Machine learning in biology - Quiz
Machine learning in biology
  • 1. What is metagenomics the study of?
A) Microbial communities from environmental DNA samples
B) Human genetic disorders and hereditary diseases
C) The evolution of complex multicellular organisms
D) Chemical synthesis of pharmaceutical compounds
  • 2. What is a major challenge in studying the microbiome according to the text?
A) High dimensionality of datasets
B) Inability to collect environmental samples
C) Lack of available supercomputers
D) Lack of interest from the scientific community
  • 3. Which disease is NOT explicitly mentioned as a focus of machine learning in gut microbiota studies?
A) Diabetes
B) Colorectal cancer
C) Alzheimer's disease
D) Inflammatory bowel disease
  • 4. What was the purpose of the Ph-CNN algorithm developed by Fioravanti et al. in 2018?
A) To sequence the entire human genome
B) To identify soil bacteria biodiversity
C) To classify healthy patients and patients with IBD symptoms
D) To predict the climate change impact on ecosystems
  • 5. What method uses phylogenetic trees and convolutional neural networks?
A) Gradient boosted tree model
B) MegaR
C) Ph-CNN
D) RF-FVS
  • 6. What influences the performance of Random Forest (RF) algorithms?
A) The number of researchers involved
B) The geographic location of the samples
C) The speed of the internet connection
D) Performance and diversity of decision trees in the ensemble
  • 7. What does the RF-FVS pipeline developed by Dang & Kishino stand for?
A) Recurrent forest with functional variable sequencing
B) Random forest coupled with forwarding variable selection
C) Random functional variable selection
D) Robust feature with forward validation system
  • 8. What datasets did Dang & Kishino use to demonstrate their 2020 pipeline performance?
A) Plant-pathogen interaction data
B) CDI and CRC datasets
C) IBD and Diabetes datasets
D) Soil and water microbiome data
  • 9. What is MegaR, developed by Dhungel et al. in 2021?
A) A new sequencing technology
B) A supercomputer specifically for metagenomics
C) A neural network architecture
D) An R package for taxonomic profiles and classification models
  • 10. What is a primary reason machine learning is less explored in environmental samples compared to clinical ones?
A) There are no microbial communities in the environment
B) Lack of available software
C) Data complexity
D) Environmental samples are not valuable
  • 11. Which of the following is a type of neural network mentioned in the text?
A) Quantum neural networks
B) Hopfield neural networks
C) Linear neural networks
D) Gaussian neural networks
  • 12. In the work by Xun et al. (2021), what did machine learning help analyze?
A) Treatment efficacy for colorectal cancer
B) The speed of DNA sequencing in labs
C) Relationship among soil, microbiome biodiversity, and ecosystem stability
D) Genetic mutations in human gut bacteria
  • 13. What happens to the computational burden as the number of features in a microbiome dataset increases?
A) It decreases linearly
B) It disappears completely
C) It increases exponentially
D) It remains constant
  • 14. What did the RF-FVS approach improve the accuracy to for CDI?
A) 99.01%
B) 90.17%
C) 75.14%
D) 81%
  • 15. What are proteins primarily composed of?
A) Carbohydrates
B) Lipids
C) Amino acids
D) Nucleotides
  • 16. Which of these is a form of secondary protein structure?
A) Protein filaments
B) Beta sheets
C) Primary chains
D) Quaternary bonds
  • 17. What is the approximate accuracy of automatic feature learning in protein secondary structure prediction?
A) 20-30%
B) 82-84%
C) 50-60%
D) 95-99%
  • 18. What are the three structural classes used for amino acid classification?
A) Primary, secondary, or tertiary
B) Folded, unfolded, or neutral
C) Alpha, beta, or gamma
D) Helix, sheet, or coil
  • 19. What is the theoretical accuracy limit for three-state protein secondary structure prediction?
A) 88–90%
B) 70–75%
C) 95–100%
D) 60–65%
  • 20. Which organization developed the AI program AlphaFold?
A) DeepMind
B) Pauling Institute
C) CASP
D) Corey Laboratories
  • 21. When was AlphaFold 2 released?
A) 2022
B) 2020
C) 1951
D) 2018
  • 22. Which proteomics problem besides secondary structure has machine learning been applied to?
A) Lipid membrane synthesis
B) RNA translation errors
C) Protein loop modeling
D) DNA sequencing optimization
  • 23. Which of the following is a proteomics application mentioned in the text?
A) Cell division modeling
B) Protein contact map prediction
C) Genome assembly
D) Metabolic pathway simulation
  • 24. Which of these is considered a level of protein structure?
A) Tertiary structure
B) Pentagonal structure
C) Atomic structure
D) Hexagonal structure
  • 25. What does HMM stand for in the context of statistical models?
A) Hierarchical Markov model
B) Hidden Machine model
C) Heuristic Markov method
D) Hidden Markov model
  • 26. What drives the observation process in an HMM?
A) Independent random variables
B) The user input
C) External noise
D) The underlying state process
  • 27. Can HMMs be formulated in continuous time?
A) Only for non-biological data
B) No
C) Only for discrete states
D) Yes
  • 28. What is a bioinformatics application of HMMs mentioned in the text?
A) Visual cortex modeling
B) Image classification
C) Metagenomic filtering
D) Profiling multiple sequence alignments
  • 29. What is the region of the visual field that a cortical neuron responds to called?
A) Convolution zone
B) Receptive field
C) Translation window
D) Feature map
  • 30. Compared to other image classification algorithms, what do CNNs require less of?
