Jingwei Zhang

Jingwei Zhang, Saarthak Kapse, Ke Ma et al.

Whole slide image (WSI) classification is a critical task in computational pathology, requiring the processing of gigapixel-sized images, which is challenging for current deep-learning methods. Current state of the art methods are based on multi-instance learning schemes (MIL), which usually rely on pretrained features to represent the instances. Due to the lack of task-specific annotated data, these features are either obtained from well-established backbones on natural images, or, more recently from self-supervised models pretrained on histopathology. However, both approaches yield task-agnostic features, resulting in performance loss compared to the appropriate task-related supervision, if available. In this paper, we show that when task-specific annotations are limited, we can inject such supervision into downstream task training, to reduce the gap between fully task-tuned and task agnostic features. We propose Prompt-MIL, an MIL framework that integrates prompts into WSI classification. Prompt-MIL adopts a prompt tuning mechanism, where only a small fraction of parameters calibrates the pretrained features to encode task-specific information, rather than the conventional full fine-tuning approaches. Extensive experiments on three WSI datasets, TCGA-BRCA, TCGA-CRC, and BRIGHT, demonstrate the superiority of Prompt-MIL over conventional MIL methods, achieving a relative improvement of 1.49%-4.03% in accuracy and 0.25%-8.97% in AUROC while using fewer than 0.3% additional parameters. Compared to conventional full fine-tuning approaches, we fine-tune less than 1.3% of the parameters, yet achieve a relative improvement of 1.29%-13.61% in accuracy and 3.22%-27.18% in AUROC and reduce GPU memory consumption by 38%-45% while training 21%-27% faster. Our code is available at https://github.com/cvlab-stonybrook/PromptMIL.

Jingwei Zhang, Xin Zhang, Ke Ma et al.

Histopathology whole slide images (WSIs) play a very important role in clinical studies and serve as the gold standard for many cancer diagnoses. However, generating automatic tools for processing WSIs is challenging due to their enormous sizes. Currently, to deal with this issue, conventional methods rely on a multiple instance learning (MIL) strategy to process a WSI at patch level. Although effective, such methods are computationally expensive, because tiling a WSI into patches takes time and does not explore the spatial relations between these tiles. To tackle these limitations, we propose a locally supervised learning framework which processes the entire slide by exploring the entire local and global information that it contains. This framework divides a pre-trained network into several modules and optimizes each module locally using an auxiliary model. We also introduce a random feature reconstruction unit (RFR) to preserve distinguishing features during training and improve the performance of our method by 1% to 3%. Extensive experiments on three publicly available WSI datasets: TCGA-NSCLC, TCGA-RCC and LKS, highlight the superiority of our method on different classification tasks. Our method outperforms the state-of-the-art MIL methods by 2% to 5% in accuracy, while being 7 to 10 times faster. Additionally, when dividing it into eight modules, our method requires as little as 20% of the total gpu memory required by end-to-end training. Our code is available at https://github.com/cvlab-stonybrook/local_learning_wsi.

Jingwei Zhang, Saarthak Kapse, Ke Ma et al.

Dense prediction tasks such as segmentation and detection of pathological entities hold crucial clinical value in computational pathology workflows. However, obtaining dense annotations on large cohorts is usually tedious and expensive. Contrastive learning (CL) is thus often employed to leverage large volumes of unlabeled data to pre-train the backbone network. To boost CL for dense prediction, some studies have proposed variations of dense matching objectives in pre-training. However, our analysis shows that employing existing dense matching strategies on histopathology images enforces invariance among incorrect pairs of dense features and, thus, is imprecise. To address this, we propose a precise location-based matching mechanism that utilizes the overlapping information between geometric transformations to precisely match regions in two augmentations. Extensive experiments on two pretraining datasets (TCGA-BRCA, NCT-CRC-HE) and three downstream datasets (GlaS, CRAG, BCSS) highlight the superiority of our method in semantic and instance segmentation tasks. Our method outperforms previous dense matching methods by up to 7.2% in average precision for detection and 5.6% in average precision for instance segmentation tasks. Additionally, by using our matching mechanism in the three popular contrastive learning frameworks, MoCo-v2, VICRegL, and ConCL, the average precision in detection is improved by 0.7% to 5.2%, and the average precision in segmentation is improved by 0.7% to 4.0%, demonstrating generalizability. Our code is available at https://github.com/cvlab-stonybrook/PLM_SSL.

