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.
Algorithm optimizes biological sequences using bootstrapped training with a score-conditioned generator.
P3BO optimizes biological sequence design by combining multiple methods.
LaMBO optimizes biological sequences using autoencoders and Bayesian optimization.
Researchers develop flexible kernels for biological sequences with guaranteed reliability.
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…
Paper uses transfer learning and Bayesian optimization to reduce DNA sequence design experiments.
Unified approach for sequence design combining likelihood-free inference and black-box optimization.
A faster method for optimizing DNA and protein sequences using machine learning.
PGEL learns embeddings to diversify protein motifs while maintaining biological function.
New tools evaluate and optimize conditional sequence models in bioinformatics.
Genomic models learn DNA sequences to predict functions.
Deep learning applied to biological data mining.
We address the problem of synthetic gene design using Bayesian optimization. The main issue when designing a gene is that the design space is defined in terms of long strings of characters of different lengths, which renders the optimization intractable. We propose a three-step approach to deal with this issue. First, …
Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current literature is fragmented when it comes to datasets and standardized evaluation tec…
With ongoing developments and innovations in single-cell RNA sequencing methods, advancements in sequencing performance could empower significant discoveries as well as new emerging possibilities to address biological and medical investigations. In the study, we will be using the dataset collected by the authors of Sys…
Proposes a novel network-based neighborhood regression for biological systems.
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…
BioBO optimizes gene perturbation design using Bayesian optimization with biological priors.
Precision oncology, the genetic sequencing of tumors to identify druggable targets, has emerged as the standard of care in the treatment of many cancers. Nonetheless, due to the pace of therapy development and variability in patient information, designing effective protocols for individual treatment assignment in a sam…
Study connects Gaussian processes and regularization for sequence-function mappings.
Biological research often involves testing a growing number of null hypotheses as new data is accumulated over time. We study the problem of online control of the familywise error rate (FWER), that is testing an apriori unbounded sequence of hypotheses (p-values) one by one over time without knowing the future, such th…
A new framework scales active search for large datasets.
New algorithms speed up learning from large screens of proteins.
Robust machine learning models improve DNA regulatory sequence prediction under various shifts.
BRAID fine-tunes diffusion models to optimize reward models in offline scenarios.
Substring kernels are classical tools for representing biological sequences or text. However, when large amounts of annotated data are available, models that allow end-to-end training such as neural networks are often preferred. Links between recurrent neural networks (RNNs) and substring kernels have recently been dra…
One of the fundamental tasks in understanding genomics is the problem of predicting Transcription Factor Binding Sites (TFBSs). With more than hundreds of Transcription Factors (TFs) as labels, genomic-sequence based TFBS prediction is a challenging multi-label classification task. There are two major biological mechan…
Optimal transport embedding learns feature sets efficiently.
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…
GeneDisco benchmarks experimental design for drug discovery.
This study benchmarks transcriptomics models for perturbation analysis, finding scVI and PCA superior.
Optimizes biomanufacturing processes with a new digital twin calibration method.
In this work, we perform an exploratory study on synthesizing deep neural networks using biological synaptic strength distributions, and the potential influence of different distributions on modelling performance particularly for the scenario associated with small data sets. Surprisingly, a CNN with convolutional layer…
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…
Maximizing the speed and precision of communication while minimizing power dissipation is a fundamental engineering design goal. Also, biological systems achieve remarkable speed, precision and power efficiency using poorly understood physical design principles. Powerful theories like information theory and thermodynam…
Path regularization improves GFlowNets exploration and generalization.
Proposes CCCVAE for better single-cell clustering with cell-cell communication.
Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design. This motivates predicting the structure of a protein from its sequence of amino…
MIK improves t-SNE's local structure preservation in biological sequence data.
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…
Two ML frameworks predict antibody properties using structural data.
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.
Given a finite sequence of graphs, e.g., coming from technological, biological, and social networks, the paper proposes a methodology to identify possible changes in stationarity in the stochastic process generating the graphs. In order to cover a large class of applications, we consider the general family of attribute…
Enhances sequence memory capacity in neural networks.
Quantitatively predicting phenotype variables by the expression changes in a set of candidate genes is of great interest in molecular biology but it is also a challenging task for several reasons. First, the collected biological observations might be heterogeneous and correspond to different biological mechanisms. Seco…