A Lightweight Measure of Classification Difficulty from Application Dataset Characteristics

no code implementations • 9 Apr 2024 • Bryan Bo Cao, Abhinav Sharma, Lawrence O'Gorman, Michael Coss, Shubham Jain

We show how this measure can help a practitioner select a computationally efficient model for a small dataset 6 to 29x faster than through repeated training and testing.

WEEP: A method for spatial interpretation of weakly supervised CNN models in computational pathology

1 code implementation • 22 Mar 2024 • Abhinav Sharma, Bojing Liu, Mattias Rantalainen

Deep learning enables the modelling of high-resolution histopathology whole-slide images (WSI).

Binary Classification Weakly-supervised Learning +1

The ACROBAT 2022 Challenge: Automatic Registration Of Breast Cancer Tissue

no code implementations • 29 May 2023 • Philippe Weitz, Masi Valkonen, Leslie Solorzano, Circe Carr, Kimmo Kartasalo, Constance Boissin, Sonja Koivukoski, Aino Kuusela, Dusan Rasic, Yanbo Feng, Sandra Sinius Pouplier, Abhinav Sharma, Kajsa Ledesma Eriksson, Stephanie Robertson, Christian Marzahl, Chandler D. Gatenbee, Alexander R. A. Anderson, Marek Wodzinski, Artur Jurgas, Niccolò Marini, Manfredo Atzori, Henning Müller, Daniel Budelmann, Nick Weiss, Stefan Heldmann, Johannes Lotz, Jelmer M. Wolterink, Bruno De Santi, Abhijeet Patil, Amit Sethi, Satoshi Kondo, Satoshi Kasai, Kousuke Hirasawa, Mahtab Farrokh, Neeraj Kumar, Russell Greiner, Leena Latonen, Anne-Vibeke Laenkholm, Johan Hartman, Pekka Ruusuvuori, Mattias Rantalainen

The alignment of tissue between histopathological whole-slide-images (WSI) is crucial for research and clinical applications.

whole slide images

ACROBAT -- a multi-stain breast cancer histological whole-slide-image data set from routine diagnostics for computational pathology

no code implementations • 24 Nov 2022 • Philippe Weitz, Masi Valkonen, Leslie Solorzano, Circe Carr, Kimmo Kartasalo, Constance Boissin, Sonja Koivukoski, Aino Kuusela, Dusan Rasic, Yanbo Feng, Sandra Kristiane Sinius Pouplier, Abhinav Sharma, Kajsa Ledesma Eriksson, Leena Latonen, Anne-Vibeke Laenkholm, Johan Hartman, Pekka Ruusuvuori, Mattias Rantalainen

In particular, there are no large, high quality publicly available data sets with WSIs of matching IHC and H&E-stained tissue sections.

Image Registration Unsupervised Pre-training

Searching k-Optimal Goals for an Orienteering Problem on a Specialized Graph with Budget Constraints

no code implementations • 2 Nov 2020 • Abhinav Sharma, Advait Deshpande, Yanming Wang, Xinyi Xu, Prashan Madumal, Anbin Hou

We propose a novel non-randomized anytime orienteering algorithm for finding k-optimal goals that maximize reward on a specialized graph with budget constraints.

COVI-AgentSim: an Agent-based Model for Evaluating Methods of Digital Contact Tracing

no code implementations • 30 Oct 2020 • Prateek Gupta, Tegan Maharaj, Martin Weiss, Nasim Rahaman, Hannah Alsdurf, Abhinav Sharma, Nanor Minoyan, Soren Harnois-Leblanc, Victor Schmidt, Pierre-Luc St. Charles, Tristan Deleu, Andrew Williams, Akshay Patel, Meng Qu, Olexa Bilaniuk, Gaétan Marceau Caron, Pierre Luc Carrier, Satya Ortiz-Gagné, Marc-Andre Rousseau, David Buckeridge, Joumana Ghosn, Yang Zhang, Bernhard Schölkopf, Jian Tang, Irina Rish, Christopher Pal, Joanna Merckx, Eilif B. Muller, Yoshua Bengio

The rapid global spread of COVID-19 has led to an unprecedented demand for effective methods to mitigate the spread of the disease, and various digital contact tracing (DCT) methods have emerged as a component of the solution.

Virology

Predicting Infectiousness for Proactive Contact Tracing

1 code implementation • ICLR 2021 • Yoshua Bengio, Prateek Gupta, Tegan Maharaj, Nasim Rahaman, Martin Weiss, Tristan Deleu, Eilif Muller, Meng Qu, Victor Schmidt, Pierre-Luc St-Charles, Hannah Alsdurf, Olexa Bilanuik, David Buckeridge, Gáetan Marceau Caron, Pierre-Luc Carrier, Joumana Ghosn, Satya Ortiz-Gagne, Chris Pal, Irina Rish, Bernhard Schölkopf, Abhinav Sharma, Jian Tang, Andrew Williams

Predictions are used to provide personalized recommendations to the individual via an app, as well as to send anonymized messages to the individual's contacts, who use this information to better predict their own infectiousness, an approach we call proactive contact tracing (PCT).

COVI White Paper

no code implementations • 18 May 2020 • Hannah Alsdurf, Edmond Belliveau, Yoshua Bengio, Tristan Deleu, Prateek Gupta, Daphne Ippolito, Richard Janda, Max Jarvie, Tyler Kolody, Sekoul Krastev, Tegan Maharaj, Robert Obryk, Dan Pilat, Valerie Pisano, Benjamin Prud'homme, Meng Qu, Nasim Rahaman, Irina Rish, Jean-Francois Rousseau, Abhinav Sharma, Brooke Struck, Jian Tang, Martin Weiss, Yun William Yu

Manual contact tracing of Covid-19 cases has significant challenges that limit the ability of public health authorities to minimize community infections.

BIG-bench Machine Learning