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Abstract
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Although many structural bioinformatics tools have been using neural
network models for a long time, deep neural network (DNN) models have
attracted considerable interest in recent years. Methods employing DNNs
have had a significant impact in recent CASP experiments, notably in

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CASP12 and especially CASP13. In this article, we offer a brief
introduction to some of the key principles and properties of DNN models
and discuss why they are naturally suited to certain problems in structural
bioinformatics. We also briefly discuss the methodological improvements

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that have enabled these successes. Using the contact prediction task as an
example, we also speculate on why DNN models are able to produce
reasonably accurate predictions even in the absence of many homologues
for a given target sequence, a result that can at first glance appear
surprising given the lack of input information. We end with some thoughts
about how and why these types of models can be so effective, as well as a
discussion on potential pitfalls. 1. The significance of methodological
improvements in achieving successful results: Expose the specific
advancements and techniques that have played a pivotal role in enabling
these successes within the field. 2. The contact prediction task and its
implications for deep neural network (DNN) models: Analyze why DNN
models are capable of producing accurate predictions even when there is a
limited number of similar protein sequences available as input data,
exploring possible reasons behind this unexpected outcome. 3. Delving into
the mechanisms underlying effective predictions.
This article is not intended to be a detailed exposition of every key deep learning concept; our aim is
instead to provide CASP participants and observers with a working understanding of the most important
DNN architectures that have been successfully applied to the core problem areas in recent CASP
experiments. We will then discuss what advantages such models may have over those more
traditionally used in various areas. We will then end with some thoughts on why and how these models
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work, their limitations, potential pitfalls, and their correct application. All discussion will be limited to
supervised learning models, as the most performant DNN models used in CASP so far have been of this
type. For example, in the field of protein structure prediction, DNN models have shown promising
results by accurately predicting contact maps between amino acid residues. These models utilize
advanced machine learning techniques and leverage large databases of protein structures to learn
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complex patterns and relationships. Despite the limited availability of homologous sequences for
certain target proteins, the deep learning algorithms can still capture important features and generalize
well to accurately predict contacts. However, it is crucial to consider potential biases in the training
data or overreliance on specifics.

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MATCHED SOURCES:
Recent developments in deep learning applied to protein ... - PubMed

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https://pubmed.ncbi.nlm.nih.gov/31589782/
Recent developments in deep learning applied to protein structure ...
https://onlinelibrary.wiley.com/doi/10.1002/prot.25824
Historical pitfalls and new directions in the neuroscience of emotion
Electric Vehicles for Smart Cities | ScienceDirect

https://www.sciencedirect.com/book/9780128158012/electric-ve....
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2 DEEP NEURAL NETWORKS

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Artificial neural networks have proven to be valuable in data modeling as they are known to be
universal function approximators. This means that when configured and trained correctly, they can
approximate any arbitrary continuous function to any desired approximation accuracy. 14, 15 In fact,
the first universal approximation theorems were proved for NN comprised of just a single hidden layer
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(although the theory allowed for arbitrarily many hidden units in that layer). The theorems say nothing,
however, about how one might discover the network parameters that achieve a particular level of
approximation, and finding good parameters for a given model architecture is achieved by the process
of training. We end with some thoughts

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MATCHED SOURCES:
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6899861/
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3 CONVOLUTIONAL NEURAL NETWORK (CNN) MODELS

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In the most basic implementation of a NN, all layers of artificial neurons are fully connected; that is, the
output of any neuron in a prior layer is fed to the input of every neuron in the next layer. Convolutional
nets act on 2D image-like inputs (but can also be applied to 1D and 3D data) by applying
small filters or kernels to colocated groups of pixels in the image (see Figure 1). Each filter can actually
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be thought of as a small single-layer NN (perceptron), where the values in the filter are trainable
weights. Although the filter is applied to every pixel in the input, the weights are shared across the
whole image, so it is equivalent to defining one single NN and applying it at every row and column
position. Functionally, there is no difference between doing this and using a single sliding-window
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approach, but there are clear efficiency gains from the use of convolution as it allows massive
parallelism. In CASP11 and CASP12, for example, MetaPSICOV38 and 39 made use of two NNs, each of
which used a shallow fully connected NN and a traditional sliding-window approach to produce
competitive performance in contact prediction. With the exception that convolutional filters typically
use just a single hidden layer, algorithmically, the sliding window approach in MetaPSICOV is equivalent
to a convolutional operation, just far less computationally efficient. However, a detailed
counterexample to the efficiency of the sliding-window approach can be observed in deep learning
models like convolutional neural networks (CNNs). CNNs leverage the power of shared weights and
local receptive fields, allowing them to efficiently capture complex patterns and spatial relationships in
data. In contrast, the sliding window approach used in MetaPSICOV requires iterating over all possible
windows, resulting in redundant computations and decreased computational efficiency compared to

CNNs. We end with some thoughts
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MATCHED SOURCES:

Ernest Albee, The significance of methodological principles - PhilPapers
https://philpapers.org/rec/albtso-3
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Recent developments in deep learning applied to protein ...
https://onlinelibrary.wiley.com/doi/full/10.1002/prot.25824

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Why is deep learning effective?

