arXiv subjects

Limin Yu

Publications and source records attributed to Limin Yu.

23 records · Page 2Linked to original sources

arXiv2023

Improved statistical benchmarking of digital pathology models using pairwise frames evaluation

Nested pairwise frames is a method for relative benchmarking of cell or tissue digital pathology models against manual pathologist annotations on a set of sampled patches. At a high level, the method compares agreement between a candidate model and pathologist annotations with agreement among pathologists' annotations. This evaluation framework addresses fundamental issues of data size and annotator variability in using manual pathologist annotations as a source of ground truth for model validation. We implemented nested pairwise frames evaluation for tissue classification, cell classification, and cell count prediction tasks and show results for cell and tissue models deployed on an H&E-stained melanoma dataset.

cs.CV↗

arXiv2022

AEDNet: Adaptive Edge-Deleting Network For Subgraph Matching

Subgraph matching is to find all subgraphs in a data graph that are isomorphic to an existing query graph. Subgraph matching is an NP-hard problem, yet has found its applications in many areas. Many learning-based methods have been proposed for graph matching, whereas few have been designed for subgraph matching. The subgraph matching problem is generally more challenging, mainly due to the different sizes between the two graphs, resulting in considerable large space of solutions. Also the extra edges existing in the data graph connecting to the matched nodes may lead to two matched nodes of two graphs having different adjacency structures and often being identified as distinct objects. Due to the extra edges, the existing learning based methods often fail to generate sufficiently similar node-level embeddings for matched nodes. This study proposes a novel Adaptive Edge-Deleting Network (AEDNet) for subgraph matching. The proposed method is trained in an end-to-end fashion. In AEDNet, a novel sample-wise adaptive edge-deleting mechanism removes extra edges to ensure consistency of adjacency structure of matched nodes, while a unidirectional cross-propagation mechanism ensures consistency of features of matched nodes. We applied the proposed method on six datasets with graph sizes varying from 20 to 2300. Our evaluations on six open datasets demonstrate that the proposed AEDNet outperforms six state-of-the-arts and is much faster than the exact methods on large graphs.

cs.DM↗

arXiv2022

Additive MIL: Intrinsically Interpretable Multiple Instance Learning for Pathology

Multiple Instance Learning (MIL) has been widely applied in pathology towards solving critical problems such as automating cancer diagnosis and grading, predicting patient prognosis, and therapy response. Deploying these models in a clinical setting requires careful inspection of these black boxes during development and deployment to identify failures and maintain physician trust. In this work, we propose a simple formulation of MIL models, which enables interpretability while maintaining similar predictive performance. Our Additive MIL models enable spatial credit assignment such that the contribution of each region in the image can be exactly computed and visualized. We show that our spatial credit assignment coincides with regions used by pathologists during diagnosis and improves upon classical attention heatmaps from attention MIL models. We show that any existing MIL model can be made additive with a simple change in function composition. We also show how these models can debug model failures, identify spurious features, and highlight class-wise regions of interest, enabling their use in high-stakes environments such as clinical decision-making.

cs.CV↗

arXiv2022

Sub-GMN: The Neural Subgraph Matching Network Model

As one of the most fundamental tasks in graph theory, subgraph matching is a crucial task in many fields, ranging from information retrieval, computer vision, biology, chemistry and natural language processing. Yet subgraph matching problem remains to be an NP-complete problem. This study proposes an end-to-end learning-based approximate method for subgraph matching task, called subgraph matching network (Sub-GMN). The proposed Sub-GMN firstly uses graph representation learning to map nodes to node-level embedding. It then combines metric learning and attention mechanisms to model the relationship between matched nodes in the data graph and query graph. To test the performance of the proposed method, we applied our method on two databases. We used two existing methods, GNN and FGNN as baseline for comparison. Our experiment shows that, on dataset 1, on average the accuracy of Sub-GMN are 12.21\% and 3.2\% higher than that of GNN and FGNN respectively. On average running time Sub-GMN runs 20-40 times faster than FGNN. In addition, the average F1-score of Sub-GMN on all experiments with dataset 2 reached 0.95, which demonstrates that Sub-GMN outputs more correct node-to-node matches. Comparing with the previous GNNs-based methods for subgraph matching task, our proposed Sub-GMN allows varying query and data graphes in the test/application stage, while most previous GNNs-based methods can only find a matched subgraph in the data graph during the test/application for the same query graph used in the training stage. Another advantage of our proposed Sub-GMN is that it can output a list of node-to-node matches, while most existing end-to-end GNNs based methods cannot provide the matched node pairs.

cs.LG↗

arXiv2020

Deep learning model trained on mobile phone-acquired frozen section images effectively detects basal cell carcinoma

Background: Margin assessment of basal cell carcinoma using the frozen section is a common task of pathology intraoperative consultation. Although frequently straight-forward, the determination of the presence or absence of basal cell carcinoma on the tissue sections can sometimes be challenging. We explore if a deep learning model trained on mobile phone-acquired frozen section images can have adequate performance for future deployment. Materials and Methods: One thousand two hundred and forty-one (1241) images of frozen sections performed for basal cell carcinoma margin status were acquired using mobile phones. The photos were taken at 100x magnification (10x objective). The images were downscaled from a 4032 x 3024 pixel resolution to 576 x 432 pixel resolution. Semantic segmentation algorithm Deeplab V3 with Xception backbone was used for model training. Results: The model uses an image as input and produces a 2-dimensional black and white output of prediction of the same dimension; the areas determined to be basal cell carcinoma were displayed with white color, in a black background. Any output with the number of white pixels exceeding 0.5% of the total number of pixels is deemed positive for basal cell carcinoma. On the test set, the model achieves area under curve of 0.99 for receiver operator curve and 0.97 for precision-recall curve at the pixel level. The accuracy of classification at the slide level is 96%. Conclusions: The deep learning model trained with mobile phone images shows satisfactory performance characteristics, and thus demonstrates the potential for deploying as a mobile phone app to assist in frozen section interpretation in real time.

cs.CV↗