Dong Liang, Jing-Wei Zhang, Ying-Peng Tang et al.

Recent aerial object detection models rely on a large amount of labeled training data, which requires unaffordable manual labeling costs in large aerial scenes with dense objects. Active learning effectively reduces the data labeling cost by selectively querying the informative and representative unlabelled samples. However, existing active learning methods are mainly with class-balanced settings and image-based querying for generic object detection tasks, which are less applicable to aerial object detection scenarios due to the long-tailed class distribution and dense small objects in aerial scenes. In this paper, we propose a novel active learning method for cost-effective aerial object detection. Specifically, both object-level and image-level informativeness are considered in the object selection to refrain from redundant and myopic querying. Besides, an easy-to-use class-balancing criterion is incorporated to favor the minority objects to alleviate the long-tailed class distribution problem in model training. We further devise a training loss to mine the latent knowledge in the unlabeled image regions. Extensive experiments are conducted on the DOTA-v1.0 and DOTA-v2.0 benchmarks to validate the effectiveness of the proposed method. For the ReDet, KLD, and SASM detectors on the DOTA-v2.0 dataset, the results show that our proposed MUS-CDB method can save nearly 75\% of the labeling cost while achieving comparable performance to other active learning methods in terms of mAP.Code is publicly online (https://github.com/ZJW700/MUS-CDB).

Jingwei Zhang, Ke Ma, Saarthak Kapse et al.

Semantic segmentations of pathological entities have crucial clinical value in computational pathology workflows. Foundation models, such as the Segment Anything Model (SAM), have been recently proposed for universal use in segmentation tasks. SAM shows remarkable promise in instance segmentation on natural images. However, the applicability of SAM to computational pathology tasks is limited due to the following factors: (1) lack of comprehensive pathology datasets used in SAM training and (2) the design of SAM is not inherently optimized for semantic segmentation tasks. In this work, we adapt SAM for semantic segmentation by introducing trainable class prompts, followed by further enhancements through the incorporation of a pathology encoder, specifically a pathology foundation model. Our framework, SAM-Path enhances SAM's ability to conduct semantic segmentation in digital pathology without human input prompts. Through experiments on two public pathology datasets, the BCSS and the CRAG datasets, we demonstrate that the fine-tuning with trainable class prompts outperforms vanilla SAM with manual prompts and post-processing by 27.52% in Dice score and 71.63% in IOU. On these two datasets, the proposed additional pathology foundation model further achieves a relative improvement of 5.07% to 5.12% in Dice score and 4.50% to 8.48% in IOU.

Saarthak Kapse, Srijan Das, Jingwei Zhang et al.

We propose DiRL, a Diversity-inducing Representation Learning technique for histopathology imaging. Self-supervised learning techniques, such as contrastive and non-contrastive approaches, have been shown to learn rich and effective representations of digitized tissue samples with limited pathologist supervision. Our analysis of vanilla SSL-pretrained models' attention distribution reveals an insightful observation: sparsity in attention, i.e, models tends to localize most of their attention to some prominent patterns in the image. Although attention sparsity can be beneficial in natural images due to these prominent patterns being the object of interest itself, this can be sub-optimal in digital pathology; this is because, unlike natural images, digital pathology scans are not object-centric, but rather a complex phenotype of various spatially intermixed biological components. Inadequate diversification of attention in these complex images could result in crucial information loss. To address this, we leverage cell segmentation to densely extract multiple histopathology-specific representations, and then propose a prior-guided dense pretext task for SSL, designed to match the multiple corresponding representations between the views. Through this, the model learns to attend to various components more closely and evenly, thus inducing adequate diversification in attention for capturing context rich representations. Through quantitative and qualitative analysis on multiple tasks across cancer types, we demonstrate the efficacy of our method and observe that the attention is more globally distributed.