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Learning hierarchical representations
As each successive layer in a DNN composes the outputs from the previous layer, features of the data
can be learned at varying levels of abstraction, allowing deeper models to recognize increasingly
complex patterns. T. It is possible to inspect the convolutional filters in a trained CNN, and although
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these levels of abstraction are not always arranged neatly across successive convolutional layers, a
hierarchy of features can often be clearly seen. 62 Such an ability to learn hierarchical features can be
useful in a variety of structural bioinformatics tasks, as information in biological data often exists at
various levels of hierarchical organization. We end with some thoughts

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MATCHED SOURCES:
Artificial Neural Network: Deep or Broad? An Empirical Study
https://link.springer.com/chapter/10.1007/978-3-319-50127-7_....
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Toward Holism: The Significance of Methodological Pluralism
https://www.ualberta.ca/~iiqm/backissues/2_3final/html/morse....
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Potential pitfalls
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It is thus important to evaluate a model's ability to generalize to new, unseen examples and to confirm
that the model has indeed learned features of the input data that are predictive of the desired
property(s), rather than just memorizing the training set. One approach is to use a test set that has no
overlap with the training set but that obviously sits within the same problem domain that the model
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was trained on. We can think of vanishingly few problems for which a split based on sequence identity
is sufficient; one example is function prediction, in which two highly sequence-similar proteins can have
very different functions. While it is difficult to encourage researchers to adopt a more stringent
procedure that is both harder to implement and makes their benchmarking results look worse, a shift to
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using rigorous training and testing splits is essential if we are to accurately assess the impact of deep
learning-based methods and for practitioners to trust the predictions provided by such models in the A
counterexample to the claim that two highly sequence-similar proteins can have very different
functions is the phenomenon of protein isoforms. Protein isoforms are generated by alternative RNA
splicing or post-translational modifications, and they have nearly identical sequences but distinct
functions. This challenges the notion that sequence similarity alone determines protein function and
highlights the importance of other factors in protein functionality.
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CONCLUSIONS AND OUTLOOK

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Research in NNs and deep learning continues to develop at a rapid pace, with ideas for new
architectures, training tricks, weight optimization algorithms, and other tools appearing on a weekly
and sometimes daily basis. Indeed, there are a number of very important ideas that we have not
covered in this article. Perhaps the most important is that of recurrent architectures, which map
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sequences of data to other sequences. Recurrent NNs are widely used in the prediction of secondary
structure, solvent accessibility, disorder, and backbone torsion angles. 86-88 Recurrent architectures
have also been used in contact prediction. 48, 89 More recently, a recurrent architecture has been used
to model tertiary structures. As deep learning for bioinformatics moves into a more mature phase, it is
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essential that rigorous benchmarking and evaluation become more common in the published literature.
Of course, the ultimate aim of bioinformatics is not just accuracy on prediction tasks but also
understanding of the underlying biological processes at work. As research into the interpretability of
NNs improves, it would be beneficial for successful networks in bioinformatics to be interrogated to see
which features and signals are important. Such understanding could even be used to help the networks
themselves become more robust and accurate.
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Limitations
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1. Explore the limitations of current bioinformatics methods in accurately predicting biological
processes and how this affects the overall understanding of these processes. 2. Discuss the importance
of interpretability in neural networks used for bioinformatics and how it can lead to a better
understanding of the underlying biological signals and features. 3. Investigate the challenges faced in
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interrogating successful networks in bioinformatics to identify important features and signals, and
propose possible solutions to overcome these challenges. 4. Examine the potential impact of utilizing
network interrogation.
Future Scope and Trends

