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.
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.
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.
End-to-end training of recurrent neural networks for biological sequences.
problem Training recurrent neural networks for biological sequence classification.
method Generalized convolutional kernel networks with recurrent structures.
result Outperforms existing methods for protein classification tasks.
Deep learning applied to biological data mining.
problem Mining complex biological data from diverse sources.
method Artificial neural networks, deep learning architectures.
result Deep learning techniques improve pattern recognition in biological data.
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.
Proposes a novel network-based neighborhood regression for biological systems.
problem Lack of comprehensive analysis on biological modules using both global and local network data.
method Develops a community-wise least square optimization approach to analyze gene modules and their regulatory strength.
result Achieves exact minimax optimality and linear consistency in identifying gene module associations.
The study compares different scRNA sequencing methods using a high-dimensional dataset.
problem To identify unique characteristics of different scRNA sequencing methods.
method Quantitative comparison through clustering analysis of a high-dimensional dataset.
result Identifies unique characteristics associated with different scRNA sequencing 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…
Study connects Gaussian processes and regularization for sequence-function mappings.
problem Understanding and interpreting sequence-function maps in biology.
method Relates Gaussian process priors, regularization, and gauge fixing in overparameterized weight space.
result Established the relationship between regularized regression and Gaussian processes in function space.
Robust machine learning models improve DNA regulatory sequence prediction under various shifts.
problem Real-world applications of DNA regulatory sequence prediction involve shifts not captured by standard i.i.d. assumptions.
method Introduces a robustness framework combining simulation benchmarks and real data analysis.
result Models remain accurate and calibrated under mild shifts but show higher error and miscalibration under strong shifts.
Optimal transport embedding learns feature sets efficiently.
problem Learning on sets of features with long-range dependencies and few labeled data.
method Parametrized fixed-size embedding that aggregates features according to optimal transport plan.
result Achieves state-of-the-art results on protein fold recognition and chromatin profiles.
Graph ConvNet improves ncRNA classification accuracy.
problem Classifying non-coding RNA sequences into families.
method Graph Convolutional Network model trained on raw RNA graphs.
result 85.73% accuracy and 85.61% F1-score over 13 classes.
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 …
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…
This study benchmarks transcriptomics models for perturbation analysis, finding scVI and PCA superior.
problem Limited evaluation of transcriptomics foundation models for perturbation analysis.
method Developed a novel evaluation framework using diverse public datasets from different sequencing techniques and cell lines.
result scVI and PCA identified as superior models for understanding biological perturbations.
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.
A fundamental aspect of biological information processing is the ubiquity of sequence-function relationships -- functions that map the sequence of DNA, RNA, or protein to a biochemically relevant activity. Most sequence-function relationships in biology are quantitative, but only recently have experimental techniques f…
Proposes CCCVAE for better single-cell clustering with cell-cell communication.
problem Improving single-cell RNA sequencing clustering by incorporating cell-cell communication.
method Integrates cell-cell communication into a variational autoencoder framework.
result Empirical results show CCCVAE outperforms standard VAEs in clustering performance.
MIK improves t-SNE's local structure preservation in biological sequence data.
problem Efficiently preserving local structure in high-dimensional biological sequence data.
method Modified Isolation Kernel (MIK) using adaptive density estimation.
result MIK preserves local and global structure better than Gaussian and isolation kernels.
High-dimensional data acquired from biological experiments such as next generation sequencing are subject to a number of confounding effects. These effects include both technical effects, such as variation across batches from instrument noise or sample processing, or institution-specific differences in sample acquisiti…
In biological research machine learning algorithms are part of nearly every analytical process. They are used to identify new insights into biological phenomena, interpret data, provide molecular diagnosis for diseases and develop personalized medicine that will enable future treatments of diseases. In this paper we (1…
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.
Learning long-term dependencies in extended temporal sequences requires credit assignment to events far back in the past. The most common method for training recurrent neural networks, back-propagation through time (BPTT), requires credit information to be propagated backwards through every single step of the forward c…
Stem uses diffusion models to infer gene expression from H&E images.
problem Inference of gene expression from H&E stained images is time-consuming and expensive.
method Conditional diffusion generative model to infer gene expression.
result Stem achieves state-of-the-art performance in spatial gene expression prediction.
Enhances sequence memory capacity in neural networks.
problem Limited sequence capacity in Hopfield-like neural networks.
method Introducing a nonlinear interaction term and a generalized pseudoinverse rule.
result Significantly increased sequence capacity with novel scaling laws.
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.
