Big Data and Biological Networks End Term: 13 April 2025 (January 2025 term)

The bond between two amino acids is called:

How many codons in the genetic code translate to amino acids?

Which of the following is a key characteristic of post-translational modifications?

Which of the following best describes the fundamental principle behind a Genome-Wide Association Study (GWAS)?

Enumerate the total number of strings that can be generated with 20 words?

Which of the following is false?

Applications of transcriptomics include:

Which of the following mutations could not affect gene expression?

Which of the following distinguish Next-Generation Sequencing from traditional Sanger sequencing?

Which of the following biological processes involve the DNA:

The number of stuck/blocked reactions in the microbe ‘A’ when grown alone is 42. The number of stuck reactions is reduced to 18 when ‘A’ is grown together with ‘B’. Also, when ‘A’ is grown together with ‘C’, the number of stuck reactions in ‘A’ is 25 . Which of the following is/are true?

Scientists are studying genetic interactions in yeast by creating knockout strains. They observe the following results:
● Single deletion of gene A: viable
● Single deletion of gene B: viable
● Single deletion of gene C: viable
● Single deletion of gene D: viable
● Double deletion of genes A and B: lethal
● Double deletion of genes B and C: viable
● Double deletion of genes C and D: lethal
● Double deletion of genes A and D: viable
Which of the following statements correctly describe synthetic lethal interactions in this system?

Researchers conducted a network motif analysis on two biological networks (Network α and Network β) and obtained the following results for a specific subgraph pattern:

Which of the following statements are correct?

NOTE: Enter the exact answer without any extra space in the beginning or at the end.

NOTE: Enter the exact answer without any extra space in the beginning or at the end.

In a Watts-Strogatz small-world network model with n nodes, k initial nearest neighbors per node (k ≪ n), and rewiring probability p, what happens to the average path length L(p) as the rewiring probability p increases from 0 to 1?

A data science team is analyzing social network interactions to compare user engagement patterns between weekday and weekend activity. They have calculated differential network centrality metrics and obtained the following results for users U1-U4:

(Values represent differences: weekend minus weekday)

Based on differential network analysis, which user most likely became a new "bridge" in the weekend network that connects previously separated community groups?

What is the average degree (regardless of the direction) of the 4-mer overlap graph constructed from “CAGATGTAT”?

What is the best global alignment score for the sequences "GTACTG" and "TAGTCTG" with the scoring scheme: matches = +2, mismatches = -1 and a constant gap penalty of -10.

Elucidate the final sequence that is obtained from the kmers: TATT, TGAT, GATC, ATGT, GTAT, CATG, ATCA, TCAT, TGTA.

Consider the following statements:
Assertion (A): Dynamic Programming based approach is required to solve the sequence alignment problem.
Reason (R): DNA sequences are very long containing thousands of bases.
Which of the following options is true:

Choose the correct option:

Choose the most appropriate option:

$X$ is the feature matrix and $I$ is the identity matrix

Consider a two-layer neural network with the following architecture:

$h_1 = W_1 x + b_1$

$z_1 = \text{ReLU}(h_1)$

$h_2 = W_2 z_1 + b_2$

$\hat{y} = \sigma(h_2)$

$\ell = -y \log(\hat{y}) - (1 - y) \log(1 - \hat{y})$

Given the following numerical values:

$W_1 = \begin{bmatrix} 0.9 & 0.2 \\ 0.1 & 0.8 \end{bmatrix}$

$b_1 = \begin{bmatrix} 0.1 \\ 0.2 \end{bmatrix}$

$W_2 = \begin{bmatrix} 0.8 & 0.1 \\ 0.5 & 0.9 \end{bmatrix}$

$b_2 = \begin{bmatrix} 0.78 \\ 0.45 \end{bmatrix}$

$x = \begin{bmatrix} 1 \\ 2 \end{bmatrix}$

What is the value of $\frac{\partial h_2}{\partial b_2}$ , $\frac{\partial z_1}{\partial h_1}$ and $\frac{\partial h_1}{\partial x}$? Note: $I_n$ is $n \times n$ Identity Matrix

A two-layer neural network with the 2 features, $x_1,\ x_2$ is defined below:

$\begin{aligned} h_1 &= W_1 x + b_1 \\ z_1 &= ReLU(h_1) \\ h_2 &= W_2 z_1 + b_2 \\ \hat{y} &= \sigma(h_2) \\ \ell &= -y.log(\hat{y}) - (1 - y).log(1 - \hat{y}) \end{aligned}$

Given the following numerical values:

$W_1 = \begin{bmatrix} 0.9 & 0.2 \\ 0.1 & 0.8 \end{bmatrix}$

$b_1 = \begin{bmatrix} 0.1 \\ 0.2 \end{bmatrix}$

$W_2 = \begin{bmatrix} 0.8 & 0.1 \\ 0.5 & 0.9 \end{bmatrix}$

$b_2 = \begin{bmatrix} 0.78 \\ 0.45 \end{bmatrix}$

$x = \begin{bmatrix} 1 \\ 2 \end{bmatrix}$

$y = 1$

Compute the values of $\frac{\partial \ell}{\partial \hat{y}}$ and $\frac{\partial \hat{y}}{\partial h_2}$.

A research team studying neural connectivity in the prefrontal cortex has mapped interactions between key neurons involved in decision-making processes. They modeled the network using a modified Watts-Strogatz approach with N=4 nodes (neurons) and the following adjacency matrix:

Based on the above data, answer the given subquestions.

When a decision task is initiated, neuron 3 shows elevated firing rates, which researchers believe coordinates the decision-making process. After analyzing the network topology, the degree centrality of protein 3 is ______________

A research team studying neural connectivity in the prefrontal cortex has mapped interactions between key neurons involved in decision-making processes. They modeled the network using a modified Watts-Strogatz approach with N=4 nodes (neurons) and the following adjacency matrix:

Based on the above data, answer the given subquestions.

The clustering coefficient of protein 3 in this network is ____________

A research team studying neural connectivity in the prefrontal cortex has mapped interactions between key neurons involved in decision-making processes. They modeled the network using a modified Watts-Strogatz approach with N=4 nodes (neurons) and the following adjacency matrix:

Based on the above data, answer the given subquestions.

The betweenness centrality of protein 3 is _____________

In a social network analysis study, researchers are examining friendship connections between users on a new platform. Initially, they observe that each user is connected to exactly k = 49 nearby users in a neighborhood-based pattern, forming a structured network with n = 100 users. However, engagement data suggest that friend recommendations introduce a small-world topology, where some connections span across distant user groups, leading to a mix of local clustering and long-range connections. To better understand this connection pattern, the researchers hypothesize that the network might instead resemble a random graph of the form G(n,p), where p is the probability of a friendship forming between any two users. Estimate the probability p that would yield the same total number of connections as in the original structured network. Report 1000p

Which of the following concepts are fundamental to understanding and performing sequence alignment?

Which of the following is true about genome assembly?

Which of the following statements about GraphSAGE are true?

Task-specific labels are scarce during the training phase. The pretraining helps to develop a general understanding of related enumerate 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.

What are the limitations of shallow embeddings?

Which of the following are true for graph filters:

What is the primary challenge in applying classical deep neural networks to graph structured data?

What is the primary purpose of introducing a normalization step in a neural network