┌─────────────────────────────────────────────────────────────────────────┐
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│ ------------------- AI Agent for Drug Discovery ------------------- │
│ │
│ │
│ 1 - Knowledge Model Agent │
│ 2 - Reasoning Agent │
│ 3 - Planning Agent │
│ 4 - Lab Agent │
│ 5 - Results Analysis Agent │
│ 6 - Exit │
│ │
│ │
└─────────────────────────────────────────────────────────────────────────┘
>> 1
------------------------------KNOWLEDGE MODEL DATA-----------------------------
Here the raw data parsed from the RDF file, [chemical, molecular_weight]:
[['Curcumine', '368'], ['Lidocaine', '234'], ['Maitotoxin', '3380'], ['Microcysin-LR', '995'], ['Morphine', '285'], ['Paclitaxel', '854'], ['Sildenafil', '475'], ['Tetrodotoxin', '319'], ['Tubocurarine', '610'], ['6-Hydroxytrypargine', '288']]
Here the adjusted data parsed from the RDF file, [chemical, molecular weight, size, possible drug candidate]:
[['Curcumine', '368', 'small molecule', 'possible drug candidate'], ['Lidocaine', '234', 'small molecule', 'possible drug candidate'], ['Maitotoxin', '3380', 'large molecule'], ['Microcysin-LR', '995', 'medium molecule'], ['Morphine', '285', 'small molecule', 'possible drug candidate'], ['Paclitaxel', '854', 'medium molecule'], ['Sildenafil', '475', 'small molecule', 'possible drug candidate'], ['Tetrodotoxin', '319', 'small molecule', 'possible drug candidate'], ['Tubocurarine', '610', 'medium molecule'], ['6-Hydroxytrypargine', '288', 'small molecule', 'possible drug candidate']]
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The graph has 74 entries
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┌─────────────────────────────────────────────────────────────────────────┐
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│ ------------------- AI Agent for Drug Discovery ------------------- │
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│ │
│ 1 - Knowledge Model Agent │
│ 2 - Reasoning Agent │
│ 3 - Planning Agent │
│ 4 - Lab Agent │
│ 5 - Results Analysis Agent │
│ 6 - Exit │
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└─────────────────────────────────────────────────────────────────────────┘
>> 2
----------------ABDUCTION REASONING------------------
Rules:
1 ) ['All drugs are', 'small molecule']
2 ) ['All drugs have', 'no more than 5 hydrogen bond donors']
Facts:
1 ) Lidocaine is a no more than 5 hydrogen bond donors
2 ) Curcumine is a no more than 5 hydrogen bond donors
3 ) Tetrodotoxin is a no more than 5 hydrogen bond donors
4 ) 6-Hydroxytrypargine is a no more than 5 hydrogen bond donors
5 ) Morphine is a more than 5 hydrogen bond donors
6 ) Maitotoxin is a more than 5 hydrogen bond donors
7 ) Microcysin-LR is a more than 5 hydrogen bond donors
8 ) Paclitaxel is a more than 5 hydrogen bond donors
9 ) Sildenafil is a more than 5 hydrogen bond donors
10 ) Tubocurarine is a more than 5 hydrogen bond donors
Potential Drugs Candidates:
1 ) Lidocaine
2 ) Tetrodotoxin
3 ) Curcumine
4 ) 6-Hydroxytrypargine
Successfully wrote hypothesis to file at:
/mnt/c/users/bhatti/desktop/ToyRs/Code/drug-ai-agent/scripts/../output/hypothesis.txt
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┌─────────────────────────────────────────────────────────────────────────┐
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│ ------------------- AI Agent for Drug Discovery ------------------- │
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│ │
│ 1 - Knowledge Model Agent │
│ 2 - Reasoning Agent │
│ 3 - Planning Agent │
│ 4 - Lab Agent │
│ 5 - Results Analysis Agent │
│ 6 - Exit │
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└─────────────────────────────────────────────────────────────────────────┘
>> 3
Hypothesis to test:
likely drug (Lidocaine)
likely drug (Tetrodotoxin)
likely drug (Curcumine)
likely drug (6-Hydroxytrypargine)
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Testable hypothesis:
measure_potency (Lidocaine, high)
measure_potency (Tetrodotoxin, high)
measure_potency (Curcumine, high)
measure_potency (6-Hydroxytrypargine, high)
Add positive control:
measure_potency (Morphine, high)
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Checking if there is a piece of equipment that can measure potency:
Equipment to measure potency available
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Checking if the chemicals are available in the list of materials:
Yes, proceed with generation of protocol
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Standard protocol:
add(ch, plate)
move(plate, incubator)
loop N times:
grow(plate, 20 min)
move(plate, reader)
measure_potency (ch, reader)
discharge(plate, trash)
Input standard protocol for measuring potency from the knowledge base
Instantiate the protocol for the given hypothesis and default number of iterations: N=5
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Experimental protocol generation...
