Xuzeng He

### Recent Advances in Using Machine Learning with Graphs --- Part 2 {#recent-advances-in-using-machine-learning-with-graphs-part-2}

#### Latest findings in multiple research directions for handling graph construction and network security issues

<figure>
<img src="https://cdn-images-1.medium.com/max/894/0*VZbI8DObQnry3gYZ" />
<figcaption>Source: Generated using DeviantArt’s DreamUp.</figcaption>
</figure>

### Author

· Xuzeng He (**ORCID:**
[0009--0005--7317--7426](https://orcid.org/0009-0005-7317-7426))

### Introduction

A graph, in short, is a description of items linked by relations, where
the items of a graph are called nodes (or vertices) and their relations
are called edges (or links). Examples of graphs can include social
networks (e.g. Instagram) or knowledge graphs (e.g. Wikipedia).
Nowadays, There is a rising trend in the research of using Machine
Learning techniques on graphs to solve various kinds of problems.

Part 1 of this article can be
found [here](https://medium.com/@researchgraph/recent-advances-in-using-machine-learning-with-graphs-5a4745e3a3d6).

In this post, we introduce two latest findings where the technique of
Machine Learning is applied to Graphs.

### AutoRD

Rare diseases (e.g. Hutchinson-Gilford Progeria Syndrome), also known as
orphan diseases, are relatively uncommon in isolation and individually
sometimes receive less attention in medical research due to their low
prevalence. In the meantime, as Large Language Models (LLMs) have
demonstrated exceptional proficiency in language understanding and
generation, current research is beginning to evaluate the capabilities
of the most powerful LLMs, such as ChatGPT and GPT-4, across various
medical applications.

In the context of rare diseases, where resources are often limited, LLMs
are able to emerge as valuable tools for extracting information about
these conditions, showcasing their utility in enhancing medical
knowledge systems. For instance, a useful tool called **Automated Rare
Disease Mining** was introduced recently for extracting information
about rare diseases and constructing corresponding knowledge graphs.
This system can process unstructured medical text as input and output
extraction results and a knowledge graph.

<figure>
<img
src="https://cdn-images-1.medium.com/max/1024/0*AneLqn1wU6fMBDMp" />
<figcaption>The AutoRD framework processes medical texts as input data
and outputs entities related to rare diseases and rare disease triples,
which are the results of the extraction process. Subsequently, it
constructs a knowledge graph based on these extraction results. During
the entity and relation extraction steps, ontologies-enhanced large
language models (LLMs) are utilised to enhance performance. (Lang Cao et
al., 2024) Article Link: <a
href="https://arxiv.org/abs/2403.00953">https://arxiv.org/abs/2403.00953</a></figcaption>
</figure>

The framework of AutoRD includes data preprocessing, entity extraction,
relation extraction, entity calibration, and knowledge graph
construction.

#### **Data Preprocessing**

- **Segmenting long documents**: Split lengthy documents into smaller
 segments to fit with the LLM being used
- **Processing medical knowledge data**: extract disease names,
 definitions, symptoms, and signs along with their definitions from
 given medical ontology files
- **Preprocessing RareDis dataset**: Correct errors in the original
 dataset annotation and split into training, test, and validation sets
 for evaluation.

#### Entity Extraction

- **Extract medical terms**: Use a string-match algorithm with negation
 detection on a medical ontology (Mondo) to find basic medical terms
 and use LLMs with a prompt to find additional medical terms, including
 those not directly in the ontology.
- **Categorise entities**: Uses LLMs with a prompt to categorise all
 extracted medical terms into entities.

#### Relation Extraction

- Use LLMs with a prompt to extract relations between identified
 entities

#### Entity Calibration

- Use LLMs with a prompt to re-analyse relationships between all
 extracted entities.
- Filter out entities identified as unrelated based on the combined
 information from entity extraction and relation extraction.

#### Knowledge Graph Construction

- Use Neo4j graph database to store and manage the relationships between
 entities as triples (entity-relation-entity) by adding them one by one
 using Neo4j API.

Experimental results show that AutoRD is able to achieve
state-of-the-art performance in terms of efficiency when constructing
rare disease knowledge graphs, opening up exciting possibilities for
future research.

For example, a possible scenario of how AutoRD works for a text about
Hutchinson-Gilford progeria syndrome could be:

**Input medical text:**

Hutchinson-Gilford progeria syndrome(HGPS) is a rare and fatal genetic
disease that causes children to age rapidly. Symptoms typically begin in
the first few months of life and include failure to thrive, wrinkled
skin, and hair loss. There is currently no cure for HGPS, but research
is ongoing.

