Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for understanding function. Existing approaches for detecting structural similarity between prot…
On-device research index
arXiv research
A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
168,695 papers · 148 categories
Trend · papers per month
48 results for “sequence similarity”
Identification of high affinity drug-target interactions is a major research question in drug discovery. Proteins are generally represented by their structures or sequences. However, structures are available only for a small subset of biomolecules and sequence similarity is not always correlated with functional similar…
The aim of this paper is to introduce and study a geometric spectral sequence in Khovanov homology. The construction was motivated by a similar spectral sequence from Khovanov homology to Heegaard Floer homology.
Second generation sequencing technologies are being increasingly used for genetic association studies, where the main research interest is to identify sets of genetic variants that contribute to various phenotype. The phenotype can be univariate disease status, multivariate responses and even high-dimensional outcomes.…
Study on the structure of classifier boundaries in DNA sequencing.
problem Understanding the structure of boundaries in a Bayes classifier for DNA sequencing.
method Examined the structure of the boundary in a Bayes classifier applied to DNA sequencing data. Introduced a new measure of uncertainty, Neighbor Similarity.
result The boundary is large and complex, and Neighbor Similarity effectively measures classifier uncertainty.
Inducing sparseness while training neural networks has been shown to yield models with a lower memory footprint but similar effectiveness to dense models. However, sparseness is typically induced starting from a dense model, and thus this advantage does not hold during training. We propose techniques to enforce sparsen…
Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a…
Researchers develop flexible kernels for biological sequences with guaranteed reliability.
problem Challenges in applying machine learning to biological sequences, including unreliable methods.
method Theoretical analysis and development of modified kernels to ensure reliability and accuracy.
result Developed kernels that are universal, characteristic, and metrize the space of distributions for biological sequences.
Emergence of Globally Attracting Fixed Points in Deep Neural Networks With Nonlinear Activationscs.LG
The paper studies how neural networks evolve representations, finding a unique fixed point for nonlinear activations.
problem Understanding how neural networks transform input data across layers.
method Theoretical framework for the evolution of the kernel sequence, using mean-field regime and Hermite polynomials.
result For nonlinear activations, the kernel sequence converges globally to a unique fixed point.
Accelerates signature kernel computation for sequences.
problem Severe computational bottleneck in computing signature kernel.
method Random Fourier features to accelerate signature kernel computation.
result Uniform approximation guarantees for unbiased estimator with linear computation time.
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons …
The problem of universal outlying sequence detection is studied, where the goal is to detect outlying sequences among sequences of samples. A sequence is considered as outlying if the observations therein are generated by a distribution different from those generating the observations in the majority of the sequenc…
Adam optimization algorithm can have non-zero average regret under certain conditions.
problem Non-zero average regret in Adam optimization algorithm.
method Used a three-periodic sequence of linear functions on [-1,1] with slopes c, -1, -1, and analyzed Adam variants.
result Adam optimization algorithm can have non-zero average regret under certain conditions.
ProGen models protein sequences for synthetic biology.
problem Generating proteins without structural annotations.
method Trained a 1.2B-parameter language model on 280M protein sequences.
result ProGen generates proteins with fine-grained control and accuracy.
We suggest a novel method of clustering and exploratory analysis of temporal event sequences data (also known as categorical time series) based on three-dimensional data grid models. A data set of temporal event sequences can be represented as a data set of three-dimensional points, each point is defined by three varia…
Develops a spectral sequence for Lie group actions on manifolds.
problem Understanding cohomology of manifolds with Lie group actions.
method Introduces a spectral sequence relating manifold cohomology to Lie algebra cohomology.
result Establishes a new description of de Rham cohomology for manifolds with Lie group actions.
Visual analytics system for comparing medical records using sequence embeddings.
problem Challenges in analyzing medical records due to high dimensionality, irregularity, and sparsity.
method Event and sequence embeddings using autoencoder and self-attention mechanism, with sequence alignment for comparison.
result Demonstrated effectiveness with real-world neonatal ICU dataset.
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does not have a close match in the database. In addition, each comparison can be costly…
Paper proposes semi-supervised learning using change points for sequence classification.
problem Limited labeled data for sequential sensor data classification.
method Change point detection for identifying class changes, semi-supervised learning with labeled and unlabeled data.
result Improved classification performance on human activity recognition datasets.
