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