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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.

168,657 papers · 148 categories

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221442663884 · Jun 202019922001200920172026
48 results for Sequence optimization

P3BO optimizes biological sequence design by combining multiple methods.

problem Variability in performance of black-box optimization methods for biological sequence design.
method Population-Based Black-Box Optimization (P3BO) that samples sequences from an ensemble of methods, weighting by past performance.
result P3BO outperforms individual methods, proposing higher quality and more diverse sequences.

OptiGAN uses GAN and RL to optimize sequence generation for specific goals.

problem Challenging in sequence generation tasks to generate sequences with specific desired goals.
method Integrates GAN and RL to optimize desired goal scores using policy gradients.
result Achieves higher desired scores in text and real-valued sequence generation.

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.

Unified approach for sequence design combining likelihood-free inference and black-box optimization.

problem Designing biological sequences efficiently and accurately.
method Unified probabilistic framework integrating likelihood-free inference and black-box optimization.
result Previous optimization methods can be adapted and new algorithms proposed within this framework.

LES optimizes designs by sampling descent sequences, achieving strong sample efficiency.

problem Optimizing large, complex design spaces is infeasible and unnecessary.
method LES uses Bayesian optimization to target solutions reachable by iterative optimizers.
result LES achieves strong sample efficiency compared to existing methods.

We present Optimal Completion Distillation (OCD), a training procedure for optimizing sequence to sequence models based on edit distance. OCD is efficient, has no hyper-parameters of its own, and does not require pretraining or joint optimization with conditional log-likelihood. Given a partial sequence generated by th…

2018-10-02abs ↗pdf ↗

Neural network optimizes learning sequence for reading words.

problem Children struggle with learning to read words due to inconsistent spelling-sound correspondences.
method Used a neural network to structure learning trials to optimize generalization accuracy.
result Significant improvement in generalization accuracy compared to random or frequency-based sequences.

A faster method for optimizing DNA and protein sequences using machine learning.

problem Designing DNA and protein sequences with improved function.
method Activation maximization with a straight-through approximation and adaptive entropy variable.
result Fast SeqProp achieves up to 100-fold faster convergence and improved fitness optima.

Given a sequential learning algorithm and a target model, sequential machine teaching aims to find the shortest training sequence to drive the learning algorithm to the target model. We present the first principled way to find such shortest training sequences. Our key insight is to formulate sequential machine teaching…

2018-10-15abs ↗pdf ↗

LaMBO optimizes biological sequences using autoencoders and Bayesian optimization.

problem Bayesian optimization for drug design is limited by discrete, high-dimensional decision variables.
method Jointly trains denoising autoencoder with a Gaussian process head for gradient-based optimization in latent space.
result LaMBO outperforms genetic optimizers and requires no large pretraining corpus.

BoGA combines evolutionary search with Bayesian optimization for efficient protein design.

problem Designing novel proteins with specific characteristics is challenging due to sequence space complexity.
method BoGA integrates a genetic algorithm with Bayesian optimization to efficiently explore sequence space.
result BoGA accelerates discovery of high-confidence binders for diverse protein design objectives.

Sequence-to-Sequence (seq2seq) modeling has rapidly become an important general-purpose NLP tool that has proven effective for many text-generation and sequence-labeling tasks. Seq2seq builds on deep neural language modeling and inherits its remarkable accuracy in estimating local, next-word distributions. In this work…

2016-06-09abs ↗pdf ↗

Paper optimizes change-point detection using learned distributions from training sequences.

problem Optimal change-point detection with unknown pre- and post-change distributions.
method Designs a change-point estimator using training sequences and test sequences.
result Optimal confidence width characterized as a function of undetected error.

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 ildeO(d2MT) ilde O(d^{2}\sqrt{MT}).

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.

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.

Paper uses transfer learning and Bayesian optimization to reduce DNA sequence design experiments.

problem Designing many similar DNA sequences for specific applications is expensive and time-consuming.
method Combines transfer learning with Bayesian optimization to reduce experiment count.
result Total number of experiments can be significantly reduced by sharing information between tasks.

Optimal Farey sequence for Γ0(2n)Γ_0(2^n) with upper bound 2n12^{n-1}.

problem Finding an optimal Farey sequence for the congruence subgroup Γ0(2n)Γ_0(2^n).
method Proving the existence of a Farey sequence with specific properties and uniqueness.
result The upper bound of the Farey sequence is optimal and equals 2n12^{n-1}.