The paper explores spectral sequences of complex manifolds with special metrics.
problem Understanding spectral sequences of compact complex manifolds with special metrics.
method Investigation of Frölicher spectral sequences and special metrics (balanced, SKT, Gauduchon) on manifolds.
result Found compact manifolds where spectral sequences do not degenerate at the second page, providing counterexamples and new families.
Seidel-Smith and Hendricks used equivariant Floer cohomology to define some spectral sequences from symplectic Khovanov homology and Heegaard Floer homology. These spectral sequences give rise to Smith-type inequalities. Similar-looking spectral sequences have been defined by Lee, Bar-Natan, Ozsváth-Szabó, Lipshitz-Tre…
This paper is based on the paper "Locally free sheaves on complex supermanifolds" of A.L.Onishchik, E.G. Vishnyakova, where two classification theorems for locally free sheaves on supermanifolds were proved and a spectral sequence for a locally free sheaf of modules E was obtained. We consider another filtration of the…
From a sequence of similarity networks, with edges representing certain similarity measures between nodes, we are interested in detecting a change-point which changes the statistical property of the networks. After the change, a subset of anomalous nodes which compares dissimilarly with the normal nodes. We study a sim…
Neural networks struggle with long sequences, but a new method improves their performance.
problem Neural networks struggle to generalize to longer sequences and unseen data.
method Proposed a learned conditional masking mechanism and binary encoding for numbers.
result Models can now generalize far outside their training range with near-perfect accuracy.
Predict human lives using sequences of life events.
problem Predicting human life outcomes based on detailed event sequences.
method Adapting natural language processing techniques to analyze life events.
result Models predict diverse outcomes with high accuracy, outperforming state-of-the-art models.
Paper presents IMRCs for evolving tasks with forward and backward learning.
problem Incremental learning of evolving tasks with few samples per task.
method Incremental minimax risk classifiers (IMRCs) that exploit forward and backward learning.
result IMRCs provide significant performance improvement, especially with reduced sample sizes.
Study of orbifold mapping class groups via arc and curve actions.
problem Understanding the structure of orbifold mapping class groups.
method Defined orbifold mapping class groups and studied their actions on arcs and curves. Established a Birman exact sequence and derived finite presentations.
result Finite presentations of orbifold mapping class groups established.
Traditional pairwise sequence alignment is based on matching individual samples from two sequences, under time monotonicity constraints. However, in many application settings matching subsequences (segments) instead of individual samples may bring in additional robustness to noise or local non-causal perturbations. Thi…
Study of BGG sequences on foliated manifolds with transverse parabolic geometry.
problem Analysis of BGG sequences on foliated manifolds with transverse parabolic structures.
method Filtered calculus and transversal index theory for filtered manifolds.
result Derived curved BGG sequences for foliated manifolds with transverse parabolic geometry.
nTreeClus clusters categorical sequences using tree-based learners and k-mers.
problem Challenges in clustering categorical and sequential data.
method nTreeClus uses Tree-based Learners, k-mers, and autoregressive models for categorical time series.
result nTreeClus outperformed baseline methods in various validation metrics.
We introduce the holonomy of a singular leaf of a singular foliation as a sequence of group morphisms from to the of the universal Lie -algebroid of the transverse foliation of . We include these morphisms in a long exact sequence, thus relating them to the holonomy groupoid of Androul…
Grammatical Error Correction (GEC) has been recently modeled using the sequence-to-sequence framework. However, unlike sequence transduction problems such as machine translation, GEC suffers from the lack of plentiful parallel data. We describe two approaches for generating large parallel datasets for GEC using publicl…
Understanding optimal prompts for binary sequence predictors is challenging.
problem Finding good prompts for binary sequence predictors is difficult.
method Viewing prompting as finding the best conditioning sequence on a near-optimal sequence predictor, using empirical and statistical analysis.
result Optimal prompts can be better understood given the pretraining distribution, which is not usually available.
