Table 1 Potentially therapeutics prioritized by LLM with cross-validation

From: Bridging the computational-experimental gap: leveraging large language model to prioritize Alzheimer’s therapeutics based on comparison of learning models

Drug Name

Graph Model

LLM-based Analysis

Hazard Ratio(p)

Clinical Trial Count (ID)

\({|T}_{i}|\)

\({R}_{u}(i)\)

\({R}_{p}(i)\)

\({R}_{n}(i)\)

Criterion 1

Criterion 2

Istradefylline

TxGNN

4

0.50

0.25

0.25

Potentially therapeutic

Potentially therapeutic

0.02 (0.95)

0

Chlorpromazine*

TxGNN

23

0.91

0.04

0.04

Potentially therapeutic

Potentially therapeutic

0.001 (0.93)

2(NCT02309723,NCT00975481)

Pimavanserin*

TxGNN

8

0.88

0.12

0

Potentially therapeutic

Potentially therapeutic

12.60 (0.01)

4(NCT02992132,NCT03325556,NCT03118947,NCT02035553)

Droxidopa

TxGNN

6

0.50

0.50

0

Potentially therapeutic

Potentially therapeutic

0.00 (0.90)

0

Apomorphine*

TxGNN

9

0.89

0.11

0

Potentially therapeutic

Potentially therapeutic

67.27 (<0.001)

2(NCT03837067,NCT04653584)

Neostigmine

CompGCN

5

0.80

0.20

0

Potentially therapeutic

Potentially therapeutic

<0.001 (0.92)

0

Carbamazepine

CompGCN

39

0.82

0.15

0.03

Potentially therapeutic

Potentially therapeutic

0.94 (0.82)

0

Memantine*

CompGCN

200

0.77

0.19

0.04

Potentially therapeutic

Potentially therapeutic

0.59 (<0.001)

97(NCT00545974,NCT01626391,NCT01409694,NCT00353665,NCT05669365)

Haloperidol

CompGCN

30

0.80

0.03

0.17

Potentially adverse effect

Potentially therapeutic

<0.001 (0.89)

4(NCT02309723,NCT00009217,NCT00000179,NCT00249145)

Riluzole*

CompGCN

7

0.71

0.29

0

Potentially therapeutic

Potentially therapeutic

1.92 (0.19)

3(NCT00353665,NCT03605667,NCT01703117)

Minocycline*

CompGCN

24

0.58

0.33

0.08

Potentially therapeutic

Potentially therapeutic

1.24 (0.57)

1(NCT01463384)

Magnesium*

CompGCN

200

0.97

0.03

0

Potentially therapeutic

Potentially therapeutic

NA

18(NCT04656860,NCT05728229,NCT00490568,NCT04606420,NCT04251182)

Carmustine

RLR

2

0.50

0.50

0

Potentially therapeutic

Potentially therapeutic

NA

0

Testosterone*

RLR

103

0.94

0.05

0.01

Potentially therapeutic

Potentially therapeutic

0.84 (0.27)

5(NCT00392912,NCT02727699,NCT02018497,NCT00539305,NCT00000177)

Naproxen*

RLR

37

0.76

0.05

0.19

Potentially adverse effect

Potentially therapeutic

0.94 (0.38)

4(NCT00007189,NCT01417130,NCT02702817,NCT00004845)

Doxycycline*

RLR

90

0.91

0.07

0.02

Potentially therapeutic

Potentially therapeutic

0.95 (0.81)

4(NCT00439166,NCT04846335,NCT00715858,NCT00692588)

Histamine*

RLR

61

0.98

0.02

0

Potentially therapeutic

Potentially therapeutic

NA

8(NCT01268020,NCT01505504,NCT00987220,NCT06169826,NCT01009255)

  1. The drugs are listed in the order ranked within each graph model. Bold drugs were significant in the cohort (\(p < 0.30\)) and prioritized by any Criteria of LLM; “*” indicates drugs were tested in clinical trials and also prioritized by any criterion of LLM. We surveyed publicly registered trials on ClinicalTrials.gov (e.g., NCT02309723) related to the drugs predicted by our model to provide contextual evidence from prior literature. These trials were not part of our dataset or analyses, and no participants from these trials were enrolled or contacted.