Oded Regev
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View article: Interpretable Distillation Reveals that Deep-learning-based Splicing Models Suffer from Pervasive Confounders and Blind Spots
Interpretable Distillation Reveals that Deep-learning-based Splicing Models Suffer from Pervasive Confounders and Blind Spots Open
Despite their growing popularity, genomic deep-learning-based models function largely as black boxes, raising concerns about their trustworthiness. Here we develop a framework to explain model prediction logic using interpretable distillat…
View article: Analysis of Large Peptide Collisional Cross Section Dataset Reveals Structural Origin of Bimodal Behavior
Analysis of Large Peptide Collisional Cross Section Dataset Reveals Structural Origin of Bimodal Behavior Open
Recent advances in ion mobility spectrometry have enabled the measurement of rotationally averaged collisional cross-sectional area (CCS) for millions of peptides, as part of routine proteomic mass spectrometry workflows. One of the most s…
View article: RNA localization to nuclear speckles follows splicing logic
RNA localization to nuclear speckles follows splicing logic Open
Summary Nuclear speckles are membraneless organelles implicated in multiple RNA processing steps. In this work, we systematically characterize the sequence logic determining RNA localization to nuclear speckles. We find extensive similarit…
View article: Abstract 1069 Context-dependent RNA localization to nuclear speckles
Abstract 1069 Context-dependent RNA localization to nuclear speckles Open
View article: Bounds on the density of smooth lattice coverings
Bounds on the density of smooth lattice coverings Open
Let $$\cal{K}$$ be a convex body in ℝ n , let L be a lattice with unit covolume, and let η > 0. We say that $$\cal{K}$$ and L form an η -smooth cover if each point x ∈ ℝ n is covered by (1 ± η )vol( $$\cal{K}$$ ) translates of $$\…
View article: Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency
Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency Open
Nuclear speckles are nuclear membraneless organelles in higher eukaryotic cells playing a vital role in gene expression. Using an in situ reverse transcription–based sequencing method, we study nuclear speckle–associated human transcripts.…
View article: RNA molecules display distinctive organization at nuclear speckles
RNA molecules display distinctive organization at nuclear speckles Open
View article: Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency
Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency Open
Nuclear speckles, a type of membraneless nuclear organelle in higher eukaryotic cells, play a vital role in gene expression regulation. Using the reverse transcription-based RNA-binding protein binding sites sequencing (ARTR-seq) method, w…
View article: On Lattices, Learning with Errors, Random Linear Codes, and Cryptography
On Lattices, Learning with Errors, Random Linear Codes, and Cryptography Open
Our main result is a reduction from worst-case lattice problems such as GapSVP and SIVP to a certain learning problem. This learning problem is a natural extension of the `learning from parity with error' problem to higher moduli. It can a…
View article: Some questions related to the reverse Minkowski theorem
Some questions related to the reverse Minkowski theorem Open
In this review we give an overview of some recent "reverse Minkowski" results on the geometry of lattices. Such results provide upper bounds on the number of short vectors a lattice can have, assuming that it does not have any sublattice o…
View article: Uncovering Distinct Peptide Charging Behaviors in Electrospray Ionization Mass Spectrometry Using a Large-Scale Dataset
Uncovering Distinct Peptide Charging Behaviors in Electrospray Ionization Mass Spectrometry Using a Large-Scale Dataset Open
Electrospray ionization is a powerful and prevalent technique used to ionize analytes in mass spectrometry. The distribution of charges that an analyte receives (charge state distribution, CSD) is an important consideration for interpretin…
View article: Bounds on the density of smooth lattice coverings
Bounds on the density of smooth lattice coverings Open
Let $K$ be a convex body in $\mathbb{R}^n$, let $L$ be a lattice with covolume one, and let $η>0$. We say that $K$ and $L$ form an $η$-smooth cover if each point $x \in \mathbb{R}^n$ is covered by $(1 \pm η) vol(K)$ translates of $K$ by $L…
View article: Deciphering RNA splicing logic with interpretable machine learning
Deciphering RNA splicing logic with interpretable machine learning Open
Machine learning methods, particularly neural networks trained on large datasets, are transforming how scientists approach scientific discovery and experimental design. However, current state-of-the-art neural networks are limited by their…
View article: An Efficient Quantum Factoring Algorithm
An Efficient Quantum Factoring Algorithm Open
We show that $n$-bit integers can be factorized by independently running a quantum circuit with $\tilde{O}(n^{3/2})$ gates for $\sqrt{n}+4$ times, and then using polynomial-time classical post-processing. The correctness of the algorithm r…
View article: A simple proof of a reverse Minkowski theorem for integral lattices
A simple proof of a reverse Minkowski theorem for integral lattices Open
We prove that for any integral lattice $\mathcal{L} \subset \mathbb{R}^n$ (that is, a lattice $\mathcal{L}$ such that the inner product $\langle \mathbf{y}_1,\mathbf{y}_2 \rangle$ is an integer for all $\mathbf{y}_1, \mathbf{y}_2 \in \math…
View article: A high-throughput approach reveals distinct peptide charging behaviors in electrospray ionization mass spectrometry
A high-throughput approach reveals distinct peptide charging behaviors in electrospray ionization mass spectrometry Open
Electrospray ionization is a powerful and prevalent technique used to ionize analytes in mass spectrometry. The distribution of charges that an analyte receives (charge state distribution, CSD) is an important consideration for interpretin…
View article: An integer parallelotope with small surface area
An integer parallelotope with small surface area Open
We prove that for any $n\in \mathbb{N}$ there is a convex body $K\subseteq \mathbb{R}^n$ whose surface area is at most $n^{\frac12+o(1)}$, yet the translates of $K$ by the integer lattice $\mathbb{Z}^n$ tile $\mathbb{R}^n$.
