We’re looking for speakers! If you’d like to present a paper, please contact Matt Scicluna (FirstNameCLastName at gmail dot com). Don’t forget the C in the middle!

Date	Speaker	Affiliation	Talk Title	Suggested Readings and Recording (if available)
25/01/2024	Matt Scicluna	University of Montreal, Mila	Phantom oscillations in principal component analysis	Phantom oscillations in principal component analysis
30/11/2023	David Hamelin	University of Montreal, Mila	Learning from prepandemic data to forecast viral escape	Learning from prepandemic data to forecast viral escape
16/11/2023	Joseph Viviano	Mila	DynGFN: Towards Bayesian Inference of Gene Regulatory Networks with GFlowNets	DynGFN: Towards Bayesian Inference of Gene Regulatory Networks with GFlowNets
2/11/2023	Alexis Nolin Lapalme	University of Montreal, Mila	HyenaDNA	HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution
22/06/2023	Stefan Bauer	TU Munich	Causal Experimental Design	Interventions, Where and How? Experimental Design for Causal Models at Scale, Trust Your ∇: Gradient-based Intervention Targeting for Causal Discovery
31/05/2023	Zeev Russak	Infiniplex	Monitoring Cancer Patients Using Liquid Biopsy and High-Multiplex qPCR	A Basic Guide to Real Time PCR in Microbial Diagnostics, Sensitivity, specificity, and accuracy of a liquid biopsy approach utilizing molecular amplification pools, UNAFold: software for nucleic acid folding and hybridization
14/12/2022	Srinivasan Sivanandan	insitro	Machine Learning enabled Pooled Optical Screening in Human Lung Cancer Cells	Optical Pooled Screens in Human Cells, The phenotypic landscape of essential human genes
30/11/2022	N/A	N/A	No meetings because NeurIPS
16/11/2022	Jason Hartford	Mila	Causal inference with instrumental variables	Recording
02/11/2022	Shadi Zabad	McGill University	Fast and Accurate Bayesian Polygenic Risk Modeling with Variational Inference	Polygenic risk scores: from research tools to clinical instruments, Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores, Course slides from Prof. Yue Li on Bayesian Polygenic Risk Scores, Slides,
29/06/2022	Assya Trofimov	University of Washington	T cell atlas: receptor sharing vs age, sex and disease	The preprint, The TLT model preprint, Immune repertoire review, Recording
15/06/2022	David Hamelin	University of Montreal	The HLA-dependent impact of emerging sars-cov-2 lineages on cellular immunity and antigenic drift	Suggested Reading 1, NetMHCPan Paper
01/06/2022	Egbert Castro	Yale University	Guided Generative Protein Design using Regularized Transformers	Suggested Reading 1, Suggested Reading 2
18/05/2022	Ionelia Buzatu	Mila	Single-cell simulation and cell state control	Suggested Reading 1
06/04/2022	Colleen Gillon	University of Toronto and Mila	Opening up the brain: An overview of an end-to-end open science neuroimaging research project	The OpenScope project, an example of open data collection initiatives, Learning from unexpected events in the neocortical microcircuit
23/03/2022	N/A	N/A	Research round table	Details on how this will work
09/03/2022	Tallulah Andrews	University of Western Ontario	The Liver Microenvironment in Health and Disease	Suggested Reading 1, Suggested Reading 2
23/02/2022	Oren Krauss	Recursion Pharmaceuticals	Cellular Phenotyping using Deep Learning	Rxrx1 dataset, Suggested Reading
26/1/2022	Dmitry Kobak	University of Tübingen	Neighbour Embeddings of scRNA-seq Data	Suggested Reading 1, Suggested Reading 2, Suggested Reading 3
12/01/2022	Michael Levin	Tufts University	Morphogenesis as Collective Intelligence: from basal cognition to general AI	Suggested Reading 1, Suggested Reading 2, Suggested Reading 3
11/11/2021	Alex Tong	Mila	Density estimation and comparison on single-cell graphs	Suggested Reading 1, Suggested Reading 2
27/10/2021	Paul Bertin	Mila	What challenges do we face when designing recommendation systems to guide laboratory experiments?	Suggested Reading
29/09/2021	Dongjoon Lim	McGill University	LSTM based context-dependent model of sequence evolution
16/09/2021	Zhaocheng Zhu, Chence Shi and Zuobai Zhang	Mila	TorchDrug
16/06/2021	Adit Radhakrishnan, Louis Cammarata	Broad	Transport problems in biology: theoretical and applied insights
02/06/2021	Joseph Viviano	Mila	Saliency is a Possible Red Herring When Diagnosing Poor Generalization
19/05/2021	N/A	N/A	No meetings because NeurIPS abstract submission deadline
05/05/2021	N/A	N/A	Research round table	Details on how this will work
21/04/2021	Guy Wolf	Mila, UdeM	Geometry-based data exploration
07/04/2021	Natasha Dudek	Mila, McGill	CRISPR genome editing tutorial
–/12/2020	N/A	N/A	No meetings because NeurIPS, exams, holidays	Check out the Ecology + ML session at the NeurIPS AI for Earth Sciences Workshop on Dec 12
26/11/2020	Cen Wan	Birkbeck, University of London	Protein function prediction is improved by creating synthetic feature samples with generative adversarial networks	This meeting will be at 11 am EST
12/11/2020	Hector Garcia Martin	Lawrence Berkeley National Lab	A machine learning Automated Recommendation Tool for synthetic biology
29/10/2020	Alexander Rives	Facebook	Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
15/10/2020	Degui Zhi	University of Texas, Houston	Gene2vec: distributed representation of genes based on co-expression
01/10/2020	Nils Strodthoff	Heinrich Hertz Institute	UDSMProt: universal deep sequence models for protein classification	This meeting will be at 11 am EST
17/09/2020	John San Soucie	MIT-WHOI	Required: Gaussian-Dirichlet Random Fields for Inference over High Dimensional Categorical Observations —————————————- Optional: Learning Seasonal Phytoplankton Communities with Topic Models Optional: Phytoplankton Hotspot Prediction With an Unsupervised Spatial Community Model
03/09/2020	N/A	N/A	Fall social	Optional: Trivia Game Winner: Assya T.
18/08/2020	Elliot Layne	McGill	Supervised learning on phylogenetically distributed data
04/08/2020	Zichao Yan	McGill	Generative models for graph-based protein design
21/07/2020	Matthew Scicluna	Mila, UdeM	Required: Genomic ULMFiT Methods Long Form Required: Building Bacterial Genome Language Model (3 min read) —————————————- Optional: Universal Language Model Fine-tuning for Text Classification (original ULMFiT paper) Optional: A primer on deep learning in genomics
07/07/2020	Natasha Dudek	Mila, McGill	Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes
24/06/2020	N/A	N/A	Initial meeting