Recently, self-supervised learning has proved to be effective to learn representations of events suitable for temporal segmentation in image sequences, where events are understood as sets of temporally adjacent images that are semantically perceived as a whole. However, although this approach does not require expensive…
Bayesian sequence prediction is a simple technique for predicting future symbols sampled from an unknown measure on infinite sequences over a countable alphabet. While strong bounds on the expected cumulative error are known, there are only limited results on the distribution of this error. We prove tight high-probabil…
Data of practical interest - such as personal records, transaction logs, and medical histories - are sequential collections of events relevant to a particular source entity. Recent studies have attempted to link sequences that represent a common entity across data sets to allow more comprehensive statistical analyses a…
In this paper we prove some general results on constant mean curvature lamination limits of certain sequences of compact surfaces embedded in with constant mean curvature and fixed finite genus, when the boundaries of these surfaces tend to infinity. Two of these theorems generalize to the non…
New spectral sequence for -manifolds, computing cohomology and harmonic forms.
problem Computing cohomology and harmonic forms of -manifolds.
method Introducing a new spectral sequence and using it to generalize theorems from -contact geometry.
result Computed cohomology ring and harmonic forms of -manifolds.
Bitcoin: A life in crisesq-fin.ST
Study examines Bitcoin's price history and identifies recurring events.
problem Understanding Bitcoin's price fluctuations and recurring events.
method Analyzed BTC price time-series (2010-2021), identified recurring events, and approximated price evolution using a Fibonacci sequence.
result BTC price history shows recurring events with similar duration and can be approximated using a Fibonacci sequence.
Study shows properties of Gromov-Hausdorff limit of frame bundles for non-collapsed manifolds.
problem Characterizing the Gromov-Hausdorff limit of orthonormal frame bundles of non-collapsed manifolds with bounded Ricci curvature.
method Analysis of the Gromov-Hausdorff limit space of orthonormal frame bundles equipped with an almost canonical metric.
result The singular set of the limit space has codimension and the complement contains an open and dense -Riemannian manifold.
Sparse Transformers can approximate dense Transformers with only O(n) connections.
problem Can sparse Transformers approximate arbitrary sequence-to-sequence functions?
method Proposed sufficient conditions for universal approximation and proved that sparse Transformers with O(n) connections can approximate dense models.
result Sparse Transformers with O(n) connections can approximate the same function class as dense models with n^2 connections.
One of the ubiquitous representation of long DNA sequence is dividing it into shorter k-mer components. Unfortunately, the straightforward vector encoding of k-mer as a one-hot vector is vulnerable to the curse of dimensionality. Worse yet, the distance between any pair of one-hot vectors is equidistant. This is partic…
Timely prediction of clinically critical events in Intensive Care Unit (ICU) is important for improving care and survival rate. Most of the existing approaches are based on the application of various classification methods on explicitly extracted statistical features from vital signals. In this work, we propose to elim…
BigBird improves transformer performance on NLP tasks with longer sequences.
problem Quadratic dependency on sequence length in transformer models.
method Sparse attention mechanism reducing quadratic dependency to linear.
result Significant improvement in performance on NLP tasks like QA and summarization.
We present a new approach to modeling sequential data: the deep equilibrium model (DEQ). Motivated by an observation that the hidden layers of many existing deep sequence models converge towards some fixed point, we propose the DEQ approach that directly finds these equilibrium points via root-finding. Such a method is…
Single Molecule Real-Time (SMRT) sequencing is a recent advancement of Next Gen technology developed by Pacific Bio (PacBio). It comes with an explosion of long and noisy reads demanding cutting edge research to get most out of it. To deal with the high error probability of SMRT data, a novel contextual Locality Sensit…
The paper examines compactness of scalar curvature sequences on conformal manifolds.
problem Compactness of sequences of Riemannian manifolds with positive scalar curvature.
method Analyzes the conformal case of Riemannian manifolds, focusing on compactness and convergence properties.
result Compactness of conformal factors and convergence away from a singular set.
A new method optimizes neural sequence models for better task performance.
problem Training neural sequence models with maximum likelihood estimation ignores task losses.
method Maximum likelihood guided parameter search (MGS) in the parameter space.
result MGS optimizes sequence-level losses, reducing repetition and non-termination.