Submitted:
04 June 2024
Posted:
04 June 2024
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Abstract
Keywords:
1. Introduction
- Automated and enhanced information extraction accuracy: By leveraging LLMs for zero-shot learning, we automate the traditional manual information extraction process, thereby enabling faster and more accurate data handling.
- Improved data accuracy through entity linking: By employing entity linking techniques, we ensure accurate connections between textual information and entities within the knowledge graph, leading to increased data consistency and reliability.
- Expanded practical applications in medicine: The developed knowledge graph has broader applicability beyond depression, potentially encompassing other mental disorders.
2. Related Works
2.1. Medical Knowledge Graphs
2.2. Zero-Shot Information Extraction
2.3. Entity Linking
3. Proposed Method
3.1. Schema Definition and Annotation Guidelines
- mystyle
- @dataclass
- class Entity:
- """
- Represents an entity in a document, which could be a person, location, organization, or any other named object.
- The ’name’ attribute holds the canonical name of the entity as identified in the document text.
- Attributes:
- name (str): The canonical name of the entity.
- """
- name: str
- mystyle
- @dataclass
- class Triple:
- """
- Represents a triple consisting of two entities and a relation in a semantic graph derived from textual data.
- A triple is typically used in knowledge representation and information extraction tasks to model factual statements.
- Attributes:
- Subject (Entity): The subject entity of the triple,
- usually the one performing or causing an action.
- Predicate (str): The relationship that connects
- the subject and object entities.
- Object (Entity): The object entity of the triple,
- usually the one experiencing or affected by the action.
- """
- Subject: Entity
- Predicate: str
- Object: Entity
3.2. Information Extraction and Entity Linking
- Context-aware recognition: The model analyzes the surrounding text to determine the precise scope and types of entities. For instance, it can distinguish whether "depression" refers to a clinical condition or a general emotional state [32].
- Entity classification: The extracted information is categorized based on predefined classes (e.g., symptoms, diagnoses, and treatments) aligned with the established schema.
3.3. Guideline-Based Model
3.4. Triple Extraction and Output
3.5. Structure of the Knowledge Graph
-
Subject nodes: These nodes represent specific medical conditions or pathological states. They categorize various forms of depression according to the DSM-5 criteria, including major depressive disorder, persistent depressive disorder, premenstrual dysphoric dis-order, and substance/medication-induced depressive disorder. Each subject node is labeled with the name of the disorder and a unique identifier.
- Object nodes: These nodes depict the symptoms or characteristics that a subject node may exhibit. Examples include emotional or behavioral responses such as depressed mood, fatigue, and loss of interest or pleasure. Each object node includes the name of the symptom and a unique identifier.
- Interaction between nodes: Within the knowledge graph, each subject node is linked to one or more object nodes that represent the manifestation of disease traits or symptoms. For instance, the "manifests as" relationship indicates how major depressive disorder might manifest as irritability, while the "is characterized by" relationship suggests that it may be characterized by a depressed mood.
4. Experiments
- Zero-shot information extraction on healthcare datasets: This experiment evaluated the effectiveness of zero-shot information extraction on various biomedical datasets.
- Zero-shot relationship extraction at the document level: This experiment focused on extracting relationships from unstructured data at the document level using a zero-shot approach.
4.1. Datasets and Settings
4.1.1. BioCreative Datasets
- BC5-Chemical and BC5-Disease [40]: Derived from the BioCreative V chemical-disease relation corpus, these datasets focus on exploring interactions between drugs and diseases. Each dataset includes 1,500 PubMed abstracts (evenly split) for training, development, and testing. We used a preprocessed version by Crichton et al., focusing on the named entity recognition (NER) of chemicals and diseases without relationship labels.
- NCBI Disease [41]: Provided by the National Center for Biotechnology Information (NCBI), this dataset includes 793 PubMed abstracts with 6,892 disease mentions linked to 790 unique disease entities. We used a preprocessed version by Crichton et al. for training, development, and testing splits.
- BC2GM [42]: Originating from the BioCreative II gene mention corpus, this dataset consists of sentences from PubMed abstracts with manually tagged genes and alternative gene entities. Our study focused on gene entity annotations using a version of the dataset separated for development by Crichton et al.
- JNLPBA [43]: Designed for applications in molecular biology, this dataset focuses on NER for entity types such as proteins, DNA, RNA, cell lines, and cell types. We focused on entity mention detection without differentiating between entity types, using the same splits as those of Crichton et al.
4.1.2. Document-Level Relationship Extraction Datasets
- DocRED [38]: This dataset was constructed using Wikipedia and Wikidata for document-level relationship extraction. It contains 9,228 documents and 57,263 relationship triples, covering 96 predefined relationship types. DocRED was used to evaluate the ability to extract relationships from complex texts spanning multiple sentences.
