GeneQuery: A General QA-based Framework for Spatial Gene Expression Predictions from Histology Images

Gene expression profiling provides profound insights into molecular mechanisms, but its time-consuming and costly nature often presents significant challenges. In contrast, whole-slide hematoxylin and eosin (H&E) stained histological images are readily accessible and allow for detailed examinations of tissue structure and composition at the microscopic level. Recent advancements have utilized these histological images to predict spatially resolved gene expression profiles. However, state-of-the-art works treat gene expression prediction as a multi-output regression problem, where each gene is learned independently with its own weights, failing to capture the shared dependencies and co-expression patterns between genes. Besides, existing works can only predict gene expression values for genes seen during training, limiting their ability to generalize to new, unseen genes. To address the above limitations, this paper presents GeneQuery, which aims to solve this gene expression prediction task in a question-answering (QA) manner for better generality and flexibility. Specifically, GeneQuery takes gene-related texts as queries and whole-slide images as contexts and then predicts the queried gene expression values. With such a transformation, GeneQuery can implicitly estimate the gene distribution by introducing the gene random variable. Besides, the proposed GeneQuery consists of two architecture implementations, i.e., spot-aware GeneQuery for capturing patterns between images and gene-aware GeneQuery for capturing patterns between genes. Comprehensive experiments on spatial transcriptomics datasets show that the proposed GeneQuery outperforms existing state-of-the-art methods on known and unseen genes. More results also demonstrate that GeneQuery can potentially analyze the tissue structure.

DistinctAD: Distinctive Audio Description Generation in Contexts

Audio Descriptions (ADs) aim to provide a narration of a movie in text form, describing non-dialogue-related narratives, such as characters, actions, or scene establishment. Automatic generation of ADs remains challenging due to: i) the domain gap between movie-AD data and existing data used to train vision-language models, and ii) the issue of contextual redundancy arising from highly similar neighboring visual clips in a long movie. In this work, we propose DistinctAD, a novel two-stage framework for generating ADs that emphasize distinctiveness to produce better narratives. To address the domain gap, we introduce a CLIP-AD adaptation strategy that does not require additional AD corpora, enabling more effective alignment between movie and AD modalities at both global and fine-grained levels. In Stage-II, DistinctAD incorporates two key innovations: (i) a Contextual Expectation-Maximization Attention (EMA) module that reduces redundancy by extracting common bases from consecutive video clips, and (ii) an explicit distinctive word prediction loss that filters out repeated words in the context, ensuring the prediction of unique terms specific to the current AD. Comprehensive evaluations on MAD-Eval, CMD-AD, and TV-AD benchmarks demonstrate the superiority of DistinctAD, with the model consistently outperforming baselines, particularly in Recall@k/N, highlighting its effectiveness in producing high-quality, distinctive ADs.

Mahalanobis Distance-based Multi-view Optimal Transport for Multi-view Crowd Localization

Multi-view crowd localization predicts the ground locations of all people in the scene. Typical methods usually estimate the crowd density maps on the ground plane first, and then obtain the crowd locations. However, the performance of existing methods is limited by the ambiguity of the density maps in crowded areas, where local peaks can be smoothed away. To mitigate the weakness of density map supervision, optimal transport-based point supervision methods have been proposed in the single-image crowd localization tasks, but have not been explored for multi-view crowd localization yet. Thus, in this paper, we propose a novel Mahalanobis distance-based multi-view optimal transport (M-MVOT) loss specifically designed for multi-view crowd localization. First, we replace the Euclidean-based transport cost with the Mahalanobis distance, which defines elliptical iso-contours in the cost function whose long-axis and short-axis directions are guided by the view ray direction. Second, the object-to-camera distance in each view is used to adjust the optimal transport cost of each location further, where the wrong predictions far away from the camera are more heavily penalized. Finally, we propose a strategy to consider all the input camera views in the model loss (M-MVOT) by computing the optimal transport cost for each ground-truth point based on its closest camera. Experiments demonstrate the advantage of the proposed method over density map-based or common Euclidean distance-based optimal transport loss on several multi-view crowd localization datasets. Project page: https://vcc.tech/research/2024/MVOT.

