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.
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.
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.
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.
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.
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.
Given the emerging global threat of antimicrobial resistance, new methods for next-generation antimicrobial design are urgently needed. We report a peptide generation framework PepCVAE, based on a semi-supervised variational autoencoder (VAE) model, for designing novel antimicrobial peptide (AMP) sequences. Our model l…
Algorithm optimizes biological sequences using bootstrapped training with a score-conditioned generator.
problem Optimizing biological sequences for a black-box score function.
method Bootstrapped training of score-conditioned generator (BootGen) algorithm.
result Our method outperforms competitive baselines on biological sequential design tasks.
Solving the RNA inverse folding problem is a critical prerequisite to RNA design, an emerging field in bioengineering with a broad range of applications from reaction catalysis to cancer therapy. Although significant progress has been made in developing machine-based inverse RNA folding algorithms, current approaches s…
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.
A new framework for efficient sequence maps using Bayesian filtering and covariance.
problem Designing efficient recurrent sequence maps from explicit memory assumptions.
method Design-model framework, exact Bayesian filtering, query-dependent readout, linear-Gaussian instantiation.
result Improved robustness and retrieval performance across various benchmarks.
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of the activation maximization ("deep dream") design method; and a joint procedure wh…
Paper proposes efficient algorithms for designing SLOPE penalty sequences.
problem Designing SLOPE penalty sequences is computationally expensive.
method Developed two efficient algorithms: PGD and CD for Gaussian and general data matrices respectively.
result Demonstrated improved mean squared error performance of SLOPE with designed penalties.
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.
Deep learning models optimize protein sequences.
problem Optimizing protein properties through sequence design.
method Deep generative models guided by machine learning.
result Improved protein sequence generation from prior knowledge.
New tools evaluate and optimize conditional sequence models in bioinformatics.
problem Evaluating and optimizing conditional sequence models in bioinformatics.
method Kernel-based discrepancy measure (ACMMD) to estimate model fit and tune hyperparameters.
result Rejects the hypothesis that ProteinMPNN fits its data for various protein families and optimizes model temperature.
Recent dialogue approaches operate by reading each word in a conversation history, and aggregating accrued dialogue information into a single state. This fixed-size vector is not expandable and must maintain a consistent format over time. Other recent approaches exploit an attention mechanism to extract useful informat…
Unified framework for sequence models using test-time regression.
problem Designing efficient sequence models with associative memory.
method Formalizing associative recall as regression over input tokens, deriving various sequence models.
result Clarifies the effectiveness of query-key normalization in softmax attention and offers new generalizations.
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.
This paper presents a novel end-to-end approach to program repair based on sequence-to-sequence learning. We devise, implement, and evaluate a system, called SequenceR, for fixing bugs based on sequence-to-sequence learning on source code. This approach uses the copy mechanism to overcome the unlimited vocabulary probl…
Deep RL optimizes compiler passes for better performance.
problem Designing optimal compiler optimization sequences is hard and often suboptimal.
method Employed deep reinforcement learning to learn optimal pass orderings.
result Achieved up to 1.32x speedup on previously unseen programs.
A new framework uses text descriptions to improve protein design.
problem Lack of effective methods to incorporate textual descriptions in protein design.
method ProteinDT framework that combines text and protein structural information.
result ProteinDT significantly improves protein design accuracy and performance.
We present a new method for design problems wherein the goal is to maximize or specify the value of one or more properties of interest. For example, in protein design, one may wish to find the protein sequence that maximizes fluorescence. We assume access to one or more, potentially black box, stochastic "oracle" predi…
We propose a conditional non-autoregressive neural sequence model based on iterative refinement. The proposed model is designed based on the principles of latent variable models and denoising autoencoders, and is generally applicable to any sequence generation task. We extensively evaluate the proposed model on machine…
Deep learning model forecasts PV power production with high accuracy.
problem Accurate forecasting of photovoltaic power production is needed for electricity infrastructure.
method Sequence to sequence model with attention mechanism using weather predictions and historical data.
result The model outperforms existing methods in forecast skill score.
Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and translation. Since an RNA's function depends on its structural properties, the RN…
Mining tasks over sequential data, such as clickstreams and gene sequences, require a careful design of embeddings usable by learning algorithms. Recent research in feature learning has been extended to sequential data, where each instance consists of a sequence of heterogeneous items with a variable length. However, m…
FLORAS uses orthogonal sequences for SISO FL, offering both DP and convergence guarantees.
problem Privacy-preserving wireless federated learning in SISO systems.
method Leverages orthogonal sequences to eliminate CSIT requirement and provide DP guarantees.
result FLORAS achieves a smooth tradeoff between convergence rate and DP levels.
Deep learning models forecast stock market orders over multiple time frames.
problem Forecasting stock market orders over varying time frames.
method Encoder-decoder models with sequence-to-sequence and Attention mechanisms, leveraging Intelligent Processing Units (IPUs) for faster training.
result Multi-horizon forecasting outperforms single-horizon models, especially for long prediction periods.