**AutoRD Output:**

1. **Entity Extraction:** AutoRD starts by extracting entities from the
 medical text. It uses a combination of string matching and LLM
 prompts. In this example, it found several entities related to rare
 diseases, including "Hutchinson-Gilford progeria syndrome",
 "disease", "wrinkled skin", "failure to thrive", and "hair loss".
2. **Relation Extraction:** Next, AutoRD uses LLMs to extract relations
 between the identified entities. It found that "Hutchinson-Gilford
 progeria syndrome" is a type of "disease" and that "disease" can
 have "hair loss" as a symptom.
3. **Knowledge Graph Construction:** Finally, AutoRD constructs a
 knowledge graph to represent the relationships between the entities.
 In this example, the knowledge graph would show that
 "Hutchinson-Gilford progeria syndrome" is a subclass of "disease"
 and that "disease" is associated with "hair loss".

### NEGSC

With the exponential growth in user hosts and network services, the
frequency and the complexity of cyberattacks are increasing.
Fortunately, Network Intrusion Detection Systems (**NIDSs**) have proven
their reliability in detecting and mitigating cyber-attacks, whose main
tasks are to capture malicious network traffic flow and apply the
identification outputs to achieve precise and prompt responses. In
recent studies, Graph Neural Networks (**GNNs**), which are a powerful
deep learning method for graph-structured data, have been introduced
into NIDS due to their suitability for representing the network
traffic flows.

<figure>
<img
src="https://cdn-images-1.medium.com/max/1024/0*QaFKYXmJY8yK48n1" />
<figcaption>Converting Netflow-based data into graph representation. An
arrow along with nodes indicates a network traffic flow from the source
host to the destination host. Normal and attack flows are denoted by
black and red arrows, respectively, where different shades of red arrows
indicate different types of attacks. (Renjie Xu et al., 2024) Article
Link: <a
href="https://arxiv.org/abs/2403.01501">https://arxiv.org/abs/2403.01501</a></figcaption>
</figure>

Although Graph Neural Networks (GNNs) are used to analyse network
traffic data (represented as a graph) to detect malicious activity, they
might not fully utilise the rich information present in network flow
data (data about traffic flow between network nodes). To further improve
the performance of GNN, a self-supervised graph representation learning
method for identifying malicious attacks and their specific types,
NetFlow-Edge Generative Subgraph Contrast (**NEGSC**), is proposed.

NEGSC does not require pre-labeled data (which can be scarce for
malicious attacks). It learns by itself by contrasting "good" and
"anomalous" subgraphs within the network traffic graph. It goes beyond
the basic graph structure and considers the specific features present in
network flows (e.g., packet size, source and destination IP addresses).
This allows for a more nuanced understanding of the traffic patterns.
NEGSC focuses on analysing the immediate neighbors (directly connected
nodes) of a central node. This helps identify suspicious patterns in
local traffic flows that might indicate an attack. It employs a learning
framework called Generative Subgraph Contrast(**GSC**) and generates
*contrastive subgraphs* for a given central node. These subgraphs
represent possible "good" and "anomalous" traffic patterns around that
node. It then uses a loss function to compare the generated contrastive
subgraphs. If the real traffic data around a node deviates significantly
from the "good" subgraph, it might indicate a potential attack.

Experimental results show that this approach significantly outperforms
the existing self-supervised learning method in terms of [Accuracy,
Precision, Recall and
F1](https://towardsdatascience.com/accuracy-precision-recall-or-f1-331fb37c5cb9)
when given a binary classification scenario.

### Conclusion

The usage of Machine Learning has witnessed significant advancements,
particularly when combined with various kinds of graphs. This can open
multiple exciting possibilities for different research directions. In
this post, we discussed two latest findings for the use of Machine
Learning when combined with graphs. Moreover, we have also shared some
promising scopes that could be used for future exploration of these
approaches. Through continuous investigation and refinement, we believe
that the use of graphs can open up exciting opportunities for us along
with different machine learning techniques.

### References

- Cao, L., Sun, J. and Cross, A. (2024). AutoRD: An Automatic and
 End-to-End System for Rare Disease Knowledge Graph Construction Based
 on Ontologies-enhanced Large Language Models. *arXiv (Cornell
 University)*. doi:https://doi.org/10.48550/arxiv.2403.00953.
- Xu, R., Wu, G., Wang, W., Gao, X., He, A. and Zhang, Z. (2024).
 Applying Self-supervised Learning to Network Intrusion Detection for
 Network Flows with Graph Neural Network. *arXiv (Cornell University)*.
 doi:https://doi.org/10.48550/arxiv.2403.01501.

