Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userInterpretable Convolutional Neural Networks for Effective Translation Initiation Site Prediction
94
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
Thanks to rapidly evolving sequencing techniques, the amount of genomic data at our disposal is growing increasingly large. Determining the gene structure is a fundamental requirement to effectively interpret gene function and regulation. An important part in that determination process is the identification of translation initiation sites. In this paper, we propose a novel approach for automatic prediction of translation initiation sites, leveraging convolutional neural networks that allow for automatic feature extraction. Our experimental results demonstrate that we are able to improve the state-of-the-art approaches with a decrease of 75.2% in false positive rate and with a decrease of 24.5% in error rate on chosen datasets. Furthermore, an in-depth analysis of the decision-making process used by our predictive model shows that our neural network implicitly learns biologically relevant features from scratch, without any prior knowledge about the problem at hand, such as the Kozak consensus sequence, the influence of stop and start codons in the sequence and the presence of donor splice site patterns. In summary, our findings yield a better understanding of the internal reasoning of a convolutional neural network when applying such a neural network to genomic data.
rate research
Read More
Predicting DNA-protein binding is an important and classic problem in bioinformatics. Convolutional neural networks have outperformed conventional methods in modeling the sequence specificity of DNA-protein binding. However, none of the studies has utilized graph convolutional networks for motif inference. In this work, we propose to use graph convolutional networks for motif inference. We build a sequence k-mer graph for the whole dataset based on k-mer co-occurrence and k-mer sequence relationship and then learn DNA Graph Convolutional Network (DNA-GCN) for the whole dataset. Our DNA-GCN is initialized with a one-hot representation for all nodes, and it then jointly learns the embeddings for both k-mers and sequences, as supervised by the known labels of sequences. We evaluate our model on 50 datasets from ENCODE. DNA-GCN shows its competitive performance compared with the baseline model. Besides, we analyze our model and design several different architectures to help fit different datasets.
We propose an image-classification method to predict the perceived-relevance of text documents from eye-movements. An eye-tracking study was conducted where participants read short news articles, and rated them as relevant or irrelevant for answering a trigger question. We encode participants eye-movement scanpaths as images, and then train a convolutional neural network classifier using these scanpath images. The trained classifier is used to predict participants perceived-relevance of news articles from the corresponding scanpath images. This method is content-independent, as the classifier does not require knowledge of the screen-content, or the users information-task. Even with little data, the image classifier can predict perceived-relevance with up to 80% accuracy. When compared to similar eye-tracking studies from the literature, this scanpath image classification method outperforms previously reported metrics by appreciable margins. We also attempt to interpret how the image classifier differentiates between scanpaths on relevant and irrelevant documents.
Convolutional neural networks (CNNs) have been successfully used in a range of tasks. However, CNNs are often viewed as black-box and lack of interpretability. One main reason is due to the filter-class entanglement -- an intricate many-to-many correspondence between filters and classes. Most existing works attempt post-hoc interpretation on a pre-trained model, while neglecting to reduce the entanglement underlying the model. In contrast, we focus on alleviating filter-class entanglement during training. Inspired by cellular differentiation, we propose a novel strategy to train interpretable CNNs by encouraging class-specific filters, among which each filter responds to only one (or few) class. Concretely, we design a learnable sparse Class-Specific Gate (CSG) structure to assign each filter with one (or few) class in a flexible way. The gate allows a filters activation to pass only when the input samples come from the specific class. Extensive experiments demonstrate the fabulous performance of our method in generating a sparse and highly class-related representation of the input, which leads to stronger interpretability. Moreover, comparing with the standard training strategy, our model displays benefits in applications like object localization and adversarial sample detection. Code link: https://github.com/hyliang96/CSGCNN.
The use of convolutional neural networks (CNNs) for classification tasks has become dominant in various medical imaging applications. At the same time, recent advances in interpretable machine learning techniques have shown great potential in explaining classifiers decisions. Layer-wise relevance propagation (LRP) has been introduced as one of these novel methods that aim to provide visual interpretation for the networks decisions. In this work we propose the application of 3D CNNs with LRP for the first time for neonatal T2-weighted magnetic resonance imaging (MRI) data analysis. Through LRP, the decisions of our trained classifier are transformed into heatmaps indicating each voxels relevance for the outcome of the decision. Our resulting LRP heatmaps reveal anatomically plausible features in distinguishing preterm neonates from term ones.
The use of machine learning methods for accelerating the design of crystalline materials usually requires manually constructed feature vectors or complex transformation of atom coordinates to input the crystal structure, which either constrains the model to certain crystal types or makes it difficult to provide chemical insights. Here, we develop a crystal graph convolutional neural networks framework to directly learn material properties from the connection of atoms in the crystal, providing a universal and interpretable representation of crystalline materials. Our method provides a highly accurate prediction of density functional theory calculated properties for eight different properties of crystals with various structure types and compositions after being trained with $10^4$ data points. Further, our framework is interpretable because one can extract the contributions from local chemical environments to global properties. Using an example of perovskites, we show how this information can be utilized to discover empirical rules for materials design.
suggested questions
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
