March 2022

Question 4
Nowadays AI systems are capable of making autonomous scientific discoveries. In this course, we considered
several AI systems capable of making automated scientific discoveries, for example, the mobile robotic chemist,
the automatic statistician, the robot scientists Adam and Eve. The research in automated scientific discovery is
flourishing, and the target is to develop systems capable of making significant scientific discoveries.

a. What are the advantages of automated discovery systems? [10]

b. What are the current limitations of automated discovery systems? [10]
c. Describe the functionality of one of the key components of the robot scientist system, e.g. a hypotheses
generator, a reasoning engine, an experiments planner, or data analysis component. What is required
for the functioning of the selected component? What are its input and output? How does it interact with
other components of the system? Outline the workings of the component. [10]

March 2023
Question 3
Robot Scientist case study
Nowadays AI systems are capable of making autonomous scientific discoveries. In this course, we
considered several AI systems capable of making automated scientific discoveries, for example, the
mobile robotic chemist, the automatic statistician, the Robot Scientists Adam and Eve. The research in
automated scientific discovery is flourishing, and the target is to develop systems capable of making
significant scientific discoveries.

a. What is a Robot Scientist? [2]

b. The Robot Scientists worked with several different applications. For each application, the developers
had to create a domain knowledge model. Why did the developers have to create a domain knowledge
model? [4]
a. Knowledge is essential for intelligent behaviour of artificial agents. Briefly explain how knowledge can be
represented and encoded so that a knowledge-based agent can access, process, and update its
knowledge base? Give examples of popular knowledge representation languages. [4]
a. The ability to reason is an advanced feature of an intelligent system. A reasoning engine can be
implemented using different logics. Give examples of such logics. [2]
a. Explain how did Robot Scientists produce and verified novel research hypotheses?
[6]
b. Briefly describe what are planning problems. What is a classical planning problem? How it can be
represented? Explain the difference between planning and scheduling problems. [4]
c. Briefly describe the input for the Robot Scientist planning agent. [4]
d. The Robot Scientist Eve worked on identifying potential drugs. How did Eve analyse the experimental
results? [2]
a. In multi-agent systems, what knowledge do agents might need to share and why?
[2]

CHAT GPT ANSWERS:

March 2022
Q1: Advantages of Automated Discovery Systems [10]
● Efficiency and Speed: Automated systems can analyze vast amounts of data rapidly,
significantly faster than humans.
 ● Consistency: They can maintain consistent analysis without being influenced by
biases or emotional factors.
● Scalability: They can easily scale to accommodate larger datasets and more complex
analysis.
● Cost-effective: They reduce long-term costs associated with human resources.
● Unbiased Analysis: They can objectively analyze data without preconceived notions
or cognitive biases.
● Repetitive Task Execution: Can efficiently execute repetitive tasks without
experiencing fatigue or decline in performance.
● Data Analysis: They can employ sophisticated data analysis methods to derive
insights and generate hypotheses.
Q2: Current Limitations of Automated Discovery Systems [10]
● Lack of Creativity: Automated systems lack the capability to think creatively or
outside predetermined parameters.
● Dependency on Quality Data: The accuracy and reliability of their analysis are highly
dependent on the quality of the input data.
● Lack of Domain Expertise: Without adequate domain knowledge models, automated
systems may miss nuances or make incorrect assumptions.
● Cost of Development and Maintenance: High initial cost and continuous maintenance
are required.
● Limited to Predefined Tasks: They are typically limited to the tasks they are
specifically designed for.
Q3: Functionality of a Hypothesis Generator [10]
● Functionality: A hypothesis generator, like in Robot Scientist Adam, is responsible for
creating plausible hypotheses based on background knowledge and observed data.
● Input: It requires a knowledge base with domain-specific knowledge (e.g., metabolic
pathways model of yeast in Adam).
● Output: It generates plausible hypotheses, which are then tested through planned
experiments.
● Interaction: It interacts with the reasoning engine to check the consistency of the
generated hypotheses with existing knowledge and with the experiment planner to
design experiments for testing hypotheses.
● Working: In Adam, it considered the possible combinations of genes and used
abduction to generate possible hypotheses about what genes may control
biosynthesis of chemicals.
March 2023
Q1: What is a Robot Scientist? [2]
A Robot Scientist is an artificial intelligence system designed to autonomously perform
scientific discoveries, encompassing the generation of hypotheses, planning and executing
experiments, analyzing data, and drawing conclusions.

Q2: Why Create a Domain Knowledge Model? [4]

Developers create domain knowledge models to equip Robot Scientists with domain-specific
knowledge and contextual understanding. This enables them to generate plausible
hypotheses, design appropriate experiments, and interpret results accurately within the
specific scientific domain they operate, like biochemistry in the case of Adam and Eve.

Q3: Representation and Encoding of Knowledge [4]

Knowledge can be represented and encoded using languages like First-Order Logic (FoL)
and Prolog, which allow defining properties, relations, and quantifiers. For instance, in
Prolog, a relation could be expressed as raises(pete, query_001). These representations
enable the knowledge-based agent to access, process, and update its knowledge base by
querying and inferring new knowledge.

Q4: Examples of Logics [2]

Examples of logics used in reasoning engines are First-Order Logic (FoL) and Descriptive
Logic (DL). FoL describes properties and relations among objects, while DL is used to define
and describe objects.

Q5: Production and Verification of Hypotheses by Robot Scientists [6]

Robot Scientists like Adam produce hypotheses using abduction, considering the
background knowledge base and existing bioinformatics databases. They generate possible
options and insert candidates into their logical models, running a reasoner to check the
plausibility of chemical synthesis. These hypotheses are then verified through designed
experiments, analyzed using data analysis components like decision trees in the case of
yeast studies.

Q6: Planning Problems & Classical Planning Problem [4]

Planning problems involve finding a sequence of actions that leads to a goal state given an
initial state and a set of actions. A classical planning problem deals with observable,
deterministic situations, represented using actions with pre-conditions and effects. Planning
differs from scheduling in that scheduling adds constraints related to time and resources to
sequential plans.

Q7: Input for Robot Scientist Planning Agent [4]

The input for a planning agent in a Robot Scientist involves a set of formulated hypotheses,
available equipment and materials, knowledge base for designing experiments, and
potentially an ontology defining experimental protocols and constraints.

Q8: Analysis of Experimental Results by Eve [2]

Eve analyzed experimental results using machine learning, specifically employing decision
trees to determine the significance of the results in identifying potential drug leads for
Malaria.The Robot Scientist Eve, focused on identifying potential drugs, specifically analyzed
experimental results using automated reasoning and machine learning techniques. It
interpreted the data to infer relationships between different biochemical compounds and their
potential therapeutic effects, thereby identifying compounds with high probabilities of being
effective drugs based on the biological assays’ outcomes. The analysis involved a
quantitative assessment of the interactions between the compounds and target proteins to
determine the likelihood of drug efficacy and to guide subsequent experiments and
investigations

Q9: Knowledge Sharing in Multi-agent Systems [2]

In multi-agent systems, agents might need to share knowledge about the goal, world
representation, and each other to coordinate and cooperate effectively. This includes sharing
domain-specific knowledge, experiment results, and communication protocols, as seen with
the SciCom protocol developed for Eve.