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.
Study improves peptide design efficiency using active and meta-learning.
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…
Major histocompatibility complex class two (MHC-II) molecules are trans-membrane proteins and key components of the cellular immune system. Upon recognition of foreign peptides expressed on the MHC-II binding groove, helper T cells mount an immune response against invading pathogens. Therefore, mechanistic identificati…
New method designs antimicrobial peptides with high potency and low toxicity.
Motivation: Post-database searching is a key procedure in peptide dentification with tandem mass spectrometry (MS/MS) strategies for refining peptide-spectrum matches (PSMs) generated by database search engines. Although many statistical and machine learning-based methods have been developed to improve the accuracy of …
The evolution of drug-resistant microbial species is one of the major challenges to global health. The development of new antimicrobial treatments such as antimicrobial peptides needs to be accelerated to combat this threat. However, the discovery of novel antimicrobial peptides is hampered by low-throughput biochemica…
Bayesian network models are finding success in characterizing enzyme-catalyzed reactions, slow conformational changes, predicting enzyme inhibition, and genomics. In this work, we apply them to statistical modeling of peptides by simultaneously identifying amino acid sequence motifs and using a motif-based model to cla…
Boosted GFlowNets improve exploration by sequentially training GFlowNets with residual rewards.
Personalized cancer vaccines are envisioned as the next generation rational cancer immunotherapy. The key step in developing personalized therapeutic cancer vaccines is to identify tumor-specific neoantigens that are on the surface of tumor cells. A promising method for this is through de novo peptide sequencing from m…
Liquid chromatography coupled with tandem mass spectrometry, also known as shotgun proteomics, is a widely-used high-throughput technology for identifying proteins in complex biological samples. Analysis of the tens of thousands of fragmentation spectra produced by a typical shotgun proteomics experiment begins by assi…
We propose a specialized string kernel for small bio-molecules, peptides and pseudo-sequences of binding interfaces. The kernel incorporates physico-chemical properties of amino acids and elegantly generalize eight kernels, such as the Oligo, the Weighted Degree, the Blended Spectrum, and the Radial Basis Function. We …
This paper presents regression models obtained from a process of blind prediction of peptide binding affinity from provided descriptors for several distinct datasets as part of the 2006 Comparative Evaluation of Prediction Algorithms (COEPRA) contest. This paper finds that kernel partial least squares, a nonlinear part…
Deep neural networks improve free energy calculations for peptide conformations.
As in many other scientific domains, we face a fundamental problem when using machine learning to identify proteins from mass spectrometry data: large ground truth datasets mapping inputs to correct outputs are extremely difficult to obtain. Instead, we have access to imperfect hand-coded models crafted by domain exper…
BoGA combines evolutionary search with Bayesian optimization for efficient protein design.
We attempt to set a mathematical foundation of immunology and amino acid chains. To measure the similarities of these chains, a kernel on strings is defined using only the sequence of the chains and a good amino acid substitution matrix (e.g. BLOSUM62). The kernel is used in learning machines to predict binding affinit…
Generative models accelerate molecular dynamics by four orders of magnitude.
Deep neural networks predict B-cell epitopes for SARS-CoV and SARS-CoV-2.
Signaling proteins are an important topic in drug development due to the increased importance of finding fast, accurate and cheap methods to evaluate new molecular targets involved in specific diseases. The complexity of the protein structure hinders the direct association of the signaling activity with the molecular s…
We introduce a machine learning approach for extracting fine-grained representations of protein evolution from molecular dynamics datasets. Metastable switching linear dynamical systems extend standard switching models with a physically-inspired stability constraint. This constraint enables the learning of nuanced repr…
The most widely used technology to identify the proteins present in a complex biological sample is tandem mass spectrometry, which quickly produces a large collection of spectra representative of the peptides (i.e., protein subsequences) present in the original sample. In this work, we greatly expand the parameter lear…
Many proteoforms - arising from alternative splicing, post-translational modifications (PTMs), or paralogous genes - have distinct biological functions, such as histone PTM proteoforms. However, their quantification by existing bottom-up mass-spectrometry (MS) methods is undermined by peptide-specific biases. To avoid …
Machine learning improves implicit solvent models for molecular dynamics.
A new approach to protein language models combines latent space prediction with masked language modeling.
Extending spatio-temporal scale limitations of models for complex atomistic systems considered in biochemistry and materials science necessitates the development of enhanced sampling methods. The potential acceleration in exploring the configurational space by enhanced sampling methods depends on the choice of collecti…
The paper introduces tests for high-dimensional independence using maximum and average distance correlations.
Recent developments in specialized computer hardware have greatly accelerated atomic level Molecular Dynamics (MD) simulations. A single GPU-attached cluster is capable of producing microsecond-length trajectories in reasonable amounts of time. Multiple protein states and a large number of microstates associated with f…
Tandem mass spectrometry (MS/MS) is a high-throughput technology used toidentify the proteins in a complex biological sample, such as a drop of blood. A collection of spectra is generated at the output of the process, each spectrum of which is representative of a peptide (protein subsequence) present in the original co…
Smooth flows for physical systems with smooth energies and forces.
Enhances diffusion-based sampling for molecular systems.
Timewarp accelerates molecular dynamics by learning to simulate long timescales.
GMVAE improves clustering in molecular simulations data.
This study interprets machine learning models to identify biomarkers for severe COVID-19 infection.
Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects -- typically neglected by conventional quan…
A framework for faster, better infographic design by non-experts and experts alike.
The paper proposes a method to reliably select design algorithms for machine learning-guided design tasks.
Unified approach to experimental design using interlacing polynomials.
We propose a new low-cost machine-learning-based methodology which assists designers in reducing the gap between the problem and the solution in the design process. Our work applies reinforcement learning (RL) to find the optimal task-oriented design solution through the construction of the design action for each task.…
Design-by-Morphing creates radical airfoil designs without geometric constraints.
MO-PaDGAN generates diverse, high-performance designs with multiple metrics.
MCD automates counterfactual design searches for multi-modal tasks.
PaDGAN generates diverse, high-quality designs with improved performance.
ANN with GA optimizes flexible disc design for lower mass and stress.
New method for mixed-variable GSA improves material design efficiency.
Deep learning models enhance engineering design automation.
Efficient deep learning computing requires algorithm and hardware co-design to enable specialization: we usually need to change the algorithm to reduce memory footprint and improve energy efficiency. However, the extra degree of freedom from the algorithm makes the design space much larger: it's not only about designin…
Enhances scenario approach for certifying design properties post-design.
DAD learns to design experiments quickly, outperforming traditional methods.