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Big Data and Biological Networks · End Term · Jan 2023 · AN

Big Data and Biological Networks · End Term · Jan 2023 AN

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0 / 46 published solutions

Question 149 MCQ · 1.0 marks

Which one of the following is most appropriate.
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Uracil base is present in RNA.
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RNA stores entire genetic information of an organism.
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Thymine base is present in RNA
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None of these

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Question 150 MCQ · 1.0 marks

Average clustering coefficient of a complete graph with 20 nodes is
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0
6406531894992.
2
6406531894993.
1
6406531894994.
0.5

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Question 151 MCQ · 1.0 marks

Given that all the nodes belong to the same module, calculate the modularity of the given graph with 6 nodes.
Source diagram or notation
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1
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0.3
6406531894997.
0.5
6406531894998.
0

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Question 152 MCQ · 1.0 marks

Consider the given set of metabolic reactions. What is the average degree of the undirected substrate graph formed?
Source diagram or notation
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2.8
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2.5
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2.2
6406531895002.
2.0

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Question 153 MCQ · 1.0 marks

If a graph with 10 nodes has two connected components with a minimum degree of 4. What is the maximum possible number of edges?
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10
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30
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20
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45

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Question 154 MCQ · 1.0 marks

Source diagram or notation
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0.125
6406531895008.
0.25
6406531895009.
0.40
6406531895010.
0.50

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Question 155 MCQ · 1.0 marks

What distance can be used to separate the nodes into three clusters/modules.
Source diagram or notation
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2
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1
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4
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6

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Question 156 MCQ · 1.0 marks

Complete the below given code (in line 1) to get the total number of triangular sub-graphs in any given network. The input to the code is a networkx graph.
Source diagram or notation
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6406531895018.Source diagram or notation

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Question 157 MCQ · 1.0 marks

What is the total number of solutions that are possible for a string reconstruction problem with 20 words ?
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6406531895060.Source diagram or notation
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6406531895062.Source diagram or notation

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Question 158 MSQ · 2.0 marks

Which of the following are true about different omics techniques. Select all the correct options.
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Genomics data is independent of the cell type
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Transcriptomics data is dependent on a specific cell type
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Epigenomics is a large-scale study of proteins
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None of these

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Question 159 MSQ · 2.0 marks

Which of the following are application of Genomics? Select all the correct options.
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To study gene-expression pattern in a context specific manner
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To study post-translation modifications
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To study association of genome changes to phenotypic traits
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To study positional change in the genome known as Single nucleotide polymorphism (SNPs)

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Question 160 MSQ · 2.0 marks

Which of the following are valid DNA sequences? Select all the correct options.
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GCGCGCGCAGCGGAAA
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AAAGGCCCTAGCGCGC
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MVHLTPEEKSAVTALWH
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KEFTPPVQAAYQKVVAGV

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Question 161 MSQ · 2.0 marks

Which of the following are true for nanopore sequencing technology? Select all the correct options.
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Sequencing is determined through change in current in protein nanopore when DNA is passed through it
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Sequence is determined through fluorescence labelled nucleotides
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Nanopore is a long-read sequencing technique
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None of these

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Question 162 MSQ · 2.0 marks

Consider the given adjacency matrix and choose the options that are true.
Source diagram or notation
6406531895019.
The graph is weighted graph
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The graph is bipartite graph
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The graph is directed graph
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The graph is a complete graph

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Question 163 MSQ · 2.0 marks

Which of the following are true?
6406531895023.Source diagram or notation
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6406531895025.Source diagram or notation
6406531895026.Source diagram or notation

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Question 164 MSQ · 2.0 marks

Consider the metabolic network characterised by the stoichiometric matrix given below.
Source diagram or notation
6406531895027.
The average degree of the substrate graph is 2
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The in-degree of the node R3 is 1 in the bi-partite representation of the given metabolic network
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If the rate of the reaction R1 is 5, then the rate of change of concentration of A is 0
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If the rate of change of concentration of C is 0, then R3 = R4

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Question 165 MSQ · 2.0 marks

Four genes ‘e’, ‘f’, ‘g’ and ‘h’ are considered for studying the lethal phenotypes of a microbe. When the genes are deleted separately, the microbe survives. But, when the genes ‘e’ and ‘h’ are deleted together, the microbe dies. Similarly, when the genes ‘f’ and ‘g’ are deleted together, the microbe dies. Which of the following are lethal phenotypes?
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Question 166 MSQ · 2.0 marks

