarize” rich intermediate features of each layer, which can then be used to train the prediction heads of downstream tasks. As VQT keeps the intermediate features intact and only learns to combine them, it enjoys memory efficiency in training, compared to many other parameter-efficient fine-tuning approaches that learn to adapt features and need back-propagation through the entire backbone. This also suggests the complementary role between VQT and those approaches in transfer learning. Empirically, VQT consistently surpasses the state-of-the-art approach that utilizes intermediate features for transfer learning and outperforms full fine-tuning in many cases. Compared to parameter-efficient approaches that adapt features, VQT achieves much higher accuracy under memory constraints. Most importantly, VQT is compatible with these approaches to attain even higher accuracy, making it a simple add-on to further boost transfer learning. Code is available at https://github.com/andytu28/VQT.

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.

Online recommendation systems are prone to create filter bubbles, whereby users are only recommended content narrowly aligned with their historical interests. In the case of media recommendation, this can reinforce political polarization by recommending topical content (e.g., on the economy) at one extreme end of the political spectrum even though this topic has broad coverage from multiple political viewpoints that would provide a more balanced and informed perspective for the user. Historically, Maximal Marginal Relevance (MMR) has been used to diversify result lists and even mitigate filter bubbles, but suffers from three key drawbacks: (1)~MMR directly sacrifices relevance for diversity, (2)~MMR typically diversifies across all content and not just targeted dimensions (e.g., political polarization), and (3)~MMR is inefficient in practice due to the need to compute pairwise similarities between recommended items. To simultaneously address these limitations, we propose a novel methodology that trains Concept Activation Vectors (CAVs) for targeted topical dimensions (e.g., political polarization). We then modulate the latent embeddings of user preferences in a state-of-the-art VAE-based recommender system to diversify along the targeted dimension while preserving topical relevance across orthogonal dimensions. Our experiments show that our Targeted Diversification VAE-based Collaborative Filtering (TD-VAE-CF) methodology better preserves relevance of content to user preferences across a range of diversification levels in comparison to both untargeted and targeted variations of Maximum Marginal Relevance (MMR); TD-VAE-CF is also much more computationally efficient than the post-hoc re-ranking approach of MMR.

Managing uncertainty in preferences is core to creating the next generation of conversational recommender systems (CRS). However, an often-overlooked element of conversational interaction is the role of clarification. Users are notoriously noisy at revealing their preferences, and a common error is being unnecessarily specific, e.g., suggesting ”chicken fingers” when a restaurant with a ”kids menu” was the intended preference. Correcting such errors requires reasoning about the level of generality and specificity of preferences and verifying that the user has expressed the correct level of generality. To this end, we propose a novel clarification-based conversational critiquing framework that allows the system to clarify user preferences as it accepts critiques. To support clarification, we propose the use of distributional embeddings that can capture the specificity and generality of concepts through distributional coverage while facilitating state-of-the-art embedding-based recommendation methods. Specifically, we incorporate Distributional Contrastive Embeddings of critiqueable keyphrases with user preference embeddings in a Variational Autoencoder recommendation framework that we term DCE-VAE. Our experiments show that our proposed DCE-VAE is (1) competitive in terms of general performance in comparison to state-of-the-art recommenders and (2) supports effective clarification-based critiquing in comparison to alternative clarification baselines. In summary, this work adds a new dimension of clarification to enhance the well-known critiquing framework along with a novel data-driven distributional embedding for clarification suggestions that significantly improves the efficacy of user interaction with critiquing-based CRSs.

As image-based deep learning becomes pervasive on every device, from cell phones to smart watches, there is a growing need to develop methods that continually learn from data while minimizing memory footprint and power consumption. While memory replay techniques have shown exceptional promise for this task of continual learning, the best method for selecting which buffered images to replay is still an open question. In this paper, we specifically focus on the online class-incremental setting where a model needs to learn new classes continually from an online data stream. To this end, we contribute a novel Adversarial Shapley value scoring method that scores memory data samples according to their ability to preserve latent decision boundaries for previously observed classes (to maintain learning stability and avoid forgetting) while interfering with latent decision boundaries of current classes being learned (to encourage plasticity and optimal learning of new class boundaries). Overall, we observe that our proposed ASER method provides competitive or improved performance compared to state-of-the-art replay-based continual learning methods on a variety of datasets.