47 citations · 127 across the 21 of their papers we have counts for
22 papers
Hyperbolic Genome Embeddings
Raiyan R. Khan, Philippe Chlenski, Itsik Pe'er
Current approaches to genomic sequence modeling often struggle to align the inductive biases of machine learning models with the evolutionarily-informed structure of biological sys…
Even Faster Hyperbolic Random Forests: A Beltrami-Klein Wrapper Approach
Philippe Chlenski, Itsik Pe'er
Decision trees and models that use them as primitives are workhorses of machine learning in Euclidean spaces. Recent work has further extended these models to the Lorentz model of…
Manify: A Python Library for Learning Non-Euclidean Representations
Philippe Chlenski, Kaizhu Du, Dylan Satow +2
We present Manify, an open-source Python library for non-Euclidean representation learning. Leveraging manifold learning techniques, Manify provides tools for learning embeddings i…
Variational Combinatorial Sequential Monte Carlo for Bayesian Phylogenetics in Hyperbolic Space
Alex Chen, Philipe Chlenski, Kenneth Munyuza +3
Hyperbolic space naturally encodes hierarchical structures such as phylogenies (binary trees), where inward-bending geodesics reflect paths through least common ancestors, and the…
Mixed-curvature decision trees and random forests
Philippe Chlenski, Quentin Chu, Raiyan R. Khan +3
Decision trees (DTs) and their random forest (RF) extensions are workhorses of classification and regression in Euclidean spaces. However, algorithms for learning in non-Euclidean…
Mixed-Curvature Decision Trees and Random Forests
Philippe Chlenski, Quentin Chu, Itsik Pe'er
We extend decision tree and random forest algorithms to product space manifolds: Cartesian products of Euclidean, hyperspherical, and hyperbolic manifolds. Such spaces have extreme…
Variational Pseudo Marginal Methods for Jet Reconstruction in Particle Physics
Hanming Yang, Antonio Khalil Moretti, Sebastian Macaluso +3
Reconstructing jets, which provide vital insights into the properties and histories of subatomic particles produced in high-energy collisions, is a main problem in data analyses in…
Distributional bias compromises leave-one-out cross-validation
George I. Austin, Itsik Pe'er, Tal Korem
Cross-validation is a common method for estimating the predictive performance of machine learning models. In a data-scarce regime, where one typically wishes to maximize the number…
Fast hyperboloid decision tree algorithms
Philippe Chlenski, Ethan Turok, Antonio Moretti +1
Hyperbolic geometry is gaining traction in machine learning for its effectiveness at capturing hierarchical structures in real-world data. Hyperbolic spaces, where neighborhoods gr…
ICLR 2022 Challenge for Computational Geometry and Topology: Design and Results
Adele Myers, Saiteja Utpala, Shubham Talbar +25
This paper presents the computational challenge on differential geometry and topology that was hosted within the ICLR 2022 workshop ``Geometric and Topological Representation Learn…
Variational Combinatorial Sequential Monte Carlo Methods for Bayesian Phylogenetic Inference
Antonio Khalil Moretti, Liyi Zhang, Christian A. Naesseth +3
Bayesian phylogenetic inference is often conducted via local or sequential search over topologies and branch lengths using algorithms such as random-walk Markov chain Monte Carlo (…
Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations
Iddo Drori, Darshan Thaker, Arjun Srivatsa +15
Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biolog…
Particle Smoothing Variational Objectives
Antonio Khalil Moretti, Zizhao Wang, Luhuan Wu +2
A body of recent work has focused on constructing a variational family of filtered distributions using Sequential Monte Carlo (SMC). Inspired by this work, we introduce Particle Sm…
High Quality Prediction of Protein Q8 Secondary Structure by Diverse Neural Network Architectures
Iddo Drori, Isht Dwivedi, Pranav Shrestha +13
We tackle the problem of protein secondary structure prediction using a common task framework. This lead to the introduction of multiple ideas for neural architectures based on sta…
Latent Space Temporal Model of Microbial Abundance to Predict Domination and Bacteremia
Ruiqi Zhong, Tyler Joseph, Joao B Xavier +1
Gut microbial composition has been linked to multiple health outcomes. Yet, temporal analysis of this composition had been limited to deterministic models. In this paper, we introd…
Parkinson's Disease Digital Biomarker Discovery with Optimized Transitions and Inferred Markov Emissions
Avinash Bukkittu, Baihan Lin, Trung Vu +1
We search for digital biomarkers from Parkinson's Disease by observing approximate repetitive patterns matching hypothesized step and stride periodic cycles. These observations wer…
A note on the distribution of admixture segment lengths and ancestry proportions under pulse and two-wave admixture models
Shai Carmi, James Xue, Itsik Pe'er
Admixed populations are formed by the merging of two or more ancestral populations, and the ancestry of each locus in an admixed genome derives from either source. Consider a simpl…
A renewal theory approach to IBD sharing
Shai Carmi, Peter Wilton, John Wakeley +1
A long genomic segment inherited by a pair of individuals from a single, recent common ancestor is said to be identical-by-descent (IBD). Shared IBD segments have numerous applicat…
GeneZip: A software package for storage-efficient processing of genotype data
Cameron Palmer, Itsik Pe'er
Genome wide association studies directly assay 10^6 single nucleotide polymorphisms (SNPs) across a study cohort. Probabilistic estimation of additional sites by genotype imputatio…
The variance of identity-by-descent sharing in the Wright-Fisher model
Shai Carmi, Pier Francesco Palamara, Vladimir Vacic +3
Widespread sharing of long, identical-by-descent (IBD) genetic segments is a hallmark of populations that have experienced recent genetic drift. Detection of these IBD segments has…
Low-pass Genomewide Sequencing and Variant Imputation Using Identity-by-descent in an Isolated Human Population
A Gusev, MJ Shah, EE Kenny +16
Whole-genome sequencing in an isolated population with few founders directly ascertains variants from the population bottleneck that may be rare elsewhere. In such populations, sha…
Age, Sex, and Genetic Architecture of Human Gene Expression in EBV Transformed Cell Lines
Manuel A. Rivas, Mark J. Daly, Itsik Pe'er
Individual expression profiles from EBV transformed cell lines are an emerging resource for genomic investigation. In this study we characterize the effects of age, sex, and geneti…