Abstract:Developing new treatments for emerging infectious diseases in infectious and noninfectious diseases has attracted a particular attention. The emergence of viral diseases is expected to accelerate; these data indicate the need for a proactive approach to develop widely active family specific and cross family therapies for future disease outbreaks. Viral disease such as pneumonia, severe acute respiratory syndrome type 2, HIV infection, and Hepatitis-C virus can cause directly and indirectly cardiovascular disea… Show more
“…To address the challenge of substantial, varying attenuation affecting optical signal transmission through water bodies, a modified CNN model is proposed for data recovery in underwater optical wireless communication [20]. Lastly, the paper discusses a deep learning-based autoencoder approach for designing a new drug source and target for molecular communication networks (MCN) under white Gaussian noise [21]. This approach aims to develop a robust mechanism for future healthcare applications, mapping MCN to molecular signaling and communication found in and around the human body.…”
Section: Related Workmentioning
confidence: 99%
“…In the second phase, the input layer, which will determine the new information, comes into play and first updates the information with the sigmoid function by employing Eq. (21). Next, the candidate data, which will contribute to creating new information, are identified using Eq.…”
Molecular communication (MC) holds promise for enabling communication in scenarios where traditional wireless methods may be impractical or ineffective, offering unique capabilities for a range of applications in both natural and engineered systems. In this research, a novel approach to MC is explored, diverging from the standard use of stationary transmitter and receiver models typically found in the field. The study introduces a dynamic MC model, where both the transmitter and receiver are mobile within a diffusion environment. This model operates using a 5-bit system. The key finding is that the mobility of these nanodevices alters their distance, which in turn impacts the likelihood of molecule reception at the receiver. The study employs deep learning techniques, specifically a combination of Convolutional Neural Networks (CNN) and Long Short-Term Memory (LSTM) networks, to categorize the mobility patterns of the receiver (Rx) and transmitter (Tx). By analyzing various mobility rates (Drx and Dtx) and distances between the Tx and Rx, the research successfully identifies the most efficient mobile MC model in terms of molecule reception rates. The use of Linear Support Vector Machine alongside the CNN and LSTM hybrid feature vector resulted in an 87.68% accuracy in predicting diffusion coefficients. Moreover, using a Cubic Support Vector with the same hybrid feature vector, the study achieved an 88.09% accuracy in estimating the distance between the transmitter and receiver. The study concludes that an increase in the mobilities of Rx and Tx correlates with a higher rate of molecule reception.
“…To address the challenge of substantial, varying attenuation affecting optical signal transmission through water bodies, a modified CNN model is proposed for data recovery in underwater optical wireless communication [20]. Lastly, the paper discusses a deep learning-based autoencoder approach for designing a new drug source and target for molecular communication networks (MCN) under white Gaussian noise [21]. This approach aims to develop a robust mechanism for future healthcare applications, mapping MCN to molecular signaling and communication found in and around the human body.…”
Section: Related Workmentioning
confidence: 99%
“…In the second phase, the input layer, which will determine the new information, comes into play and first updates the information with the sigmoid function by employing Eq. (21). Next, the candidate data, which will contribute to creating new information, are identified using Eq.…”
Molecular communication (MC) holds promise for enabling communication in scenarios where traditional wireless methods may be impractical or ineffective, offering unique capabilities for a range of applications in both natural and engineered systems. In this research, a novel approach to MC is explored, diverging from the standard use of stationary transmitter and receiver models typically found in the field. The study introduces a dynamic MC model, where both the transmitter and receiver are mobile within a diffusion environment. This model operates using a 5-bit system. The key finding is that the mobility of these nanodevices alters their distance, which in turn impacts the likelihood of molecule reception at the receiver. The study employs deep learning techniques, specifically a combination of Convolutional Neural Networks (CNN) and Long Short-Term Memory (LSTM) networks, to categorize the mobility patterns of the receiver (Rx) and transmitter (Tx). By analyzing various mobility rates (Drx and Dtx) and distances between the Tx and Rx, the research successfully identifies the most efficient mobile MC model in terms of molecule reception rates. The use of Linear Support Vector Machine alongside the CNN and LSTM hybrid feature vector resulted in an 87.68% accuracy in predicting diffusion coefficients. Moreover, using a Cubic Support Vector with the same hybrid feature vector, the study achieved an 88.09% accuracy in estimating the distance between the transmitter and receiver. The study concludes that an increase in the mobilities of Rx and Tx correlates with a higher rate of molecule reception.
“…For a critical introduction to the application of interpretable genomics, see [48]. Another subfield, the Deep Learning in drug response prediction is discussed in [49][50][51][52].…”
Background
There is an increasing interest in the use of Deep Learning (DL) based methods as a supporting analytical framework in oncology. However, most direct applications of DL will deliver models with limited transparency and explainability, which constrain their deployment in biomedical settings.
Methods
This systematic review discusses DL models used to support inference in cancer biology with a particular emphasis on multi-omics analysis. It focuses on how existing models address the need for better dialogue with prior knowledge, biological plausibility and interpretability, fundamental properties in the biomedical domain. For this, we retrieved and analyzed 42 studies focusing on emerging architectural and methodological advances, the encoding of biological domain knowledge and the integration of explainability methods.
Results
We discuss the recent evolutionary arch of DL models in the direction of integrating prior biological relational and network knowledge to support better generalisation (e.g. pathways or Protein-Protein-Interaction networks) and interpretability. This represents a fundamental functional shift towards models which can integrate mechanistic and statistical inference aspects. We introduce a concept of bio-centric interpretability and according to its taxonomy, we discuss representational methodologies for the integration of domain prior knowledge in such models.
Conclusions
The paper provides a critical outlook into contemporary methods for explainability and interpretability used in DL for cancer. The analysis points in the direction of a convergence between encoding prior knowledge and improved interpretability. We introduce bio-centric interpretability which is an important step towards formalisation of biological interpretability of DL models and developing methods that are less problem- or application-specific.
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