Identify the protein-protein interactions using the given set of genomes by gene-neighbourhood method.
Source diagram or notation
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A-D
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A-C
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D-E
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B-E

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Question 167 MSQ · 2.0 marks

The z-score of a bi-fan sub-graph in the two graphs (A and B) are -4 and 4, respectively. The Bi-fan sub-graph is a motif in ___________
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Graph A
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Graph B
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Both Graph A and Graph B
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None of these

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Question 168 MSQ · 2.0 marks

Transcriptional regulatory network (TRN) can be inferred in different levels of detail. Which of the following are true about the TRN?
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Nodes are the genes and enzymes
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Modules of the network are interconnected motifs
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A transcription factor in the network can have both incoming and outgoing edge
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Edges corresponds to the regulatory information

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Question 169 MSQ · 2.0 marks

Which of the following are true?
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Expression of genes is controlled by transcription factors
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Signals from external environment is transmitted via metabolic networks
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Protein networks defined only the functional interactions
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Gene regulatory network contains information on the type of gene-gene interaction

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Question 170 MSQ · 2.0 marks

Task-specific labels are scarce during the training phase. The pretraining helps to develop a general understanding of related tasks with abundant unlabelled data. Then, fine-tuning can be performed for a downstream task of interest. For the molecular property prediction task, which of the following are valid pretraining strategies.
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Reconstructing the adjacency matrix for each graph using an encoder-decoder approach
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Mask nodes and predict the features of masked nodes during training
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Predict the structural similarity between different graphs
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Use subgraphs to predict surrounding graph structures

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Question 171 MSQ · 2.0 marks

Which of the following are valid regularization approaches for graphs:
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Add L2 norm of trainable parameters to supervised loss term
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Randomly drop edges during training
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Constrain the neighbouring nodes to share similar embedding
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Randomly mask node features during training

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Question 172 MSQ · 2.0 marks

Which of the following statements is true?
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Global alignment is more applicable for sequences with similar lengths
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Traceback in the score matrix is the only place that the Smith-Waterman algorithm differs from the Needleman-Wunsch algorithm.
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Affine gap penalties are more widely used than constant gap penalties
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Sequence alignment cannot be used for identifying frameshift mutations

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Question 173 MSQ · 3.0 marks

Which of the following are true about Illumina sequencing? Select all the correct options.
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It sequences a single DNA fragment at a time
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It has faster true around times for high-sample volumes
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It has an ability to sequence several thousand genes simultaneously
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It is used widely for whole genome sequencing projects

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Question 174 MSQ · 3.0 marks

Which of the following are correct statements. Select all the correct options.
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Genetics is a study of heredity that involves a limited set of genes
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Genomics is a large-scale study of all the DNA of the organism
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High-throughput sequencing required for Genomics is made possible due to Next-generation sequencing techniques
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Aberrant epigenomic markers linked to diseases are studied using Genomics

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Question 175 MSQ · 3.0 marks

Which of the following can we use alignment for?
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To identify mutations in a given sequence
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To search in a database based on a query
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To discover conserved regions in a gene
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Predicting mutations in a gene sequence

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Question 176 SHORT_TEXT · 3.0 marks

Source diagram or notation

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Question 177 SUBJECTIVE · 3.0 marks

Dr. A has a hypothesis that betweenness centrality is a very good determiner of a node’s importance in a network and that targeting top betweenness centrality nodes will be a successful strategy to quickly disrupt a network. Can you suggest some computational experiments that Dr. A should perform to test the validity of her hypothesis? **NOTE:** Your answer should not exceed 150 words.

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Question 178 SUBJECTIVE · 3.0 marks

Consider a bipartite graph to study disease spread (GPL). One group of nodes indicate persons and the other group indicate locations. Edge connecting a person with a locality indicate that the person has been to the particular locality. Edge labels indicate at what time the person was present in the given locality. Using this graph, devise a strategy to: a) Impose time stratified lockdowns during a pandemic b) Identify super spreader. (Super spreader is the person who can transmit a disease to a large number of people) c) Identify which road to block at what time to control the spread **NOTE:** Your answer should not exceed 150 words.

