12,690 research outputs found
Estimating notch fatigue limits via a machine learning-based approach structured according to the classic Kf formulas
This paper deals with the problem of estimating notch fatigue limits via machine learning. The proposed strategy is based on those constitutive elements that were used by the pioneers like Peterson, Neuber, Heywood, and Topper to devise their well-known formulas. The machine learning algorithms being considered were trained and tested using a database containing 238 notch fatigue limits taken from the literature. The outcomes from this study confirm that machine learning is a promising approach for designing notched components against fatigue. In particular, the accuracy in the estimates can easily be increased by simply increasing size and quality of the calibration dataset. Further, since machine learning regression models are highly flexible and can handle high-dimensional datasets with many input features, they can capture complex relationships between input features and the target variable. This means that the accuracy in estimating notch fatigue limit can be increased by including in the analyses further input features like, for instance, grain size or hardness. Finally, machine learning’s generalization ability is crucial for regression tasks where the goal is to predict values for new materials
UMSL Bulletin 2023-2024
The 2023-2024 Bulletin and Course Catalog for the University of Missouri St. Louis.https://irl.umsl.edu/bulletin/1088/thumbnail.jp
Protein-DNA binding sites prediction based on pre-trained protein language model and contrastive learning
Protein-DNA interaction is critical for life activities such as replication,
transcription, and splicing. Identifying protein-DNA binding residues is
essential for modeling their interaction and downstream studies. However,
developing accurate and efficient computational methods for this task remains
challenging. Improvements in this area have the potential to drive novel
applications in biotechnology and drug design. In this study, we propose a
novel approach called CLAPE, which combines a pre-trained protein language
model and the contrastive learning method to predict DNA binding residues. We
trained the CLAPE-DB model on the protein-DNA binding sites dataset and
evaluated the model performance and generalization ability through various
experiments. The results showed that the AUC values of the CLAPE-DB model on
the two benchmark datasets reached 0.871 and 0.881, respectively, indicating
superior performance compared to other existing models. CLAPE-DB showed better
generalization ability and was specific to DNA-binding sites. In addition, we
trained CLAPE on different protein-ligand binding sites datasets, demonstrating
that CLAPE is a general framework for binding sites prediction. To facilitate
the scientific community, the benchmark datasets and codes are freely available
at https://github.com/YAndrewL/clape
Highly Accurate Quantum Chemical Property Prediction with Uni-Mol+
Recent developments in deep learning have made remarkable progress in
speeding up the prediction of quantum chemical (QC) properties by removing the
need for expensive electronic structure calculations like density functional
theory. However, previous methods learned from 1D SMILES sequences or 2D
molecular graphs failed to achieve high accuracy as QC properties primarily
depend on the 3D equilibrium conformations optimized by electronic structure
methods, far different from the sequence-type and graph-type data. In this
paper, we propose a novel approach called Uni-Mol+ to tackle this challenge.
Uni-Mol+ first generates a raw 3D molecule conformation from inexpensive
methods such as RDKit. Then, the raw conformation is iteratively updated to its
target DFT equilibrium conformation using neural networks, and the learned
conformation will be used to predict the QC properties. To effectively learn
this update process towards the equilibrium conformation, we introduce a
two-track Transformer model backbone and train it with the QC property
prediction task. We also design a novel approach to guide the model's training
process. Our extensive benchmarking results demonstrate that the proposed
Uni-Mol+ significantly improves the accuracy of QC property prediction in
various datasets. We have made the code and model publicly available at
\url{https://github.com/dptech-corp/Uni-Mol}
Initial Value Problem Enhanced Sampling for Closed-Loop Optimal Control Design with Deep Neural Networks
Closed-loop optimal control design for high-dimensional nonlinear systems has
been a long-standing challenge. Traditional methods, such as solving the
associated Hamilton-Jacobi-Bellman equation, suffer from the curse of
dimensionality. Recent literature proposed a new promising approach based on
supervised learning, by leveraging powerful open-loop optimal control solvers
to generate training data and neural networks as efficient high-dimensional
function approximators to fit the closed-loop optimal control. This approach
successfully handles certain high-dimensional optimal control problems but
still performs poorly on more challenging problems. One of the crucial reasons
for the failure is the so-called distribution mismatch phenomenon brought by
the controlled dynamics. In this paper, we investigate this phenomenon and
propose the initial value problem enhanced sampling method to mitigate this
problem. We theoretically prove that this sampling strategy improves over the
vanilla strategy on the classical linear-quadratic regulator by a factor
proportional to the total time duration. We further numerically demonstrate
that the proposed sampling strategy significantly improves the performance on
tested control problems, including the optimal landing problem of a quadrotor
and the optimal reaching problem of a 7 DoF manipulator
MolFM: A Multimodal Molecular Foundation Model
Molecular knowledge resides within three different modalities of information
sources: molecular structures, biomedical documents, and knowledge bases.
Effective incorporation of molecular knowledge from these modalities holds
paramount significance in facilitating biomedical research. However, existing
multimodal molecular foundation models exhibit limitations in capturing
intricate connections between molecular structures and texts, and more
importantly, none of them attempt to leverage a wealth of molecular expertise
derived from knowledge graphs. In this study, we introduce MolFM, a multimodal
molecular foundation model designed to facilitate joint representation learning
from molecular structures, biomedical texts, and knowledge graphs. We propose
cross-modal attention between atoms of molecular structures, neighbors of
molecule entities and semantically related texts to facilitate cross-modal
comprehension. We provide theoretical analysis that our cross-modal
pre-training captures local and global molecular knowledge by minimizing the
distance in the feature space between different modalities of the same
molecule, as well as molecules sharing similar structures or functions. MolFM
achieves state-of-the-art performance on various downstream tasks. On
cross-modal retrieval, MolFM outperforms existing models with 12.13% and 5.04%
absolute gains under the zero-shot and fine-tuning settings, respectively.
Furthermore, qualitative analysis showcases MolFM's implicit ability to provide
grounding from molecular substructures and knowledge graphs. Code and models
are available on https://github.com/BioFM/OpenBioMed.Comment: 31 pages, 15 figures, and 15 table
Smart Farm-Care using a Deep Learning Model on Mobile Phones
Deep learning and its models have provided exciting solutions in various image processing applications like image segmentation, classification, labeling, etc., which paved the way to apply these models in agriculture to identify diseases in agricultural plants. The most visible symptoms of the disease initially appear on the leaves. To identify diseases found in leaf images, an accurate classification system with less size and complexity is developed using smartphones. A labeled dataset consisting of 3171 apple leaf images belonging to 4 different classes of diseases, including the healthy ones, is used for classification. In this work, four variants of MobileNet models - pre-trained on the ImageNet database, are retrained to diagnose diseases. The model’s variants differ based on their depth and resolution multiplier. The results show that the proposed model with 0.5 depth and 224 resolution performs well - achieving an accuracy of 99.6%. Later, the K-means algorithm is used to extract additional features, which helps improve the accuracy to 99.7% and also measures the number of pixels forming diseased spots, which helps in severity prediction. Doi: 10.28991/ESJ-2023-07-02-013 Full Text: PD
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