Successfully wrote experimental protocol to file at:
/mnt/c/users/bhatti/desktop/ToyRs/Code/drug-ai-agent/scripts/../output/protocol.txt
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┌─────────────────────────────────────────────────────────────────────────┐
│ │
│ ------------------- AI Agent for Drug Discovery ------------------- │
│ │
│ │
│ 1 - Knowledge Model Agent │
│ 2 - Reasoning Agent │
│ 3 - Planning Agent │
│ 4 - Lab Agent │
│ 5 - Results Analysis Agent │
│ 6 - Exit │
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│ │
└─────────────────────────────────────────────────────────────────────────┘
>> 4
Generating experimental results table from the protocol...
This table contains the chemicals and their potency values:
| Lidocaine | 0.8 | 0.8 | 0.75 | 0.76 | 0.82 | 0.78 | 0.8 | 0.8 | 0.82 | 0.81 | 0.8 | 0.82 | 0.85 | 0.85 | 0.86 |
| Curcumine | 0.7 | 0.72 | 0.7 | 0.71 | 0.73 | 0.75 | 0.76 | 0.71 | 0.72 | 0.71 | 0.75 | 0.79 | 0.78 | 0.8 | 0.79 |
| Tetrodotoxin | 0.2 | 0.2 | 0.2 | 0.19 | 0.2 | 0.21 | 0.23 | 0.2 | 0.19 | 0.15 | 0.14 | 0.16 | 0.14 | 0.14 | 0.15 |
| 6-Hydroxytrypargine | 0.2 | 0.18 | 0.2 | 0.19 | 0.18 | 0.21 | 0.23 | 0.2 | 0.19 | 0.15 | 0.15 | 0.16 | 0.14 | 0.14 | 0.15 |
| Morphine | 0.73 | 0.72 | 0.75 | 0.71 | 0.73 | 0.76 | 0.76 | 0.71 | 0.72 | 0.76 | 0.75 | 0.79 | 0.78 | 0.8 | 0.81 |
Successfully wrote experimental results to file at:
/mnt/c/users/bhatti/desktop/ToyRs/Code/drug-ai-agent/scripts/../output/experimental_results.txt
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┌─────────────────────────────────────────────────────────────────────────┐
│ │
│ ------------------- AI Agent for Drug Discovery ------------------- │
│ │
│ │
│ 1 - Knowledge Model Agent │
│ 2 - Reasoning Agent │
│ 3 - Planning Agent │
│ 4 - Lab Agent │
│ 5 - Results Analysis Agent │
│ 6 - Exit │
│ │
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└─────────────────────────────────────────────────────────────────────────┘
>> 5
Generating analysis results table from the experimental results...
Processed results:
['Lidocaine', 0.8, 0.8, 0.75, 0.76, 0.82, 0.78, 0.8, 0.8, 0.82, 0.81, 0.8, 0.82, 0.85, 0.85, 0.86]
['Curcumine', 0.7, 0.72, 0.7, 0.71, 0.73, 0.75, 0.76, 0.71, 0.72, 0.71, 0.75, 0.79, 0.78, 0.8, 0.79]
['Tetrodotoxin', 0.2, 0.2, 0.2, 0.19, 0.2, 0.21, 0.23, 0.2, 0.19, 0.15, 0.14, 0.16, 0.14, 0.14, 0.15]
['6-Hydroxytrypargine', 0.2, 0.18, 0.2, 0.19, 0.18, 0.21, 0.23, 0.2, 0.19, 0.15, 0.15, 0.16, 0.14, 0.14, 0.15]
['Morphine', 0.73, 0.72, 0.75, 0.71, 0.73, 0.76, 0.76, 0.71, 0.72, 0.76, 0.75, 0.79, 0.78, 0.8, 0.81]
The list of selected chemicals (potency above ~0.5) are:
['Lidocaine', 'Curcumine']
Results Analysis (Statistical Based Analysis):
Morphine was added as a control chemical, so its potency measurements was filtered from experimental results
| Chemical | is a drug candidate? |
|---------------------+------------------------|
| Lidocaine | Confirmed |
| Curcumine | Confirmed |
| Tetrodotoxin | Rejected |
| 6-Hydroxytrypargine | Rejected |
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┌─────────────────────────────────────────────────────────────────────────┐
│ │
│ ------------------- AI Agent for Drug Discovery ------------------- │
│ │
│ │
│ 1 - Knowledge Model Agent │
│ 2 - Reasoning Agent │
│ 3 - Planning Agent │
│ 4 - Lab Agent │
│ 5 - Results Analysis Agent │
│ 6 - Exit │
│ │
│ │
└─────────────────────────────────────────────────────────────────────────┘
>> 6