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Question 179 SUBJECTIVE · 3.0 marks

Pattern lock is a commonly used security measure to protect Android devices. A typical pattern lock has 9 nodes in it (Graph A). Any pattern drawn on these nodes is a graph and will have following properties: 1) It has a single connected component 2) it is a directed graph 3) Only one directed edge is possible between two nodes. Mr(s) AAA found that because of the given spatial arrangement of nodes few combinations would be missed. For example, node ‘3’ cannot have an edge with nodes ‘1’, ‘7’ and ‘9’ given that the path did not cover these nodes. Hence Mr(s) AAA came up with a new spatial arrangement with a lesser number of nodes (Graph B). No three nodes in Graph B lie on a same line. How can Mr(s) AAA prove that Graph B is more secure than Graph A. Here, more secure refers to more possible combinations of nodes.
Source diagram or notation
**NOTE:** Your answer should not exceed 150 words.

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Question 180 SHORT_TEXT · 3.0 marks

Elucidate the final sequence that is obtained using the following set of the k-mers: {‘ATCG’, ‘TACA’, ‘TCGG’, ‘CGGT’, ‘CAAC’, ‘GGTA’, ‘GTAC’, ‘ACAA’, ‘AACT’, ‘ACTC’}.

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Question 181 SUBJECTIVE · 3.0 marks

Highlight the differences between inductive and transductive node embedding and mention their limitations. **NOTE:** Your answer should not exceed 150 words.

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Question 182 SUBJECTIVE · 3.0 marks

Provide an overview for the graph classification problem a) Describe the training dataset b) Objective of graph classification c) Loss function d) Parameter learning e) Key elements of the Graph Neural Network model **NOTE:** Your answer should not exceed 150 words.

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Question 183 MSQ · 1.0 marks

Choose the correct pairs:
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Drug-Drug interaction → Binary graph classification
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Molecule toxicity prediction → Graph classification
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Protein interface prediction → Link prediction
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Drug-Target binding affinity prediction → Graph classification

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Question 184 MCQ · 2.0 marks

Which of the following is true?
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Diffpool uses importance scores to coarsen the input graph
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Pooling is used to generate node representations from a graph representation
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The assignment matrix is used to map super nodes to the original graph
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Eigenpooling uses spectral clustering to generate super nodes

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Question 185 MCQ · 2.0 marks

Source diagram or notation
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6406531895070.Source diagram or notation

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Question 186 MCQ · 2.0 marks

Given two sequences TATTT and AGTA, in the graph representation of their sequence alignment, how many nodes are present?
6406531895083.
10
6406531895084.
30
6406531895085.
20
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40

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Question 187 MCQ · 3.0 marks

What is the average degree (regardless of the direction) of the 3-mer overlap graph constructed from “GAATTCAGTTA”?
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2.22
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2.45
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3.12
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1.57

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Question 188 MCQ · 3.0 marks

What is the best local alignment score for the sequences "GTACTG" and "TAGT" with the scoring scheme: **matches** = +2, **mismatches** = -1, and a constant gap penalty = -10.
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3
6406531895096.
4
6406531895097.
5
6406531895098.
6

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Question 189 MCQ · 3.0 marks

Consider the following statements: **Assertion (A):** Eulerian Path algorithm is preferred over the Hamiltonian Path algorithm for the genome assembly problem. **Reason (R):** A Hamiltonian Path is defined as the path that passes through all the nodes of a graph. Now, which of the following options is true?:
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Both A and R are true and R is the correct explanation for A
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Both A and R are true and R is not the correct explanation for R
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A is true but R is false
6406531895103.
Both the statements are false

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Question 190 MCQ · 3.0 marks

Source diagram or notation
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6406531895108.Source diagram or notation

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Question 191 MCQ · 3.0 marks

Source diagram or notation
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6406531895112.Source diagram or notation

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Question 192 MCQ · 3.0 marks

Source diagram or notation
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(1), (A),(i);(2),(B),(ii);(3),(A),(ii);(4),(B),(i);
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(1), (B),(i);(2),(B),(ii);(3),(A),(ii);(4),(A),(ii);
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(1), (A),(ii);(2),(A),(i);(3),(B),(i);(4),(A),(i);
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(1), (B),(ii);(2),(B),(i);(3),(B),(i);(4),(A),(ii);

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Question 193 MCQ · 3.0 marks

Source diagram or notation
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6406531895120.Source diagram or notation

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Question 194 MCQ · 3.0 marks

Source diagram or notation
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      **Fin Forensics** **Section Id :** 64065338436 **Section Number :** 9 **Section type :** Online **Mandatory or Optional :** Mandatory **Number of Questions :** 41 **Number of Questions to be attempted :** 41 **Section Marks :** 40 **Display Number Panel :** Yes **Group All Questions :** No **Enable Mark as Answered Mark for Review and** Yes **Clear Response :** **Maximum Instruction Time :** 0

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