AntBO optimizes antibody design using Bayesian optimization for efficient and effective CDRH3 sequence generation.

problem Designing optimal antigen-specific CDRH3 regions in antibody design due to combinatorial sequence space.
method Combinatorial Bayesian optimization framework with trust region for developability.
result AntBO designs CDRH3 regions with diverse biophysical properties and outperforms existing methods.

Hybridizes CEM and gradient descent for efficient model-predictive control.

problem Efficiently planning optimal action sequences in high-dimensional spaces.
method Interleaves Cross-Entropy Method (CEM) and gradient descent steps.
result Faster convergence and avoidance of local optima compared to CEM.

Optimizes sliding window approach for tracking Gaussian densities.

problem Improving tracking performance of Gaussian density estimation.
method Theoretical analysis of sliding window Gaussian Kernel Density Estimators.
result Empirical evidence shows improved tracking performance with optimal weight sequence.

Existing imitation learning approaches often require that the complete demonstration data, including sequences of actions and states, are available. In this paper, we consider a more realistic and difficult scenario where a reinforcement learning agent only has access to the state sequences of an expert, while the expe…

2019-03-11abs ↗pdf ↗

This paper focuses on learning rate analysis of distributed kernel ridge regression for strong mixing sequences. Using a recently developed integral operator approach and a classical covariance inequality for Banach-valued strong mixing sequences, we succeed in deriving optimal learning rate for distributed kernel ridg…

2020-02-10abs ↗pdf ↗

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.

Paper analyzes regret bounds for unconstrained online optimization.

problem Minimizing regret in dynamic online learning for strongly convex and smooth functions.
method Preconditioned OGD, Online Optimistic Newton (OON), multiple gradient queries.
result Achieves O(C2,T)O(C^*_{2,T}) regret bound with one gradient query per round.

Reinforcement Patching optimizes dynamic sequence patching for efficient time series forecasting.

problem Efficiently learning data-adaptive representations for long-horizon sequence data, especially continuous sequences.
method Reinforcement Patching (ReinPatch) uses reinforcement learning to optimize dynamic patching policies and sequence backbones.
result ReinPatch achieves compelling performance in time-series forecasting compared to state-of-the-art methods.

We obtain an index of the complexity of a random sequence by allowing the role of the measure in classical probability theory to be played by a function we call the generating mechanism. Typically, this generating mechanism will be a finite automata. We generate a set of biased sequences by applying a finite state auto…

2008-12-10abs ↗pdf ↗

The paper tackles online learning problems with monotone arm sequences, achieving optimal or near-optimal regret bounds.

problem Online learning problems with ordinal and monotone arm sequences, such as dynamic pricing and clinical trials.
method Proposes algorithms for continuum-armed bandit problems with monotone arm sequences, achieving optimal or near-optimal regret bounds.
result Achieves optimal or near-optimal regret bounds for monotone arm sequences, differing from the continuous-armed bandit literature.

Survey and benchmark high-dimensional Bayesian optimization of discrete sequences.

problem Heterogeneous experimental set-ups and technical barriers in high-dimensional Bayesian optimization of discrete sequences.
method Unified framework and software libraries to test and benchmark methods.
result Unified framework and software libraries for testing and benchmarking high-dimensional Bayesian optimization methods.

As deep learning techniques advance more than ever, hyper-parameter optimization is the new major workload in deep learning clusters. Although hyper-parameter optimization is crucial in training deep learning models for high model performance, effectively executing such a computation-heavy workload still remains a chal…

2019-11-24abs ↗pdf ↗

A latent-variable model is introduced for text matching, inferring sentence representations by jointly optimizing generative and discriminative objectives. To alleviate typical optimization challenges in latent-variable models for text, we employ deconvolutional networks as the sequence decoder (generator), providing l…

2017-09-21abs ↗pdf ↗

An online framework optimizes efficiency in conformal prediction with a target miscoverage rate.

problem Achieving coverage and minimizing interval length in a sequential, online setting.
method Optimizes efficiency by directly optimizing the average length of intervals while maintaining coverage.
result Shows a gap between optimal performance for exchangeable and arbitrary sequences, and provides a matching algorithm for the Pareto-optimal settings.