View article: A high-throughput approach reveals distinct peptide charging behaviors in electrospray ionization mass spectrometry
A high-throughput approach reveals distinct peptide charging behaviors in electrospray ionization mass spectrometry Open
Electrospray ionization is a powerful and prevalent technique used to ionize analytes prior to measurement through mass spectrometry. The distribution of charges that an analyte receives (charge state distribution, CSD) is an important con…
View article: RNA molecules display distinctive organization at nuclear speckles
RNA molecules display distinctive organization at nuclear speckles Open
RNA molecules often play critical roles in assisting the formation of membraneless organelles in eukaryotic cells. Yet, little is known about the organization of RNAs within membraneless organelles. Here, using super-resolution imaging and…
View article: Machine learning for discovery: deciphering RNA splicing logic
Machine learning for discovery: deciphering RNA splicing logic Open
Summary Machine learning methods, particularly neural networks trained on large datasets, are transforming how scientists approach scientific discovery and experimental design. However, current state-of-the-art neural networks are limited …
View article: A Tight Reverse Minkowski Inequality for the Epstein Zeta Function
A Tight Reverse Minkowski Inequality for the Epstein Zeta Function Open
We prove that if $\mathcal{L} \subset \mathbb{R}^n$ is a lattice such that $\det(\mathcal{L}') \geq 1$ for all sublattices $\mathcal{L}' \subseteq \mathcal{L}$, then \[ \sum_{\substack{\mathbf{y}\in\mathcal{L}\\\mathbf{y}\neq\mathbf0}} (\|…
View article: On the Gaussian surface area of spectrahedra
On the Gaussian surface area of spectrahedra Open
We show that for sufficiently large $n\geq 1$ and $d=C n^{3/4}$ for some universal constant $C>0$, a random spectrahedron with matrices drawn from Gaussian orthogonal ensemble has Gaussian surface area $Θ(n^{1/8})$ with high probability.
View article: New bounds on the density of lattice coverings
New bounds on the density of lattice coverings Open
We obtain new upper bounds on the minimal density of lattice coverings of Euclidean space by dilates of a convex body K. We also obtain bounds on the probability (with respect to the natural Haar-Siegel measure on the space of lattices) th…
View article: Splicing at the phase-separated nuclear speckle interface: a model
Splicing at the phase-separated nuclear speckle interface: a model Open
Phase-separated membraneless bodies play important roles in nucleic acid biology. While current models for the roles of phase separation largely focus on the compartmentalization of constituent proteins, we reason that other properties of …
View article: Concentration of Markov chains with bounded moments
Concentration of Markov chains with bounded moments Open
Let $\{W_t\}_{t=1}^{\infty}$ be a finite state stationary Markov chain, and suppose that $f$ is a real-valued function on the state space. If $f$ is bounded, then Gillman's expander Chernoff bound (1993) provides concentration estimates fo…
View article: Continuous LWE
Continuous LWE Open
We introduce a continuous analogue of the Learning with Errors (LWE) problem,
which we name CLWE. We give a polynomial-time quantum reduction from worst-case
lattice problems to CLWE, showing that CLWE enjoys similar hardness guarantees
to…
View article: Continuous LWE
Continuous LWE Open
We introduce a continuous analogue of the Learning with Errors (LWE) problem, which we name CLWE. We give a polynomial-time quantum reduction from worst-case lattice problems to CLWE, showing that CLWE enjoys similar hardness guarantees to…
View article: Nearly Optimal Embeddings of Flat Tori
Nearly Optimal Embeddings of Flat Tori Open
We show that for any $n$-dimensional lattice $\mathcal{L} \subseteq \mathbb{R}^n$, the torus $\mathbb{R}^n/\mathcal{L}$ can be embedded into Hilbert space with $O(\sqrt{n\log n})$ distortion. This improves the previously best known upper b…
View article: Nearly Optimal Embeddings of Flat Tori
Nearly Optimal Embeddings of Flat Tori Open
We show that for any n-dimensional lattice ℒ ⊆ ℝⁿ, the torus ℝⁿ/ℒ can be embedded into Hilbert space with O(√{nlog n}) distortion. This improves the previously best known upper bound of O(n√{log n}) shown by Haviv and Regev (APPROX 2010, J…
View article: ASGCT 22nd Annual Meeting Abstracts
ASGCT 22nd Annual Meeting Abstracts Open