Jingwei Zhang, Cheuk Ting Li, Farzan Farnia

The massive developments of generative model frameworks require principled methods for the evaluation of a model's novelty compared to a reference dataset. While the literature has extensively studied the evaluation of the quality, diversity, and generalizability of generative models, the assessment of a model's novelty compared to a reference model has not been adequately explored in the machine learning community. In this work, we focus on the novelty assessment for multi-modal distributions and attempt to address the following differential clustering task: Given samples of a generative model $P_\mathcal{G}$ and a reference model $P_\mathrm{ref}$, how can we discover the sample types expressed by $P_\mathcal{G}$ more frequently than in $P_\mathrm{ref}$? We introduce a spectral approach to the differential clustering task and propose the Kernel-based Entropic Novelty (KEN) score to quantify the mode-based novelty of $P_\mathcal{G}$ with respect to $P_\mathrm{ref}$. We analyze the KEN score for mixture distributions with well-separable components and develop a kernel-based method to compute the KEN score from empirical data. We support the KEN framework by presenting numerical results on synthetic and real image datasets, indicating the framework's effectiveness in detecting novel modes and comparing generative models. The paper's code is available at: www.github.com/buyeah1109/KEN

Jingwei Zhang, Mohammad Jalali, Cheuk Ting Li et al.

A fine-grained comparison of generative models requires the identification of sample types generated differently by each of the involved models. While quantitative scores have been proposed in the literature to rank different generative models, score-based evaluation and ranking do not reveal the nuanced differences between the generative models in producing different sample types. In this work, we propose solving a differential clustering problem to detect sample types generated differently by two generative models. To solve the differential clustering problem, we develop a spectral method called Fourier-based Identification of Novel Clusters (FINC) to identify modes produced by a generative model with a higher frequency in comparison to a reference distribution. FINC provides a scalable algorithm based on random Fourier features to estimate the eigenspace of kernel covariance matrices of two generative models and utilize the principal eigendirections to detect the sample types present more dominantly in each model. We demonstrate the application of the FINC method to large-scale computer vision datasets and generative modeling frameworks. Our numerical results suggest the scalability of the developed Fourier-based method in highlighting the sample types produced with different frequencies by generative models. The project code is available at https://github.com/buyeah1109/FINC.

Zixiao Wang, Jingwei Zhang, Wenqian Zhao et al.

Few-shot gradient methods have been extensively utilized in existing model pruning methods, where the model weights are regarded as static values and the effects of potential weight perturbations are not considered. However, the widely used large language models (LLMs) have several billion model parameters, which could increase the fragility of few-shot gradient pruning. In this work, we experimentally show that one-shot gradient pruning algorithms could lead to unstable results under perturbations to model weights. And the minor error of switching between data formats bfloat16 and float16 could result in drastically different outcomes. To address such instabilities, we leverage optimization analysis and propose an LLM structural pruning method, called MoreauPruner, with provable robustness against weight perturbations. In MoreauPruner, the model weight importance is estimated based on the neural network's Moreau envelope, which can be flexibly combined with $\ell_1$-norm regularization techniques to induce the sparsity required in the pruning task. We extensively evaluate the MoreauPruner algorithm on several well-known LLMs, including LLaMA-7B, LLaMA-13B, LLaMA3-8B, and Vicuna-7B. Our numerical results suggest the robustness of MoreauPruner against weight perturbations, and indicate the MoreauPruner's successful accuracy-based scores in comparison to several existing pruning methods. We have released the code in \url{https://github.com/ShiningSord/MoreauPruner}.

Saarthak Kapse, Pushpak Pati, Srijan Das et al.

Introducing interpretability and reasoning into Multiple Instance Learning (MIL) methods for Whole Slide Image (WSI) analysis is challenging, given the complexity of gigapixel slides. Traditionally, MIL interpretability is limited to identifying salient regions deemed pertinent for downstream tasks, offering little insight to the end-user (pathologist) regarding the rationale behind these selections. To address this, we propose Self-Interpretable MIL (SI-MIL), a method intrinsically designed for interpretability from the very outset. SI-MIL employs a deep MIL framework to guide an interpretable branch grounded on handcrafted pathological features, facilitating linear predictions. Beyond identifying salient regions, SI-MIL uniquely provides feature-level interpretations rooted in pathological insights for WSIs. Notably, SI-MIL, with its linear prediction constraints, challenges the prevalent myth of an inevitable trade-off between model interpretability and performance, demonstrating competitive results compared to state-of-the-art methods on WSI-level prediction tasks across three cancer types. In addition, we thoroughly benchmark the local and global-interpretability of SI-MIL in terms of statistical analysis, a domain expert study, and desiderata of interpretability, namely, user-friendliness and faithfulness.