- Re-DocRED [39]: Re-DocRED, which is an expanded version of DocRED, includes additional positive cases (11,854 documents and 70,608 relationship triples) and incorporates relationship types and scenarios that are not addressed by DocRED. This dataset is useful for research aimed at identifying diverse and in-depth relationship patterns within documents.
4.2. Experimental Results
4.2.1. Zero-Shot Information Extraction on Healthcare Datasets
| Supervised Evaluation | Zero-shot Evaluation | |||
|---|---|---|---|---|
| BioBERT | PubMedBERT | In-context learning | Proposed method | |
| NCBI | 89.1 | 97.8 | 51.4 | 85.4 |
| BC5-disease | 84.7 | 85.6 | 73.0 | 87.3 |
| BC5-chem | 92.9 | 93.3 | 43.6 | 88.5 |
| BC2GM | 83.8 | 84.5 | 41.1 | 67.2 |
| JNLPBA | 78.6 | 79.1 | 48.3 | 49.7 |
4.2.2. Zero-Shot Relationship Extraction at the Document Level
| Existing Large Language Model | Proposed Method | ||||
|---|---|---|---|---|---|
| LLaMA2-7B | Flan-T5-XXL | LLaMA2-13B | without entity linking | with entity linking | |
| DocRED | 1.2 | 4.4 | 4.0 | 7.8 | 9.8 |
| RE-DocRED | 1.9 | 4.3 | 3.5 | 7.5 | 9.2 |
5. Discussion
-
Performance evaluation and interpretationThe results confirm that incorporating entity linking with LLMs significantly enhances zero-shot information extraction for medical data. The performance of our model surpassed that of traditional zero-shot approaches, demonstrating that these techniques can compete with conventional supervised learning methods. This is particularly valuable in healthcare, where data labeling is expensive and data privacy is paramount.
-
Importance of entity linkingEntity linking plays a vital role in ensuring data consistency and boosting the model performance. In this study, this went beyond simple identification tasks. By significantly improving the overall data accuracy, entity linking underscores its importance in maintaining the integrity and usefulness of medical information systems.
-
Methodological limitations and future directionsThis study used a limited set of datasets, which potentially affected the generalizability of the findings. Future studies should address this issue by exploring a broader range of medical datasets and incorporating a wider variety of entity types. This will help to validate and extend the applicability of the proposed method.
-
Potential applications in healthcareThe constructed medical knowledge graph serves as a critical tool for the systematic analysis of complex medical data and disease states. It has the potential to be integrated into real-time patient management systems to improve both diagnosis and ongoing patient care. Furthermore, the model of synergized LLMs and knowledge graphs suggests the potential benefits of integrating LLMs with knowledge graphs [49]. This approach can leverage the NLP capabilities of LLMs to interpret complex medical data and provide more accurate disease diagnosis and treatment predictions. This holds promise for more precise analysis of the diverse manifestations of depression and the development of effective personalized treatment plans.
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
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| 1 | World mental health report: Transforming mental health for all; https://www.who.int/publications/i/item/9789240049338
|
| 2 | WHO and ILO call for new measures to tackle mental health issues at work; https://www.who.int/news/item/28-09-2022-who-and-ilo-call-for-new-measures-to-tackle-mental-health-issues-at-work
|


| Number | Subject | Object | Relation |
|---|---|---|---|
| 1 | Major depressive disorder | Irritability | manifests as |
| 2 | Major depressive disorder | Depressed mood | manifests as |
| 3 | Major depressive disorder | Loss of interest or pleasure | manifests as |
| 4 | Major depressive disorder | Changes in sleep patterns | manifests as |
| 5 | Major depressive disorder | Decreased energy levels | manifests as |
| ... | ... | ... | ... |
| 483 | Unspecified depressive disorder | Appetite change | lasts |
| 484 | Unspecified depressive disorder | Weight change | lasts |
| 485 | Unspecified depressive disorder | Sexual interest or desire | lasts |
| 486 | Unspecified depressive disorder | Sleep disturbance | includes |
| 487 | Unspecified depressive disorder | Psychomotor changes | includes |
| Category | Dataset Name | Source | Document Count | Primary Entity Type | Entity Count |
|---|---|---|---|---|---|
| Biomedical Dataset | BC5-Chemical [40] | PubMed Abstracts | 1,500 | Chemicals (Drugs) | N/A |
| BC5-Disease [40] | PubMed Abstracts | 1,500 | Diseases | N/A | |
| NCBI-Disease [41] | PubMed Abstracts | 793 | Diseases | 6,892 | |
| BC2GM [42] | PubMed Abstracts | N/A | Genes and Alternative Gene Products | N/A | |
| JNLPBA [43] | PubMed Abstracts | N/A | Proteins, DNA, RNA, Cell Lines, Cell Types | N/A | |
| Document-level Information Extraction | DocRED [38] | Wikipedia | 9,228 | Relationships | 57,263 Triples |
| Re-DocRED [39] | Wikipedia | 11,854 | Relationships | 70,608 Triples |
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