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