![](https://medium.com/_/stat?event=post.clientViewed&referrerSource=full_rss&postId=88e27d32ed9f){width="1"
height="1"}

Recent Advances in Using Machine Learning with Graphs — Part 2 Latest findings in multiple research directions for handling graph construction and network security issues Author · Xuzeng He (

 ORCID:

0009–0005–7317–7426) Introduction A graph, in short, is a description of items linked by relations, where the items of a graph are called nodes (or vertices) and their relations are called edges (or links). Examples of

Recent Advances in Using Machine Learning with Graphs — Part 2

Stephen Royle

The database <a href="https://clinicaltrials.gov">clinicaltrials.gov</a> is a web resource of clinical trials around the world. It has a REST API that gives access to clinical trial data. There are some resources available to interact with this resource using R, such as <a href="https://github.com/sachsmc/rclinicaltrials">rclinicaltrials</a> and <a href="https://github.com/seandavi/ClinicalTrialsAPI">ClinicalTrialsAPI</a>.



We were interested at looking clinical trials for rare diseases and particularly whether this year, COVID-19 had affected these trials.



<figure class="wp-block-image size-large"><img loading="lazy" decoding="async" width="640" height="287" data-attachment-id="2257" data-permalink="https://quantixed.org/2020/11/29/all-my-trials-impact-of-covid-19-on-rare-disease-clinical-trials/clinicaltrials/" data-orig-file="https://i0.wp.com/quantixed.org/wp-content/uploads/2020/11/clinicalTrials.png?fit=820%2C368&amp;ssl=1" data-orig-size="820,368" data-comments-opened="1" data-image-meta="{&quot;aperture&quot;:&quot;0&quot;,&quot;credit&quot;:&quot;&quot;,&quot;camera&quot;:&quot;&quot;,&quot;caption&quot;:&quot;&quot;,&quot;created_timestamp&quot;:&quot;0&quot;,&quot;copyright&quot;:&quot;&quot;,&quot;focal_length&quot;:&quot;0&quot;,&quot;iso&quot;:&quot;0&quot;,&quot;shutter_speed&quot;:&quot;0&quot;,&quot;title&quot;:&quot;&quot;,&quot;orientation&quot;:&quot;0&quot;}" data-image-title="clinicalTrials" data-image-description="" data-image-caption="" data-medium-file="https://i0.wp.com/quantixed.org/wp-content/uploads/2020/11/clinicalTrials.png?fit=300%2C135&amp;ssl=1" data-large-file="https://i0.wp.com/quantixed.org/wp-content/uploads/2020/11/clinicalTrials.png?fit=640%2C287&amp;ssl=1" src="https://i0.wp.com/quantixed.org/wp-content/uploads/2020/11/clinicalTrials.png?resize=640%2C287&#038;ssl=1" alt="" class="wp-image-2257" srcset="https://i0.wp.com/quantixed.org/wp-content/uploads/2020/11/clinicalTrials.png?w=820&amp;ssl=1 820w, https://i0.wp.com/quantixed.org/wp-content/uploads/2020/11/clinicalTrials.png?resize=300%2C135&amp;ssl=1 300w, https://i0.wp.com/quantixed.org/wp-content/uploads/2020/11/clinicalTrials.png?resize=768%2C345&amp;ssl=1 768w" sizes="(max-width: 640px) 100vw, 640px" data-recalc-dims="1" /></figure>



I retrieved data sets for Rare Disease trials (n = 4029) and for COVID-19 trials (n = 2259). There are some trials that are investigating both things, so the intersecting trials were found and then the trials looking purely at Rare Diseases or at COVID-19 could be segregated.



I used the start date for each trial to count the number of trials in each of the three categories. The data are shown as the sum of trials starting in each quarter. Rare disease trials are shown on the left axis, COVID-19 trials on the right. The trials that are at the intersection are stacked on top of the Rare Disease only data.



Note the large difference in number of trials. There were 1801 COVID-19 trials starting in Q2 of 2020, whereas the busiest quarter for new trials in the rare disease area was 73 in Q1 of 2019.



The data do not show that COVID-19 has &#8220;wiped out&#8221; clinical trials in rare diseases. Some rare disease trial activity in 2020 now encompasses COVID-19, but the number of trials starting in each quarter this year is similar to previous years.