Generative adversarial nets (GAN) has been successfully introduced for generating text to alleviate the exposure bias. However, discriminators in these models only evaluate the entire sequence, which causes feedback sparsity and mode collapse. To tackle these problems, we propose a novel mechanism. It first segments th…
Study on continuous sequence classification with distribution uncertainty.
problem Classifying continuous sequences with varying distribution uncertainty.
method Proposes distribution-free tests for three test designs: fixed-length, sequential, and two-phase tests.
result Error probabilities decay exponentially fast for all test designs.
A new method achieves optimal uniformity in designs with minimal flexibility.
problem Achieving optimal uniformity in designs with minimal flexibility.
method Derive a lower bound on the uniformity constant and use a greedy construction to achieve this bound, then extend the scheme for more flexibility.
result A simple greedy construction achieves the optimal uniformity constant.
Deep conditional generative models are developed to simultaneously learn the temporal dependencies of multiple sequences. The model is designed by introducing a three-way weight tensor to capture the multiplicative interactions between side information and sequences. The proposed model builds on the Temporal Sigmoid Be…
Genomic models learn DNA sequences to predict functions.
problem Understanding complex genetic interactions.
method Training LLMs on DNA sequences to predict functions.
result gLMs can predict functions of DNA elements.
We propose an input design method for a general class of parametric probabilistic models, including nonlinear dynamical systems with process noise. The goal of the procedure is to select inputs such that the parameter posterior distribution concentrates about the true value of the parameters; however, exact computation…
Algorithm provides online learning guarantees against general comparators in full and bandit feedback.
problem Adversarial online learning with data-dependent regret guarantees.
method Completely online algorithm with data-dependent regret guarantees for full and bandit feedback.
result Algorithm achieves expected performance against arbitrary comparator sequences in full and bandit feedback settings.
Time-based model improves recommendation performance.
problem Efficiently handling sequences of varying lengths in recommendation systems.
method Embedding layer and TSL attention-like mechanism with inner products.
result Model outperforms complex models on Taobao User Behavior dataset.
New algorithm handles bandit problems under translations and scales.
problem Adversarial multi-armed bandit problems with arbitrary translations and scales.
method Innovative online algorithm invariant to translations and scales, using universal prediction.
result Second-order regret bounds, unaffected by affine transformations of losses.
Paper proposes using LSTM for LSH-based sequence alignment.
problem Sequence alignment using deep learning models.
method Deep bidirectional LSTM for feature learning and LSH-based sequence alignment.
result Higher accuracy achieved with LSTM-based model.
JADAI optimizes design and inference for parameter estimation.
problem Parameter estimation with active optimization of design variables.
method Jointly trains a policy, history network, and inference network to minimize posterior error.
result Achieves superior or competitive performance across benchmarks.
Study designs neural networks for fault localization, state estimation, and optimal PMU placement in power systems.
problem Fault localization, state estimation, and optimal PMU placement in power systems.
method Designs and compares various neural networks for fault localization, builds machine learning schemes for state estimation and parameter estimation, and designs an algorithm for optimal PMU placement.
result Comprehensive comparison of neural networks for fault localization shows that Graphical Convolutional NN and Neural Graph-based ODE perform best.
Paper presents robust confidence sequences for means with known moment bounds and arbitrary corruption.
problem Tackles robustness to outliers and adversarial corruptions in mean estimation.
method Designs new robust exponential supermartingales to create confidence sequences.
result Achieves optimal width and shows smaller margin of error compared to fixed-time robust methods.
Neural Module Networks, originally proposed for the task of visual question answering, are a class of neural network architectures that involve human-specified neural modules, each designed for a specific form of reasoning. In current formulations of such networks only the parameters of the neural modules and/or the or…
New framework infers causal shifts in event sequences under out-of-domain interventions.
problem Inferring causal relationships in event sequences without considering out-of-domain interventions.
method Proposes a new causal framework to define ATE, designs an unbiased ATE estimator, and uses a Transformer-based neural network model.
result Demonstrates superior performance in ATE estimation and goodness-of-fit under out-of-domain-augmented point processes.
DFMs enable flow-based models for multimodal discrete and continuous data.
problem Combining discrete and continuous data for generative models.
method Discrete Flow Models (DFMs) using Continuous Time Markov Chains.
result DFMs achieve state-of-the-art co-design performance for protein structure and sequence generation.
A quantum model classifies financial sentiment by mapping text chunks to quantum circuits.
problem Classifying financial texts with high accuracy and preserving semantic information.
method Chunked diagrams are mapped to quantum circuits, with a Transformer encoder and type embeddings added for context.
result The hybrid model improves sentiment classification over a simple averaging baseline.
New method optimizes experiments under constraints.
problem Adapting BED to dynamic constraints in real-world tasks.
method Offline pre-training of an amortized policy and posterior network with online multi-step lookahead planning.
result Significantly more informative design sequences than existing methods.
A Semi-Hidden Markov Model (SHMM) for bursty error channels is defined by a state transition probability matrix A, a prior probability vector Π, and the state dependent output symbol error probability matrix B. Several processes are utilized for estimating A, Π and B from a given empirically obtained or sim…