A talk about how researchers can benefit from natural language processing tools such as ChatGPT or Bard and other AI approaches to improve their productivity, scientific writing and research. This presentation was given by Sonja Aits at a training and team building retreat for ~150 life science researchers from Lund University on Aug 22, 2023.

1. AI in research:
ChatGPT and more
Sonja Aits
Cell Death, Lysosomes and Artificial Intelligence Group,
Lund University
AI Lund – Coordinator for AI in Medicine and
Life Science
COMPUTE research school – Study director
sonja.aits@med.lu.se
@Aitslab

2. Life science today

3. AI image analysis: classification/scoring
Damaged tissue
Normal tissue
Images from collaborator Darcy Wagner
Damage score:
34
Damage score:
2

4. AI image analysis: object detection

5. Natural language processing

7. Text loading &
Preprocessing
Named entity
recognition
Named entity
linking
Relation
extraction
SiRNAs targeting four kinesins (KIF11/Eg5,
KIF20A, KIF21A, KIF25), myosin 1G (MYO1G),
myosin heavy chain 1 (MYH1) and
tropomyosin 2 (TPM2) were identified as
effective inducers of non-apoptotic cell
death. All seven killed human cervix cancer
(HeLa) and osteosarcoma (U-2-OS) cells and
sensitized cancer cells to other lysosome-
destabilizing treatments, i.e. siramesine,
etoposide or cisplatin.
SiRNAs targeting four kinesins
(KIF11/Eg5, KIF20A, KIF21A,
KIF25), myosin 1G (MYO1G),
myosin heavy chain 1 (MYH1)
and tropomyosin 2 (TPM2)
were identified as effective
inducers of non-apoptotic cell
death. All seven killed human
cervix cancer (HeLa) and
osteosarcoma (U-2-OS) cells
and sensitized cancer cells to
other lysosome-destabilizing
treatments, i.e. siramesine,
etoposide or cisplatin.
SiRNAs targeting four kinesins
(KIF11/Eg5, KIF20A, KIF21A,
KIF25), myosin 1G (MYO1G),
myosin heavy chain 1 (MYH1)
and tropomyosin 2 (TPM2)
were identified as effective
inducers of non-apoptotic cell
death. All seven killed human
cervix cancer (HeLa) and
osteosarcoma (U-2-OS) cells
and sensitized cancer cells to
other lysosome-destabilizing
treatments, i.e. siramesine,
etoposide or cisplatin.
SiRNAs targeting four kinesins
(KIF11/Eg5, KIF20A, KIF21A,
KIF25), myosin 1G (MYO1G),
myosin heavy chain 1 (MYH1)
and tropomyosin 2 (TPM2)
were identified as effective
inducers of non-apoptotic cell
death. All seven killed human
cervix cancer (HeLa) and
osteosarcoma (U-2-OS) cells
and sensitized cancer cells to
other lysosome-destabilizing
treatments, i.e. siramesine,
etoposide or cisplatin.
SiRNAs targeting four kinesins
(KIF11/Eg5, KIF20A, KIF21A,
KIF25), myosin 1G (MYO1G),
myosin heavy chain 1 (MYH1)
and tropomyosin 2 (TPM2)
were identified as effective
inducers of non-apoptotic cell
death. All seven killed human
cervix cancer (HeLa) and
osteosarcoma (U-2-OS) cells
and sensitized cancer cells to
other lysosome-destabilizing
treatments, i.e. siramesine,
etoposide or cisplatin.
SiRNAs targeting four kinesins
(KIF11/Eg5, KIF20A, KIF21A,
KIF25), myosin 1G (MYO1G),
myosin heavy chain 1 (MYH1)
and tropomyosin 2 (TPM2)
were identified as effective
inducers of non-apoptotic cell
death. All seven killed human
cervix cancer (HeLa) and
osteosarcoma (U-2-OS) cells
and sensitized cancer cells to
other lysosome-destabilizing
treatments, i.e. siramesine,
etoposide or cisplatin.
SiRNAs targeting four kinesins
(KIF11/Eg5, KIF20A, KIF21A,
KIF25), myosin 1G (MYO1G),
myosin heavy chain 1 (MYH1)
and tropomyosin 2 (TPM2)
were identified as effective
inducers of non-apoptotic cell
death. All seven killed human
cervix cancer (HeLa) and
osteosarcoma (U-2-OS) cells
and sensitized cancer cells to
other lysosome-destabilizing
treatments, i.e. siramesine,
etoposide or cisplatin.
Chemicals
Proteins/Genes
Diseases
Species
Tissues
Cell processes
Symptoms
PubChem
Drugbank
UniProt
NCBI Gene
ICD-10
MeSH
NCBI Taxonomy
Activation
Inhibition
Binding
Part-of
Phosphorylation
Upregulation
Cleavage
AI for medical information extraction
“Text mining”
Ahmed R et al. Arxiv 2023
SciLifeLab/KAW National COVID-19 Research Program
Pubmed
PMC
CORD-19
Pdf
Text
Swedish/English
EasyNER

8. AI chatbots
ChatGPT
Bard
HuggingChat
Bing Chat

9. ChatGPT for beginners
https://chat.openai.com/

10. Writing assistant: Title suggestions
ChatGPT

11. Writing assistant: Outline generation
ChatGPT Bard
Prompt: “write an outline for a scientific review on cell death”

12. ChatGPT
Writing assistant:
Summarization + style change + translation

13. Writing assistant:
Production of complete text
Hi everyone, and welcome to this video about gene expression. Gene
expression is the process by which DNA is converted into proteins.
Proteins are the building blocks of cells and tissues, and they play a role
in almost every function of the body.
The first step in gene expression is transcription…
Bard
Prompt:
“write a script for a 2 min video that explains the process of gene expression in a
clear and concise way to biomedical university students ”

14. Scientific
discussion
partner
“how can lysosomal cell death be measured in cultured cancer cells?”
”which of these assays is best?”
ChatGPT

15. Personal teacher
“explain what a Western Blot is”

16. Programming assistant
“generate a script that does the following: 1. loads the values from a pandas dataframe called
df which has two columns called "control" and "treated". 2. plots the two columns as two data
series in a violin plot with the control column values in red and the treated column values in
blue”
ChatGPT

17. AI chatbots can support you in many ways
• Writing assistant
• Title suggestions
• Content suggestions
• Outline generation
• Rephrasing/Correction/Shortening
• Summarization/Style change/Translation
• Production of complete text
• Discussion partner
• Personal teacher
• Programming assistant

18. AI tools for image generation
DALL-E2
“a cartoon image of a
white robot looking
into a microscope”

19. A few words of caution…
• Incorrect/biased results
• Prompts are stored – do not provide sensitive information!
• Check journal policies for AI
• Ethical/legal/societal issues

20. AI Lund
www.ai.lu.se
COMPUTE research school
www.compute.lu.se

21. Cell death, Lysosomes and Artificial
Intelligence Group
Natural language processing
Image analysis
Knowledge integration
AI training
http://research.med.lu.se/sonja-aits
https://github.com/Aitslab/
https://www.youtube.com/Aitslab
sonja.aits@med.lu.se