The increased affordability of whole genome sequencing has motivated its use for phenotypic studies. We address the problem of learning interpretable models for discrete phenotypes from whole genomes. We propose a general approach that relies on the Set Covering Machine and a k-mer representation of the genomes. We sho…
Optimization approach for efficient sampling in optical mapping for structural variant detection.
problem Efficient sampling strategy for structural variant detection using optical mapping.
method Developed an optimization approach using a hyper-geometric distribution and probabilistic concentration inequalities.
result Optimal sampling strategy requires sampling most chromosomal fragments to detect variants at high confidence with little biological material.
PGEL learns embeddings to diversify protein motifs while maintaining biological function.
problem Generating diverse protein structures while preserving biological function.
method Embedding learning framework that enhances motif diversity in a diffusion model's frozen denoiser.
result PGEL achieves greater structural diversity, better designability, and improved self-consistency compared to partial diffusion.
Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads", which constitute a fundamentally discrete measure of the level of gene expression. A…
We propose a novel framework for combining datasets via alignment of their intrinsic geometry. This alignment can be used to fuse data originating from disparate modalities, or to correct batch effects while preserving intrinsic data structure. Importantly, we do not assume any pointwise correspondence between datasets…
TAPE benchmarks protein learning tasks, finds self-supervised pretraining boosts performance.
problem Fragmented datasets and lack of standardized evaluation in protein modeling.
method TAPE introduces five semi-supervised learning tasks, curates splits, benchmarks models.
result Self-supervised pretraining more than doubles performance in some cases.
Neural network uses local credit assignment to learn distant cause-effect relationships.
problem Learning distant cause-effect relationships in sequential data.
method Sparse coding in a recurrent neural network memory with local and immediate credit assignment.
result Network can predict partially-observable higher-order sequences and navigate mazes.
sgdGMF efficiently estimates generalized matrix factorization models for single-cell RNA sequencing data.
problem Challenges in dimensionality reduction for large single-cell RNA sequencing datasets.
method Scalable adaptive stochastic gradient descent algorithm for generalized matrix factorization models.
result sgdGMF outperforms existing methods in scalability and accuracy for large datasets.
scICML integrates multi-omics data from single cells using co-clustering.
problem High noise and sparsity in multi-omics data from single cells.
method Information-theoretic co-clustering-based multi-view learning.
result Improves clustering performance and provides biological insights.
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.
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.
NESS improves neighbor embedding for smooth cell-state transitions in single-cell data.
problem Challenges in extracting smooth, low-dimensional representations from noisy single-cell data.
method Builds on PCS framework to develop NESS, a stable machine learning approach.
result NESS consistently yields useful biological insights across diverse single-cell datasets.
The functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects. While recent models have relaxed this constraint to also account for pairwise in…
A new framework scales active search for large datasets.
problem Scaling active search for large, high-dimensional data sets.
method Hierarchical Batch Bandit Search (HBBS) framework.
result HBBS improves performance and scalability for batch search.
New Performer model tackles long-sequence protein modeling.
problem Challenges of training complex Transformer models for long sequences.
method Linearly scalable long-context Transformer architecture, Performer.
result Performer provides strong theoretical guarantees and is effective for protein sequence modeling.
RNA-binding proteins (RBPs) play crucial roles in many biological processes, e.g. gene regulation. Computational identification of RBP binding sites on RNAs are urgently needed. In particular, RBPs bind to RNAs by recognizing sequence motifs. Thus, fast locating those motifs on RNA sequences is crucial and time-efficie…
We introduce GeNet, a method for shotgun metagenomic classification from raw DNA sequences that exploits the known hierarchical structure between labels for training. We provide a comparison with state-of-the-art methods Kraken and Centrifuge on datasets obtained from several sequencing technologies, in which dataset s…
A new smooth edit distance for easier optimization in machine learning.
problem Hard optimization of edit distance for variable-length sequences.
method Soft edit distance (SED) as a differentiable approximation.
result SED can be optimized with gradient methods and used for clustering.
Predicting the biological function of molecules, be it proteins or drug-like compounds, from their atomic structure is an important and long-standing problem. Function is dictated by structure, since it is by spatial interactions that molecules interact with each other, both in terms of steric complementarity, as well …
Motivation: Prediction of the interaction affinity between proteins and compounds is a major challenge in the drug discovery process. WideDTA is a deep-learning based prediction model that employs chemical and biological textual sequence information to predict binding affinity. Results: WideDTA uses four text-based inf…
As high-throughput biological sequencing becomes faster and cheaper, the need to extract useful information from sequencing becomes ever more paramount, often limited by low-throughput experimental characterizations. For proteins, accurate prediction of their functions directly from their primary amino-acid sequences h…