In this work, sequence-to-sequence (seq2seq) models, originally developed for language translation, are used to predict the temporal evolution of complex, multi-physics computer simulations. The predictive performance of seq2seq models is compared to state transition models for datasets generated with multi-physics cod…
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48 results for “sequence evolution”
Bayesian-Deep Learning model predicts Covid-19 evolution in Spain.
problem Estimating the future evolution of Covid-19 in Spain.
method Combines DL techniques with Bayesian Poisson-Gamma model for counts.
result Allows prediction of future evolution and estimation of scenarios.
This paper explores the problem of unknotting closed braids and classical knots in mathematical knot theory. We apply evolutionary computation methods to learn sequences of moves that simplify knot diagrams, and show that this can be effective both when the evolution is carried out for individual knots and when a gener…
This paper uses bandit theory and Thompson Sampling to optimize protein sequences.
problem Optimizing protein sequences using machine learning and directed evolution.
method Proposes a Thompson Sampling-guided Directed Evolution (TS-DE) framework.
result TS-DE achieves a nearly optimal Bayesian regret of order .
MutaGAN predicts mutations of evolving protein populations using GANs.
problem Predicting mutations in evolving protein populations.
method Generative adversarial networks (GANs) with recurrent neural networks (RNNs).
result MutaGAN generates complete protein sequences with mutations.
Framework learns dynamic graph attributes and links co-evolution.
problem Forecasting change of node attributes and link formation in dynamic graphs.
method CoEvoGNN framework with temporal self-attention and joint optimization.
result Framework outperforms baselines on predicting unseen graph snapshots.
Emergenet predicts animal influenza strain emergence, outperforming current methods.
problem Limited ability to quantitatively assess animal influenza strain emergence.
method Infer digital twin of sequence evolution using 220,151 HA sequences.
result Emergenet predictions outperform WHO seasonal vaccine recommendations and CDC IRAT scores.
New models predict future events with uncertainty.
problem Predicting future events in asynchronous sequences with uncertainty.
method Two new architectures, WGP-LN and FD-Dir, modeling time-dependent distributions.
result Models outperform other approaches in various datasets.
New algorithm estimates intrinsic dimension of discrete datasets.
problem Inaccuracies in using continuous methods for discrete datasets.
method Introduced an algorithm to infer intrinsic dimension of discrete spaces.
result Demonstrated accuracy on benchmark datasets and found a small intrinsic dimension in a metagenomic dataset.
In this paper we study properties of the area evolute (AE) and the center symmetry set (CSS) of a convex planar curve . The main tool is to define a Minkowski plane where becomes a constant width curve. In this Minkowski plane, the CSS is the evolute of and the AE is an involute of the CSS. We prove that the…
AI helps forecasters understand TC convective evolution before intensification.
problem Challenges in extracting scientific insights from complex TC data.
method Combining AI prediction algorithms and classical statistical inference.
result Identifies patterns in TC convective structure leading to intensification.
Deep learning adapts HVAC models to new buildings.
problem Adapting thermal dynamics models to new buildings with limited data.
method Deep supervised domain adaptation (DSDA) using LSTM-based Sequence to Sequence model.
result Deep supervised domain adaptation improves predictive performance over learning from scratch.
The inverse Potts problem to infer a Boltzmann distribution for homologous protein sequences from their single-site and pairwise amino acid frequencies recently attracts a great deal of attention in the studies of protein structure and evolution. We study regularization and learning methods and how to tune regularizati…
Unbiased Gradient Estimation in Unrolled Computation Graphs with Persistent Evolution Strategiescs.LG
PES method reduces bias in gradient estimation for unrolled graphs.
problem High variance and bias in gradient estimation for unrolled computation graphs.
method Divide graph into unrolls, apply ES update, accumulate correction terms.
result PES provides unbiased, low-variance gradient estimates.
Study geometric mKdV flows for Legendrian curves in a 3-sphere.
problem Investigate geometric evolution equations for Legendrian curves.
method Define a symplectic structure and show mKdV and associated flows.
result Show mKdV equation as curvature evolution induced by Hamiltonian flows.
