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Mining Mass Spectra for Peptide Facts
The current mainstream software for peptide-centric tandem mass spectrometry data analysis can be categorized as either …
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Mining Mass Spectra for Peptide Facts
Pepid - a Highly Modifiable Bioinformatics-Oriented Peptide Search Engine
Motivation Current peptide search engines are optimized for wet-lab work ows, i.e. they operate in an endto-end manner to achieve …
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Pepid - a Highly Modifiable Bioinformatics-Oriented Peptide Search Engine
Baseline Acute Myeloid Leukemia Prognosis Models using Transcriptomic and Clinical Profiles by Studying the Impacts of Dimensionality Reductions and Gene Signatures on Cox-Proportional Hazard
Gene marker extraction to evaluate risk in cancer can refine the diagnosis process and lead to adapted therapies and better survival. …
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The TCGA Meta-Dataset Clinical Benchmark
Machine learning is bringing a paradigm shift to healthcare by changing the process of disease diagnosis and prognosis in clinics and …
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Holographic Neural Architectures
Representation learning is at the heart of what makes deep learning effective. In this work, we introduce a new framework for …
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Target variant detection in leukemia using unaligned RNA-Seq reads
Mutations identified in each Acute Myeloid Leukemia (AML) patients are useful for prognosis and to select targeted therapies. Detection …
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Towards the Latent Transcriptome
In this work we propose a method to compute continuous embeddings for kmers from raw RNA-seq data, without the need for alignment to a …
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Warp - a method for neural network interpretability applied to gene expression profiles
We show a proof of principle for warping, a method to interpret the inner working of neural networks in the context of gene expression …
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myCircos - Facilitating the Creation and Use of Circos Plots Online
Circos plots were designed to display large amounts of processed genomic information on a single graphical representation. The creation …
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Theano - A Python framework for fast computation of mathematical expressions
Theano is a Python library that allows to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays …
The Theano Development Team, Al-Rfou Rami, Alain Guillaume, Almahairi Amjad, Angermueller Christof, Bahdanau Dzmitry, Ballas Nicolas, Bastien Frédéric, Bayer Justin, Belikov Anatoly, Belopolsky Alexander, Bengio Yoshua, Bergeron Arnaud, Bergstra James, Bisson Valentin, Snyder Josh Bleecher, Bouchard Nicolas, Boulanger-Lewandowski Nicolas, Bouthillier Xavier, de Brébisson Alexandre, Breuleux Olivier, Carrier Pierre-Luc, Cho Kyunghyun, Chorowski Jan, Christiano Paul, Cooijmans Tim, Côté Marc-Alexandre, Côté Myriam, Courville Aaron, Delalleau Olivier, Demouth Julien, Desjardins Guillaume, Dieleman Sander, Dinh Laurent, Ducoffe Mélanie, Dumoulin Vincent, Kahou Samira Ebrahimi, Erhan Dumitru, Fan Ziye, Firat Orhan, Germain Mathieu, Glorot Xavier, Goodfellow Ian, Graham Matt, Gulcehre Caglar, Hamel Philippe, Harlouchet Iban, Heng Jean-Philippe, Hidasi Balázs, Honari Sina, Jain Arjun, Jean Sébastien, Jia Kai, Korobov Mikhail, Kulkarni Vivek, Lamb Alex, Lamblin Pascal, Larsen Eric, Laurent César, Lee Sean, Lefrancois Simon, Lemieux Simon, Léonard Nicholas, Lin Zhouhan, Lorenz Cory, Lowin Jeremiah, Ma Qianli, Manzagol Pierre-Antoine, Mastropietro Olivier, Memisevic Roland, van Merriënboer Bart, Michalski Vincent, Mirza Mehdi, Orlandi Alberto, Pal Christopher, Pascanu Razvan, Pezeshki Mohammad, Raffel Colin, Renshaw Daniel, Rocklin Matthew, Romero Adriana, Roth Markus, Sadowski Peter, Salvatier John, Savard François, Schlüter Jan, Schulman John, Schwartz Gabriel, Serban Iulian Vlad, Serdyuk Dmitriy, Shabanian Samira, Simon Étienne, Spieckermann Sigurd, Subramanyam S. Ramana, Sygnowski Jakub, Tanguay Jérémie, van Tulder Gijs, Turian Joseph, Urban Sebastian, Vincent Pascal, Visin Francesco, de Vries Harm, Warde-Farley David, Willson Matthew, Xu Kelvin, Xue Lijun, Yao Li, Zhang Saizheng, Zhang Ying
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