Zhan Shi, Jingwei Zhang, Jun Kong et al.

In digital pathology, the multiple instance learning (MIL) strategy is widely used in the weakly supervised histopathology whole slide image (WSI) classification task where giga-pixel WSIs are only labeled at the slide level. However, existing attention-based MIL approaches often overlook contextual information and intrinsic spatial relationships between neighboring tissue tiles, while graph-based MIL frameworks have limited power to recognize the long-range dependencies. In this paper, we introduce the integrative graph-transformer framework that simultaneously captures the context-aware relational features and global WSI representations through a novel Graph Transformer Integration (GTI) block. Specifically, each GTI block consists of a Graph Convolutional Network (GCN) layer modeling neighboring relations at the local instance level and an efficient global attention model capturing comprehensive global information from extensive feature embeddings. Extensive experiments on three publicly available WSI datasets: TCGA-NSCLC, TCGA-RCC and BRIGHT, demonstrate the superiority of our approach over current state-of-the-art MIL methods, achieving an improvement of 1.0% to 2.6% in accuracy and 0.7%-1.6% in AUROC.

Xi Han, Jingwei Zhang, Dimitris Samaras et al.

The neural operator (NO) framework has emerged as a powerful tool for solving partial differential equations (PDEs). Recent NOs are dominated by the Transformer architecture, which offers NOs the capability to capture long-range dependencies in PDE dynamics. However, existing Transformer-based NOs suffer from quadratic complexity, lack geometric rigor, and thus suffer from sub-optimal performance on regular grids. As a remedy, we propose the Geometric Mamba Neural Operator (GeoMaNO) framework, which empowers NOs with Mamba's modeling capability, linear complexity, plus geometric rigor. We evaluate GeoMaNO's performance on multiple standard and popularly employed PDE benchmarks, spanning from Darcy flow problems to Navier-Stokes problems. GeoMaNO improves existing baselines in solution operator approximation by as much as 58.9%.

Qiaomu Miao, Alexandros Graikos, Jingwei Zhang et al.

Training gaze following models requires a large number of images with gaze target coordinates annotated by human annotators, which is a laborious and inherently ambiguous process. We propose the first semi-supervised method for gaze following by introducing two novel priors to the task. We obtain the first prior using a large pretrained Visual Question Answering (VQA) model, where we compute Grad-CAM heatmaps by `prompting' the VQA model with a gaze following question. These heatmaps can be noisy and not suited for use in training. The need to refine these noisy annotations leads us to incorporate a second prior. We utilize a diffusion model trained on limited human annotations and modify the reverse sampling process to refine the Grad-CAM heatmaps. By tuning the diffusion process we achieve a trade-off between the human annotation prior and the VQA heatmap prior, which retains the useful VQA prior information while exhibiting similar properties to the training data distribution. Our method outperforms simple pseudo-annotation generation baselines on the GazeFollow image dataset. More importantly, our pseudo-annotation strategy, applied to a widely used supervised gaze following model (VAT), reduces the annotation need by 50%. Our method also performs the best on the VideoAttentionTarget dataset.

Lei Tai, Jingwei Zhang, Ming Liu et al.

We present an approach for mobile robots to learn to navigate in dynamic environments with pedestrians via raw depth inputs, in a socially compliant manner. To achieve this, we adopt a generative adversarial imitation learning (GAIL) strategy, which improves upon a pre-trained behavior cloning policy. Our approach overcomes the disadvantages of previous methods, as they heavily depend on the full knowledge of the location and velocity information of nearby pedestrians, which not only requires specific sensors, but also the extraction of such state information from raw sensory input could consume much computation time. In this paper, our proposed GAIL-based model performs directly on raw depth inputs and plans in real-time. Experiments show that our GAIL-based approach greatly improves the safety and efficiency of the behavior of mobile robots from pure behavior cloning. The real-world deployment also shows that our method is capable of guiding autonomous vehicles to navigate in a socially compliant manner directly through raw depth inputs. In addition, we release a simulation plugin for modeling pedestrian behaviors based on the social force model.