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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) Microbial communities from environmental DNA samples
C) Chemical synthesis of pharmaceutical compounds
D) The evolution of complex multicellular organisms
  • 2. What is a major challenge in studying the microbiome according to the text?
A) Inability to collect environmental samples
B) Lack of interest from the scientific community
C) High dimensionality of datasets
D) Lack of available supercomputers
  • 3. Which disease is NOT explicitly mentioned as a focus of machine learning in gut microbiota studies?
A) Alzheimer's disease
B) Colorectal cancer
C) Inflammatory bowel disease
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 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) Ph-CNN
B) MegaR
C) RF-FVS
D) Gradient boosted tree model
  • 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 functional variable selection
B) Robust feature with forward validation system
C) Random forest coupled with forwarding variable selection
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) Plant-pathogen interaction data
C) CDI and CRC 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) Environmental samples are not valuable
C) Data complexity
D) Lack of available software
  • 11. Which of the following is a type of neural network mentioned in the text?
A) Linear neural networks
B) Hopfield neural networks
C) Quantum 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) Genetic mutations in human gut bacteria
C) Relationship among soil, microbiome biodiversity, and ecosystem stability
D) The speed of DNA sequencing in labs
  • 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) 75.14%
B) 99.01%
C) 81%
D) 90.17%
  • 15. What are proteins primarily composed of?
A) Amino acids
B) Lipids
C) Nucleotides
D) Carbohydrates
  • 16. Which of these is a form of secondary protein structure?
A) Quaternary bonds
B) Beta sheets
C) Primary chains
D) Protein filaments
  • 17. What is the approximate accuracy of automatic feature learning in protein secondary structure prediction?
A) 82-84%
B) 50-60%
C) 20-30%
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) Helix, sheet, or coil
D) Alpha, beta, or gamma
  • 19. What is the theoretical accuracy limit for three-state protein secondary structure prediction?
A) 95–100%
B) 70–75%
C) 60–65%
D) 88–90%
  • 20. Which organization developed the AI program AlphaFold?
A) CASP
B) Pauling Institute
C) DeepMind
D) Corey Laboratories
  • 21. When was AlphaFold 2 released?
A) 1951
B) 2020
C) 2018
D) 2022
  • 22. Which proteomics problem besides secondary structure has machine learning been applied to?
A) Lipid membrane synthesis
B) RNA translation errors
C) DNA sequencing optimization
D) Protein loop modeling
  • 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) Hexagonal structure
B) Atomic structure
C) Tertiary structure
D) Pentagonal structure
  • 25. What does HMM stand for in the context of statistical models?
A) Hidden Machine model
B) Heuristic Markov method
C) Hidden Markov model
D) Hierarchical Markov model
  • 26. What drives the observation process in an HMM?
A) The underlying state process
B) Independent random variables
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) Yes
D) No
  • 28. What is a bioinformatics application of HMMs mentioned in the text?
A) Profiling multiple sequence alignments
B) Visual cortex modeling
C) Image classification
D) Metagenomic filtering
  • 29. What is the region of the visual field that a cortical neuron responds to called?
A) Receptive field
B) Feature map
C) Convolution zone
D) Translation window
  • 30. Compared to other image classification algorithms, what do CNNs require less of?
A) Validation
B) Computational power
C) Training data
D) Pre-processing
  • 31. How are filters optimized in a CNN?
A) Through automated learning
B) Hand-engineered by humans
C) Pre-determined by the analyst
D) Via manual feature extraction
  • 32. In a Ph-CNN, what is used to select k-neighborhoods?
A) GC content
B) Sequence identity
C) Random selection
D) Patristic distance
  • 33. How were bioinformatics algorithms traditionally created before machine learning?
A) Derived from hardware limitations
B) Generated by artificial intelligence
C) Programmed by hand
D) Calculated by physical modeling
  • 34. What type of output does a classification algorithm produce?
A) A raw string of data
B) A numerical value
C) An analog signal
D) A categorical class
  • 35. What is the output of a prediction algorithm in bioinformatics?
A) A discrete class label
B) A numerical valued feature
C) A symbolic proof
D) A hardware interrupt
  • 36. What technique is used to reduce the high dimensionality of k-mer vectors?
A) Linear regression
B) Principal component analysis
C) Binary serialization
D) Data encryption
  • 37. What is the approximate dimensionality of a vector of k-mers when k=12?
A) 12 thousand
B) 16 million
C) 16 thousand
D) 4 billion
  • 38. Which of these is NOT explicitly mentioned as a field within machine learning in biology?
A) Proteomics
B) Quantum computing
C) Text mining
D) Genomics
  • 39. How do deep learning systems build sophisticated predictions?
A) By following pre-defined manual rules
B) By combining low-level features into abstract features
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) To initialize the weights
B) To compress the memory
C) To increase the gradient
D) Scaling
  • 41. How many linear transformations does the feed-forward network consist of?
A) Two
B) Four
C) Three
D) One
  • 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) Support vector machines
B) Principal component analysis
C) Neural networking
D) Bootstrap aggregating
  • 44. What can random forest proximities be used for?
A) Increasing the number of decision trees
B) Calculating gradient descent
C) Imputing missing values
D) Removing outliers from the original dataset
  • 45. Which clustering approach begins with each element as a separate cluster?
A) Partitional
B) Agglomerative
C) Affinity propagation
D) Divisive
  • 46. What is a characteristic of partitional clustering algorithms?
A) They cannot be used on large datasets
B) They determine all clusters at once
C) They are always hierarchical
D) They start with one large cluster
  • 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) ESMFold2
B) GeneFormer
C) BIRCH
D) MAMMAL
  • 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) HyenaDNA
C) ESMFold2
D) GeneFormer
  • 51. Which of these is a source of error in biological data?
A) Algorithm efficiency
B) Standardized databases
C) Erroneous interpretation
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) Cancer genomic studies
B) Meteorological prediction
C) Stock market analysis
D) Plant hybridization
  • 54. In which field have deep learning applications been used?
A) Cellular imaging
B) Urban planning
C) Soil chemistry
D) Acoustic engineering
  • 55. What is a specific application of deep learning in genomics mentioned in the text?
A) Transportation logistics
B) Energy grid management
C) Variant calling
D) Hardware manufacturing
  • 56. What has helped to understand protein-protein interactions?
A) Manual database entry
B) Physical paper files
C) Natural language processing
D) Random guess algorithms
  • 57. What does precision medicine consider?
A) Geographical location
B) Individual genomic variability
C) Hospital budget limits
D) Administrative paperwork
  • 58. How often has the number of bases in GenBank doubled on average since 1982?
A) Every 5 years
B) Every 6 months
C) Every 10 years
D) Every 18 months
  • 59. What can machine learning be used to detect and visualize?
A) Genome rearrangements
B) Mechanical vibration
C) Atmospheric pressure
D) Global population trends
  • 60. What are microarrays commonly known as?
A) Lab-on-a-chip
B) Protein synthesizers
C) Cellular microscopes
D) Genetic sequencers
  • 61. Which of the following is a machine learning application for microarrays mentioned in the text?
A) DNA chemical synthesis
B) Genetic network induction
C) Microchip physical manufacturing
D) Biological tissue harvesting
  • 62. In the context of cancer diagnosis, what do microarrays monitor?
A) Gene expression
B) Cell division frequency
C) Viral replication cycles
D) Protein folding rates
  • 63. Besides classification, what is another application of machine learning in microarray analysis?
A) Microchip heat reduction
B) Data storage compression
C) Hardware circuit design
D) Expression pattern identification
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