Motivation. Protein contact map describes the pairwise spatial and functional relationship of residues in a protein and contains key information for protein 3D structure prediction. Although studied extensively, it remains very challenging to predict contact map using only sequence information. Most existing methods pr…
The goal of this note is to prove a compact embedding result for spaces of forward rate curves. As a consequence of this result, we show that any forward rate evolution can be approximated by a sequence of finite dimensional processes in the larger state space.
A new method estimates protein evolutionary fields and couplings from alignments.
problem Estimating evolutionary fields and couplings from protein sequence alignments.
method Boltzmann machine with parallel, persistent Markov chain Monte Carlo method.
result Improved precision in predicting contact residue pairs.
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.
Protein contacts contain important information for protein structure and functional study, but contact prediction from sequence remains very challenging. Both evolutionary coupling (EC) analysis and supervised machine learning methods are developed to predict contacts, making use of different types of information, resp…
Paper shows no finite time singularities for smooth conformal heat flow of harmonic maps.
problem Smoothness of conformal heat flow of harmonic maps.
method Combines harmonic map flow with metric evolution in conformal direction.
result No finite time singularity occurs for the flow, and under certain conditions, maps converge to a point.
Hamiltonian in Financial Marketscond-mat.stat-mech
A statistical physics model for the time evolutions of stock portfolios is proposed. In this model the time series of price changes are coded into the sequences of up and down spins. The Hamiltonian of the system is introduced and is expressed by spin-spin interactions as in spin glass models of disordered magnetic sys…
Wittgenstein's Rule Following evolves datasets by extrapolating structural descriptors.
problem Generating meaningful continuations of evolving datasets.
method Wittgenstein's Rule Following (WRF) uses structural descriptors to extrapolate trajectories and average historical descriptors.
result WRF can generate meaningful continuations of evolving datasets.
PMCE: efficient inference of expressive models of cancer evolution with high prognostic powerstat.ML
Motivation: Driver (epi)genomic alterations underlie the positive selection of cancer subpopulations, which promotes drug resistance and relapse. Even though substantial heterogeneity is witnessed in most cancer types, mutation accumulation patterns can be regularly found and can be exploited to reconstruct predictive …
Generative Link Sequence Modeling predicts future links in evolving networks.
problem Predicting future links in networks with evolving structures.
method Sequence modeling framework with self-tokenization to capture temporal link formation patterns.
result GLSM achieves best performance on AUC metrics compared to existing methods.
This paper is devoted to the horizontal (``characteristic'') cohomology of systems of differential equations. Recent results on computing the horizontal cohomology via the compatibility complex are generalized. New results on the Vinogradov C-spectral sequence and the Krasil'shchik C-cohomology are obtained. As an appl…
SDIFT generates full-field dynamics from sparse, irregular data.
problem Modeling and reconstructing physical dynamics from sparse, off-grid observations.
method SDIFT uses a functional Tucker model and sequential diffusion for generating full-field evolution from irregular sparse observations.
result Significant improvements in reconstruction accuracy and computational efficiency compared to state-of-the-art approaches.
A framework infers causal direction from symbolic sequences using compression measures.
problem Inferring causal direction from two observed discrete symbolic sequences.
method Lossless compressors for inferring context-free grammars (CFGs) and quantifying compression extent.
result Grammar inferred from one sequence better compresses the other sequence, indicating causal direction.
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 …
Neural SDEs model continuous sequences using neural networks.
problem Modeling continuous-time dynamics in sequence data.
method Interprets time-series as samples from a continuous dynamical system, parameterized by Neural SDE.
result Demonstrates superior performance in diverse sequence modeling tasks.
We consider the problem of training input-output recurrent neural networks (RNN) for sequence labeling tasks. We propose a novel spectral approach for learning the network parameters. It is based on decomposition of the cross-moment tensor between the output and a non-linear transformation of the input, based on score …
This paper introduces a new neural ODE model for continuous-time sequence generation.
problem Representing and predicting continuous-time sequences with high accuracy.
method A neural emission model and neural ODE define the latent state evolution, with an Energy-based model for prior distribution.
result The model outperforms existing methods in various tasks, including long-horizon predictions.