Multi-View People Detection in Large Scenes via Supervised View-Wise Contribution Weighting

Recent deep learning-based multi-view people detection (MVD) methods have shown promising results on existing datasets. However, current methods are mainly trained and evaluated on small, single scenes with a limited number of multi-view frames and fixed camera views. As a result, these methods may not be practical for detecting people in larger, more complex scenes with severe occlusions and camera calibration errors. This paper focuses on improving multi-view people detection by developing a supervised view-wise contribution weighting approach that better fuses multi-camera information under large scenes. Besides, a large synthetic dataset is adopted to enhance the model's generalization ability and enable more practical evaluation and comparison. The model's performance on new testing scenes is further improved with a simple domain adaptation technique. Experimental results demonstrate the effectiveness of our approach in achieving promising cross-scene multi-view people detection performance. See code here: https://vcc.tech/research/2024/MVD.

The Pitfalls and Promise of Conformal Inference Under Adversarial Attacks

In safety-critical applications such as medical imaging and autonomous driving, where decisions have profound implications for patient health and road safety, it is imperative to maintain both high adversarial robustness to protect against potential adversarial attacks and reliable uncertainty quantification in decision-making. With extensive research focused on enhancing adversarial robustness through various forms of adversarial training (AT), a notable knowledge gap remains concerning the uncertainty inherent in adversarially trained models. To address this gap, this study investigates the uncertainty of deep learning models by examining the performance of conformal prediction (CP) in the context of standard adversarial attacks within the adversarial defense community. It is first unveiled that existing CP methods do not produce informative prediction sets under the commonly used $l_{\infty}$-norm bounded attack if the model is not adversarially trained, which underpins the importance of adversarial training for CP. Our paper next demonstrates that the prediction set size (PSS) of CP using adversarially trained models with AT variants is often worse than using standard AT, inspiring us to research into CP-efficient AT for improved PSS. We propose to optimize a Beta-weighting loss with an entropy minimization regularizer during AT to improve CP-efficiency, where the Beta-weighting loss is shown to be an upper bound of PSS at the population level by our theoretical analysis. Moreover, our empirical study on four image classification datasets across three popular AT baselines validates the effectiveness of the proposed Uncertainty-Reducing AT (AT-UR).

FreeDiff: Progressive Frequency Truncation for Image Editing with Diffusion Models

Precise image editing with text-to-image models has attracted increasing interest due to their remarkable generative capabilities and user-friendly nature. However, such attempts face the pivotal challenge of misalignment between the intended precise editing target regions and the broader area impacted by the guidance in practice. Despite excellent methods leveraging attention mechanisms that have been developed to refine the editing guidance, these approaches necessitate modifications through complex network architecture and are limited to specific editing tasks. In this work, we re-examine the diffusion process and misalignment problem from a frequency perspective, revealing that, due to the power law of natural images and the decaying noise schedule, the denoising network primarily recovers low-frequency image components during the earlier timesteps and thus brings excessive low-frequency signals for editing. Leveraging this insight, we introduce a novel fine-tuning free approach that employs progressive $\textbf{Fre}$qu$\textbf{e}$ncy truncation to refine the guidance of $\textbf{Diff}$usion models for universal editing tasks ($\textbf{FreeDiff}$). Our method achieves comparable results with state-of-the-art methods across a variety of editing tasks and on a diverse set of images, highlighting its potential as a versatile tool in image editing applications.

