Darpan Sanghavi

Ylaine Gerardin, John Shamshoian, Judy Shen et al.

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.

Dinkar Juyal, Harshith Padigela, Chintan Shah et al.

Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology Whole Slide Image (WSI) is gigapixel-sized and often contains hundreds of thousands to millions of objects of interest across multiple resolutions. In this work, we propose PathoLogy Universal TransfOrmer (PLUTO): a light-weight pathology FM that is pre-trained on a diverse dataset of 195 million image tiles collected from multiple sites and extracts meaningful representations across multiple WSI scales that enable a large variety of downstream pathology tasks. In particular, we design task-specific adaptation heads that utilize PLUTO's output embeddings for tasks which span pathology scales ranging from subcellular to slide-scale, including instance segmentation, tile classification, and slide-level prediction. We compare PLUTO's performance to other state-of-the-art methods on a diverse set of external and internal benchmarks covering multiple biologically relevant tasks, tissue types, resolutions, stains, and scanners. We find that PLUTO matches or outperforms existing task-specific baselines and pathology-specific foundation models, some of which use orders-of-magnitude larger datasets and model sizes when compared to PLUTO. Our findings present a path towards a universal embedding to power pathology image analysis, and motivate further exploration around pathology foundation models in terms of data diversity, architectural improvements, sample efficiency, and practical deployability in real-world applications.

Hananel Hazan, Daniel J. Saunders, Darpan T. Sanghavi et al.

Spiking neural networks (SNNs) with a lattice architecture are introduced in this work, combining several desirable properties of SNNs and self-organized maps (SOMs). Networks are trained with biologically motivated, unsupervised learning rules to obtain a self-organized grid of filters via cooperative and competitive excitatory-inhibitory interactions. Several inhibition strategies are developed and tested, such as (i) incrementally increasing inhibition level over the course of network training, and (ii) switching the inhibition level from low to high (two-level) after an initial training segment. During the labeling phase, the spiking activity generated by data with known labels is used to assign neurons to categories of data, which are then used to evaluate the network's classification ability on a held-out set of test data. Several biologically plausible evaluation rules are proposed and compared, including a population-level confidence rating, and an $n$-gram inspired method. The effectiveness of the proposed self-organized learning mechanism is tested using the MNIST benchmark dataset, as well as using images produced by playing the Atari Breakout game.

Hananel Hazan, Daniel J. Saunders, Darpan T. Sanghavi et al.

We present a system comprising a hybridization of self-organized map (SOM) properties with spiking neural networks (SNNs) that retain many of the features of SOMs. Networks are trained in an unsupervised manner to learn a self-organized lattice of filters via excitatory-inhibitory interactions among populations of neurons. We develop and test various inhibition strategies, such as growing with inter-neuron distance and two distinct levels of inhibition. The quality of the unsupervised learning algorithm is evaluated using examples with known labels. Several biologically-inspired classification tools are proposed and compared, including population-level confidence rating, and n-grams using spike motif algorithm. Using the optimal choice of parameters, our approach produces improvements over state-of-art spiking neural networks.