Search Results for author: Asa Ben-Hur

Found 7 papers, 5 papers with code

Insights into performance evaluation of com-pound-protein interaction prediction methods

1 code implementation28 Jan 2022 Adiba Yaseen, Imran Amin, Naeem Akhter, Asa Ben-Hur, Fayyaz Minhas

We also show that random pairing for gen-erating synthetic negative examples for training and performance evaluation results in models with better generalization performance in comparison to more sophisticated strategies used in existing studies.

Ten ways to fool the masses with machine learning

no code implementations7 Jan 2019 Fayyaz Minhas, Amina Asif, Asa Ben-Hur

If you want to tell people the truth, make them laugh, otherwise they'll kill you.

BIG-bench Machine Learning

Protein Interface Prediction using Graph Convolutional Networks

2 code implementations NeurIPS 2017 Alex Fout, Jonathon Byrd, Basir Shariat, Asa Ben-Hur

We consider the prediction of interfaces between proteins, a challenging problem with important applications in drug discovery and design, and examine the performance of existing and newly proposed spatial graph convolution operators for this task.

Drug Discovery Protein Interface Prediction

pyLEMMINGS: Large Margin Multiple Instance Classification and Ranking for Bioinformatics Applications

no code implementations14 Nov 2017 Amina Asif, Wajid Arshad Abbasi, Farzeen Munir, Asa Ben-Hur, Fayyaz ul Amir Afsar Minhas

Motivation: A major challenge in the development of machine learning based methods in computational biology is that data may not be accurately labeled due to the time and resources required for experimentally annotating properties of proteins and DNA sequences.

General Classification Multiple Instance Learning

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

1 code implementation3 Jan 2016 Yuxiang Jiang, Tal Ronnen Oron, Wyatt T Clark, Asma R Bankapur, Daniel D'Andrea, Rosalba Lepore, Christopher S Funk, Indika Kahanda, Karin M Verspoor, Asa Ben-Hur, Emily Koo, Duncan Penfold-Brown, Dennis Shasha, Noah Youngs, Richard Bonneau, Alexandra Lin, Sayed ME Sahraeian, Pier Luigi Martelli, Giuseppe Profiti, Rita Casadio, Renzhi Cao, Zhaolong Zhong, Jianlin Cheng, Adrian Altenhoff, Nives Skunca, Christophe Dessimoz, Tunca Dogan, Kai Hakala, Suwisa Kaewphan, Farrokh Mehryary, Tapio Salakoski, Filip Ginter, Hai Fang, Ben Smithers, Matt Oates, Julian Gough, Petri Törönen, Patrik Koskinen, Liisa Holm, Ching-Tai Chen, Wen-Lian Hsu, Kevin Bryson, Domenico Cozzetto, Federico Minneci, David T Jones, Samuel Chapman, Dukka B K. C., Ishita K Khan, Daisuke Kihara, Dan Ofer, Nadav Rappoport, Amos Stern, Elena Cibrian-Uhalte, Paul Denny, Rebecca E Foulger, Reija Hieta, Duncan Legge, Ruth C Lovering, Michele Magrane, Anna N Melidoni, Prudence Mutowo-Meullenet, Klemens Pichler, Aleksandra Shypitsyna, Biao Li, Pooya Zakeri, Sarah ElShal, Léon-Charles Tranchevent, Sayoni Das, Natalie L Dawson, David Lee, Jonathan G Lees, Ian Sillitoe, Prajwal Bhat, Tamás Nepusz, Alfonso E Romero, Rajkumar Sasidharan, Haixuan Yang, Alberto Paccanaro, Jesse Gillis, Adriana E Sedeño-Cortés, Paul Pavlidis, Shou Feng, Juan M Cejuela, Tatyana Goldberg, Tobias Hamp, Lothar Richter, Asaf Salamov, Toni Gabaldon, Marina Marcet-Houben, Fran Supek, Qingtian Gong, Wei Ning, Yuanpeng Zhou, Weidong Tian, Marco Falda, Paolo Fontana, Enrico Lavezzo, Stefano Toppo, Carlo Ferrari, Manuel Giollo, Damiano Piovesan, Silvio Tosatto, Angela del Pozo, José M Fernández, Paolo Maietta, Alfonso Valencia, Michael L Tress, Alfredo Benso, Stefano Di Carlo, Gianfranco Politano, Alessandro Savino, Hafeez Ur Rehman, Matteo Re, Marco Mesiti, Giorgio Valentini, Joachim W Bargsten, Aalt DJ van Dijk, Branislava Gemovic, Sanja Glisic, Vladmir Perovic, Veljko Veljkovic, Nevena Veljkovic, Danillo C Almeida-e-Silva, Ricardo ZN Vencio, Malvika Sharan, Jörg Vogel, Lakesh Kansakar, Shanshan Zhang, Slobodan Vucetic, Zheng Wang, Michael JE Sternberg, Mark N Wass, Rachael P Huntley, Maria J Martin, Claire O'Donovan, Peter N. Robinson, Yves Moreau, Anna Tramontano, Patricia C Babbitt, Steven E Brenner, Michal Linial, Christine A Orengo, Burkhard Rost, Casey S Greene, Sean D Mooney, Iddo Friedberg, Predrag Radivojac

To review progress in the field, the analysis also compared the best methods participating in CAFA1 to those of CAFA2.

Quantitative Methods

Support Vector Clustering

1 code implementation JMLR 2001 Asa Ben-Hur, David Horn, Hava T. Siegelmann, Vladimir Vapnik

We present a novel clustering method using the approach of support vector machines.

Clustering

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