Learning Tracking Representations from Single Point Annotations

Existing deep trackers are typically trained with largescale video frames with annotated bounding boxes. However, these bounding boxes are expensive and time-consuming to annotate, in particular for large scale datasets. In this paper, we propose to learn tracking representations from single point annotations (i.e., 4.5x faster to annotate than the traditional bounding box) in a weakly supervised manner. Specifically, we propose a soft contrastive learning (SoCL) framework that incorporates target objectness prior into end-to-end contrastive learning. Our SoCL consists of adaptive positive and negative sample generation, which is memory-efficient and effective for learning tracking representations. We apply the learned representation of SoCL to visual tracking and show that our method can 1) achieve better performance than the fully supervised baseline trained with box annotations under the same annotation time cost; 2) achieve comparable performance of the fully supervised baseline by using the same number of training frames and meanwhile reducing annotation time cost by 78% and total fees by 85%; 3) be robust to annotation noise.

A Fixed-Point Approach to Unified Prompt-Based Counting

Existing class-agnostic counting models typically rely on a single type of prompt, e.g., box annotations. This paper aims to establish a comprehensive prompt-based counting framework capable of generating density maps for concerned objects indicated by various prompt types, such as box, point, and text. To achieve this goal, we begin by converting prompts from different modalities into prompt masks without requiring training. These masks are then integrated into a class-agnostic counting methodology for predicting density maps. Furthermore, we introduce a fixed-point inference along with an associated loss function to improve counting accuracy, all without introducing new parameters. The effectiveness of this method is substantiated both theoretically and experimentally. Additionally, a contrastive training scheme is implemented to mitigate dataset bias inherent in current class-agnostic counting datasets, a strategy whose effectiveness is confirmed by our ablation study. Our model excels in prominent class-agnostic datasets and exhibits superior performance in cross-dataset adaptation tasks.

Robust Unsupervised Crowd Counting and Localization with Adaptive Resolution SAM

The existing crowd counting models require extensive training data, which is time-consuming to annotate. To tackle this issue, we propose a simple yet effective crowd counting method by utilizing the Segment-Everything-Everywhere Model (SEEM), an adaptation of the Segmentation Anything Model (SAM), to generate pseudo-labels for training crowd counting models. However, our initial investigation reveals that SEEM's performance in dense crowd scenes is limited, primarily due to the omission of many persons in high-density areas. To overcome this limitation, we propose an adaptive resolution SEEM to handle the scale variations, occlusions, and overlapping of people within crowd scenes. Alongside this, we introduce a robust localization method, based on Gaussian Mixture Models, for predicting the head positions in the predicted people masks. Given the mask and point pseudo-labels, we propose a robust loss function, which is designed to exclude uncertain regions based on SEEM's predictions, thereby enhancing the training process of the counting networks. Finally, we propose an iterative method for generating pseudo-labels. This method aims at improving the quality of the segmentation masks by identifying more tiny persons in high-density regions, which are often missed in the first pseudo-labeling stage. Overall, our proposed method achieves the best unsupervised performance in crowd counting, while also being comparable results to some supervised methods. This makes it a highly effective and versatile tool for crowd counting, especially in situations where labeled data is not available.

Human Attention-Guided Explainable Artificial Intelligence for Computer Vision Models

We examined whether embedding human attention knowledge into saliency-based explainable AI (XAI) methods for computer vision models could enhance their plausibility and faithfulness. We first developed new gradient-based XAI methods for object detection models to generate object-specific explanations by extending the current methods for image classification models. Interestingly, while these gradient-based methods worked well for explaining image classification models, when being used for explaining object detection models, the resulting saliency maps generally had lower faithfulness than human attention maps when performing the same task. We then developed Human Attention-Guided XAI (HAG-XAI) to learn from human attention how to best combine explanatory information from the models to enhance explanation plausibility by using trainable activation functions and smoothing kernels to maximize XAI saliency map's similarity to human attention maps. While for image classification models, HAG-XAI enhanced explanation plausibility at the expense of faithfulness, for object detection models it enhanced plausibility and faithfulness simultaneously and outperformed existing methods. The learned functions were model-specific, well generalizable to other databases.