Conditional COT-GAN predicts sequences using past data and kernel smoothing.
problem Predicting sequences given past data.
method Conditional COT-GAN with kernel smoothing.
result Improved convergence results for sequence prediction.
ReGENN improves time series forecasting by considering inter and intra-temporal relationships.
problem Achieving reliable predictions in real-world time series applications.
method ReGENN combines graph evolution with deep recurrent learning to model dynamic dependencies among multiple variables.
result Sound improvement of up to 64.87% over competing algorithms in time-series forecasting.
In this article we investigate a family of nonlinear evolutions of polygons in the plane called the -polygon flow and obtain some results analogous to results for the smooth curve shortening flow: (1) any planar polygon shrinks to a point and (2) a regular polygon with five or more vertices is asymptotically stable …
We develop a second-order model for limit order books in a single scaling regime.
problem Modeling price and volume dynamics in a limit order book with market and limit orders at a common time scale.
method Established a first- and second-order approximation for an infinite dimensional limit order book model.
result Proved the existence and uniqueness of a solution for the second-order approximation.
Consider a convex polygon P in the plane, and denote by U a homothetical copy of the vector sum of P and (-P). Then the polygon U, as unit ball, induces a norm such that, with respect to this norm, P has constant Minkowskian width. We define notions like Minkowskian curvature, evolutes and involutes for polygons of con…
Mathematical methods characterize RNNs' asymptotics as hidden units and data grow.
problem Characterize recurrent neural networks' behavior as hidden units and data grow.
method Developed mathematical methods to analyze RNNs' convergence to an infinite-dimensional ODE coupled with a fixed point of a random algebraic equation.
result RNNs converge to an infinite-dimensional ODE coupled with a fixed point of a random algebraic equation.
Rapid progress in deep learning has spurred its application to bioinformatics problems including protein structure prediction and design. In classic machine learning problems like computer vision, progress has been driven by standardized data sets that facilitate fair assessment of new methods and lower the barrier to …
Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, that can be applied to WGS data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutation…
Bayesian optimization of antibodies learns from immune system evolution.
problem Efficiently optimizing antibody sequences in a large space of possibilities.
method Bayesian optimization guided by a generative model of evolving antibody sequences.
result CloneBO optimizes antibodies more efficiently than previous methods.
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.
Modeling a sequence of interactions between users and items (e.g., products, posts, or courses) is crucial in domains such as e-commerce, social networking, and education to predict future interactions. Representation learning presents an attractive solution to model the dynamic evolution of user and item properties, w…
Generalized Frenet frames for singular space curves
problem Revisiting the Frenet frame for singular space curves
method Introducing a generalized Frenet frame and frame sequence
result Unified framework for Frenet and Bishop frames
Neural Physicist learns physical dynamics from images.
problem Learning meaningful physical state representations and accurate state transitions from image sequences.
method Neural Physicist uses VAE for state extraction, NP for parameters, and SSM for dynamics.
result Achieves long-term predictions and identifies system degrees of freedom.
CMC hierarchymath.DG
We propose an extension of the differential system for constant mean curvature (CMC) surfaces in a three dimensional space form to an associated hierarchy of evolution equations by the higher-order commuting symmetries. The infinite sequence of higher-order conservation laws of CMC surfaces admit the corresponding exte…
Click-through rate~(CTR) prediction, whose goal is to estimate the probability of the user clicks, has become one of the core tasks in advertising systems. For CTR prediction model, it is necessary to capture the latent user interest behind the user behavior data. Besides, considering the changing of the external envir…
Many studies in Economics and other disciplines have been reporting distributions following power-law behavior (i.e distributions of incomes (Pareto's law), city sizes (Zipf's law), frequencies of words in long sequences of text etc.)[1, 6, 7]. This widespread observed regularity has been explained in many ways: genera…