A) Pre-processing
B) Computational power
C) Training data
D) Validation
  • 31. How are filters optimized in a CNN?
A) Pre-determined by the analyst
B) Hand-engineered by humans
C) Via manual feature extraction
D) Through automated learning
  • 32. In a Ph-CNN, what is used to select k-neighborhoods?
A) Patristic distance
B) Random selection
C) GC content
D) Sequence identity
  • 33. How were bioinformatics algorithms traditionally created before machine learning?
A) Calculated by physical modeling
B) Generated by artificial intelligence
C) Derived from hardware limitations
D) Programmed by hand
  • 34. What type of output does a classification algorithm produce?
A) A categorical class
B) A raw string of data
C) A numerical value
D) An analog signal
  • 35. What is the output of a prediction algorithm in bioinformatics?
A) A numerical valued feature
B) A discrete class label
C) A symbolic proof
D) A hardware interrupt
  • 36. What technique is used to reduce the high dimensionality of k-mer vectors?
A) Binary serialization
B) Principal component analysis
C) Data encryption
D) Linear regression
  • 37. What is the approximate dimensionality of a vector of k-mers when k=12?
A) 4 billion
B) 16 million
C) 12 thousand
D) 16 thousand
  • 38. Which of these is NOT explicitly mentioned as a field within machine learning in biology?
A) Quantum computing
B) Text mining
C) Proteomics
D) Genomics
  • 39. How do deep learning systems build sophisticated predictions?
A) By combining low-level features into abstract features
B) By following pre-defined manual rules
C) By simulating the organism's physical structure
D) By ignoring complex dataset patterns
  • 40. In the attention formula, what is the purpose of dividing the dot product by the square root of the key dimension?
A) Scaling
B) To compress the memory
C) To initialize the weights
D) To increase the gradient
  • 41. How many linear transformations does the feed-forward network consist of?
A) Four
B) Two
C) One
D) Three
  • 42. Which variable represents the input to the multi-head self-attention or FFN in the provided formulas?
A) X
B) Y
C) b2
D) W1
  • 43. What technique is random forest a modification of?
A) Support vector machines
B) Neural networking
C) Principal component analysis
D) Bootstrap aggregating
  • 44. What can random forest proximities be used for?
A) Increasing the number of decision trees
B) Calculating gradient descent
C) Removing outliers from the original dataset
D) Imputing missing values
  • 45. Which clustering approach begins with each element as a separate cluster?
A) Divisive
B) Affinity propagation
C) Partitional
D) Agglomerative
  • 46. What is a characteristic of partitional clustering algorithms?
A) They start with one large cluster
B) They are always hierarchical
C) They determine all clusters at once
D) They cannot be used on large datasets
  • 47. Which algorithm does not require the user to specify an initial number of groups?
A) K-medoids
B) Affinity propagation
C) K-means
D) BIRCH
  • 48. Which of these is an example of a foundation model for transcriptomics?
A) MAMMAL
B) ESMFold2
C) GeneFormer
D) BIRCH
  • 49. Divisive hierarchical algorithms start with which state?
A) Each element as a separate cluster
B) A random subset
C) The whole set
D) An empty dataset
  • 50. Which of these is a foundation model used for proteomics?
A) HyenaDNA
B) Evo2
C) GeneFormer
D) ESMFold2
  • 51. Which of these is a source of error in biological data?
A) Standardized databases
B) Erroneous interpretation
C) Algorithm efficiency
D) High-speed processing
  • 52. Which method is mentioned as a source of 3D structure data in the PDB?
A) Optical microscopy
B) X-ray diffraction
C) Manual observation
D) Paper-based recording
  • 53. What have support vector machines been extensively used for?
A) Cancer genomic studies
B) Plant hybridization
C) Stock market analysis
D) Meteorological prediction
  • 54. In which field have deep learning applications been used?
A) Acoustic engineering
B) Soil chemistry
C) Urban planning
D) Cellular imaging
  • 55. What is a specific application of deep learning in genomics mentioned in the text?
A) Hardware manufacturing
B) Energy grid management
C) Variant calling
D) Transportation logistics
  • 56. What has helped to understand protein-protein interactions?
A) Manual database entry
B) Natural language processing
C) Random guess algorithms
D) Physical paper files
  • 57. What does precision medicine consider?
A) Individual genomic variability
B) Hospital budget limits
C) Geographical location
D) Administrative paperwork
  • 58. How often has the number of bases in GenBank doubled on average since 1982?
A) Every 6 months
B) Every 10 years
C) Every 18 months
D) Every 5 years
  • 59. What can machine learning be used to detect and visualize?
A) Atmospheric pressure
B) Genome rearrangements
C) Global population trends
D) Mechanical vibration
  • 60. What are microarrays commonly known as?
A) Genetic sequencers
B) Cellular microscopes
C) Lab-on-a-chip
D) Protein synthesizers
  • 61. Which of the following is a machine learning application for microarrays mentioned in the text?
A) Genetic network induction
B) DNA chemical synthesis
C) Biological tissue harvesting
D) Microchip physical manufacturing
  • 62. In the context of cancer diagnosis, what do microarrays monitor?
A) Protein folding rates
B) Cell division frequency
C) Viral replication cycles
D) Gene expression
  • 63. Besides classification, what is another application of machine learning in microarray analysis?
A) Microchip heat reduction
B) Expression pattern identification
C) Data storage compression
D) Hardware circuit design
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