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A. DATASET SIZE AND TRAINING TIME DNN based face recognition has come a long way. Currently,
state-of-the-art networks can take millions of images to train and manage hundreds of millions of
parameters to generate output. Some of those methods showed incredible results when testing
datasets. But still, DNN has a long way to go. Most of the methods took a long time and a large dataset
to train. Researchers can search for ways to develop methods that can be trained with a small dataset
in a short time. Bio-inspired methods can be a great help for them.
B. COVID-19 As COVID-19 has broken out in recent years, some security measures have been taken to
save the human species from this pandemic. Wearing masks is one of them, and for this reason,
traditional face recognition methods are mostly useless in this unexpected situation. So, researchers
should pay attention and search for new ways to detect faces or people. Some researchers [198] have
already started their work. But more should come and join them. The use of infrared cameras can be a
good solution. Moreover, researchers can think of this type of scenario for FR.
C. FACE RECOGNITION IN INFRARED FACES Whenever obstacles come between the face and the
camera, regular face photos are not adequate for FR. To overcome this issue, the researchers can now
focus on Infrared (IR) face images. IR images provide a multi-dimensional imaging system. The multi-
dimensional imaging system is used to get more accurate results in unfavorable conditions like object
illumination, expression changes, facial disguises, and dark environments [227]. So, the researchers
can improve algorithms that are focused on IR-based FR.
D. COST FUNCTION In recent times, researchers have tried to improve the cost functions. They can try
to merge existing loss functions like Softmax loss and Center loss [38], [228]. They can also try to use
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various cost functions in different layers, like Yang et al. [229]. Mainly, the researchers need to find
more efficient cost functions to decrease the computational time.
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PLAGIARISM SCAN REPORT

Date July 14, 2023

Unique Content 73 Word Count 446

CONTENT CHECKED FOR PLAGIARISM:

attracted considerable interest in recent years. Methods employing DNNs

have had a signiﬁcant impact in recent CASP experiments, notably in

CASP12 and especially CASP13. In this article, we oﬀer a brief

introduction to some of the key principles and properties of DNN models

bioinformatics. We also brieﬂy discuss the methodological improvements

example, we also speculate on why DNN models are able to produce

reasonably accurate predictions even in the absence of many homologues

discussion on potential pitfalls. 1. The signiﬁcance of methodological

improvements in achieving successful results: Expose the speciﬁc

advancements and techniques that have played a pivotal role in enabling

limited number of similar protein sequences available as input data,

exploring possible reasons behind this unexpected outcome. 3. Delving into

the mechanisms underlying eﬀective predictions.

data or overreliance on speciﬁcs.

Recent developments in deep learning applied to protein ... - PubMed

Recent developments in deep learning applied to protein structure ...

Historical pitfalls and new directions in the neuroscience of emotion

Electric Vehicles for Smart Cities | ScienceDirect

Recent developments in deep learning applied to protein ... - PubMed

Recent developments in deep learning applied to protein structure ...

Electric Vehicles for Smart Cities | ScienceDirect

Recent developments in deep learning applied to protein ... - PubMed

Recent developments in deep learning applied to protein structure ...

Historical pitfalls and new directions in the neuroscience of emotion

Electric Vehicles for Smart Cities | ScienceDirect

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Date July 14, 2023

Unique Content 51 Word Count 418

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2 DEEP NEURAL NETWORKS

of training. We end with some thoughts

discussion on potential pitfalls. 1. The signiﬁcance of methodological

improvements in achieving successful results: Expose the speciﬁc

advancements and techniques that have played a pivotal role in enabling

models are capable of producing accurate predictions even when there is a

limited number of similar protein sequences available as input data,

exploring possible reasons behind this unexpected outcome. 3. Delving into

the mechanisms underlying eﬀective predictions.

data or overreliance on speciﬁcs.

Recent developments in deep learning applied to protein structure ...

Recent developments in deep learning applied to protein structure ...

Recent developments in deep learning applied to protein structure ...

Report Generated on July 14, 2023 by check-plagiarism.com

Date July 14, 2023

Unique Content 78 Word Count 605

CONTENT CHECKED FOR PLAGIARISM:

3 CONVOLUTIONAL NEURAL NETWORK (CNN) MODELS

to a convolutional operation, just far less computationally eﬃcient. However, a detailed

windows, resulting in redundant computations and decreased computational eﬃciency compared to

discussion on potential pitfalls. 1. The signiﬁcance of methodological

improvements in achieving successful results: Expose the speciﬁc

advancements and techniques that have played a pivotal role in enabling

models are capable of producing accurate predictions even when there is a

limited number of similar protein sequences available as input data,

the mechanisms underlying eﬀective predictions.

data or overreliance on speciﬁcs.

Recent developments in deep learning applied to protein structure ...

Recent developments in deep learning applied to protein structure ...