&#8212;



The post title comes from &#8220;All My Trials&#8221; from Cerys Matthews&#8217; LP Cockahoop.

The database [clinicaltrials.gov](https://clinicaltrials.gov) is a web
resource of clinical trials around the world. It has a REST API that
gives access to clinical trial data. There are some resources available
to interact with this resource using R, such as
[rclinicaltrials](https://github.com/sachsmc/rclinicaltrials) and
[ClinicalTrialsAPI](https://github.com/seandavi/ClinicalTrialsAPI).

We were interested at looking clinical trials for rare diseases and
particularly whether this year, COVID-19 had affected these trials.

<figure class="wp-block-image size-large">
<img
src="https://i0.wp.com/quantixed.org/wp-content/uploads/2020/11/clinicalTrials.png?resize=640%2C287&amp;ssl=1"
class="wp-image-2257" loading="lazy" decoding="async"
data-attachment-id="2257"
data-permalink="https://quantixed.org/2020/11/29/all-my-trials-impact-of-covid-19-on-rare-disease-clinical-trials/clinicaltrials/"
data-orig-file="https://i0.wp.com/quantixed.org/wp-content/uploads/2020/11/clinicalTrials.png?fit=820%2C368&amp;ssl=1"
data-orig-size="820,368" data-comments-opened="1"
data-image-meta="{&quot;aperture&quot;:&quot;0&quot;,&quot;credit&quot;:&quot;&quot;,&quot;camera&quot;:&quot;&quot;,&quot;caption&quot;:&quot;&quot;,&quot;created_timestamp&quot;:&quot;0&quot;,&quot;copyright&quot;:&quot;&quot;,&quot;focal_length&quot;:&quot;0&quot;,&quot;iso&quot;:&quot;0&quot;,&quot;shutter_speed&quot;:&quot;0&quot;,&quot;title&quot;:&quot;&quot;,&quot;orientation&quot;:&quot;0&quot;}"
data-image-title="clinicalTrials" data-image-description=""
data-image-caption=""
data-medium-file="https://i0.wp.com/quantixed.org/wp-content/uploads/2020/11/clinicalTrials.png?fit=300%2C135&amp;ssl=1"
data-large-file="https://i0.wp.com/quantixed.org/wp-content/uploads/2020/11/clinicalTrials.png?fit=640%2C287&amp;ssl=1"
srcset="https://i0.wp.com/quantixed.org/wp-content/uploads/2020/11/clinicalTrials.png?w=820&amp;ssl=1 820w, https://i0.wp.com/quantixed.org/wp-content/uploads/2020/11/clinicalTrials.png?resize=300%2C135&amp;ssl=1 300w, https://i0.wp.com/quantixed.org/wp-content/uploads/2020/11/clinicalTrials.png?resize=768%2C345&amp;ssl=1 768w"
sizes="(max-width: 640px) 100vw, 640px" data-recalc-dims="1" width="640"
height="287" />
</figure>

I retrieved data sets for Rare Disease trials (n = 4029) and for
COVID-19 trials (n = 2259). There are some trials that are investigating
both things, so the intersecting trials were found and then the trials
looking purely at Rare Diseases or at COVID-19 could be segregated.

I used the start date for each trial to count the number of trials in
each of the three categories. The data are shown as the sum of trials
starting in each quarter. Rare disease trials are shown on the left
axis, COVID-19 trials on the right. The trials that are at the
intersection are stacked on top of the Rare Disease only data.

**Note the large difference in number of trials.** There were 1801
COVID-19 trials starting in Q2 of 2020, whereas the busiest quarter for
new trials in the rare disease area was 73 in Q1 of 2019.

The data do not show that COVID-19 has "wiped out" clinical trials in
rare diseases. Some rare disease trial activity in 2020 now encompasses
COVID-19, but the number of trials starting in each quarter this year is
similar to previous years.

---

The post title comes from "All My Trials" from Cerys Matthews' LP
Cockahoop.

The database clinicaltrials.gov is a web resource of clinical trials around the world. It has a REST API that gives access to clinical trial data. There are some resources available to interact with this resource using R, such as rclinicaltrials and ClinicalTrialsAPI. We were interested at looking clinical trials for rare diseases and particularly whether this year, COVID-19 had affected these trials.


Rogue Scholar Posts

Recent Advances in Using Machine Learning with Graphs — Part 2

All My Trials: Impact of COVID-19 on rare disease clinical trials