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Biomedical Engineering

Citation Management Tools

Citation management tools allow you to download, organize, and share references. Some have greater capabilities that allow you to attach PDFs or work with your word processing system and google doc to format papers properly, including formatting bibliographies in multiple styles. Below are a selection of subscription-based and free citation management tools.

Citation Managers offer a more comprehensive look at Zotero and PaperPile.

Paperpile

Paperpile is a web-based reference citation management system, with emphasis on integration with Google apps.

Getting Started:
~Select the Start Free Trial option. You will need to login with your SJSU email address.
~Next,  go to Settings > Account info  and click on "Activate site license"
~Enter your SJSU email address, and then click the activation link you will receive via email.

EndNote

Endnote is an online bibliographic management tools often used in engineering and data sciences. You can create an account through SJSU Library’s subscription to Web of Science. This is a premium account that grants access to Web of Science and up to 1 million references. The online account works as a citation library. Software is available for your desktop and offers greater capabilities. See the EndNote libguide 

BibTeX

BibTex is reference management software typically used together with the LaTeX typesetting system for documentation and bibliography creation. EndNote, RefWorks and OneSearch have BibTeX output style.

OverLeaf

Overleaf is a free collaborative cloud-based LaTeX editor used for writing and editing technical publications.  Subscription-based plans with greater capability are available. Learn more about LaTeX and reference managers with Overleaf.

Zotero

Zotero is a free, open source citation manager with a desktop app, browser extension, and integration with Google Docs, Microsoft Word, and LibreOffice. Learn more about Zotero using the how-to-guide. For a comprehensive guide, go to Georgia State University Zotero Guide.

Another citation management tool with a free version is Mendeley.

Plagiarism

San José State University defines plagiarism as the act of representing the work of another as one’s own without giving appropriate credit, regardless of how that work was obtained, and submitting it to fulfill academic requirements. 

SJSU Academic Integrity Policy 

IEEE Plagiarism Definition

ACM Policy on Plagiarism, Misrepresentation, and Falsification

Background

Why do we use sources and cite them?
Builds credibility and authority as a writer by showing we have done our background work and learned about our topic. Connects our writing to bigger topics in the field. Allows readers to find our good sources.

Plagiarism: Using people’s words and/or ideas without giving credit or misrepresenting their ideas in our writing.

Paraphrasing: Rephrasing other’s ideas while giving credit and adding analysis or combining it with other sources.


When does something stop being plagiarism and start being paraphrasing?

Pitfalls between plagiarism and paraphrasing Steps to paraphrase
Only switching words for synonyms Carefully read the text
Keeping mostly the same idea order Take notes
Keeping mostly the same sentence structure Turn the paper over, write using your notes
Summarizing ideas with no citations   Combine information with other sources using quotation and add your own analysis
Copying phrases directly without both quotation marks and citing Cite your source
Misrepresenting information  Make sure the reader is able to identify borrowed ideas and your interpretation/analysis

Example Quote from a Source:

Smart objects provide a distributed architectural model for the Internet of Things. Due to their dual nature as physical and digital entities, such objects highlight the fact that the Internet of Things can’t be viewed only as a technical system but must also be considered as a human-centered interactive one. This implies that we must expand smart-object design beyond hardware and software to include interaction design as well as social aspects” (Kortuem, Kawsar, and Fitton, 2010, 46).

Kortuem, G., Kawsar, F., & Fitton, D. (2010). Smart objects as building blocks for the internet of things. IEEE Computer Society 12(1), 44-51.

Plagiarized

Smart objects have two natures, both as physical and digital entities; such objects show why the Internet of Things is not only a technical system but must also be considered a human system. This implies that we must expand smart-object design to include hardware, software, and social aspects in recognizing the distributed architectural model of the Internet of Things.

  1. Only shuffles the idea order slightly.         3. Mostly just uses synonyms.          5. Does not cite.
  2. Has almost identical sentence structure.    4. Uses some exact phrasing.

Paraphrased

Koretuem et al (2010) highlights how with the rapid growth of the Internet of Things (IoT), designers can no longer simply just think about the technical aspects. Smart objects blend together people’s physical and digital lives, which makes the interaction point between human and machines increasingly important (Kortuem et al, 2010). In order be competitive, computer science students should explore the human interaction and social expectations of the IoT in their projects.

  1. Cites source.                                            3. Varies idea order, sentence structure and words
  2. Blends source and personal analysis.    

Adapted from SJSU Writing Center

Proper Ways to Use AI tools

You can also use AI tools in the following ways: 

  • You can use a text generator for research ideas: you can ask a tool where to search for sources, to give you a list of possibly useful sources for a topic, to create a source map, or to help you narrow down a topic for a writing assignment
  • You can use a text generator to suggest an outline for a paragraph or a paper
  • You can use AI text spinners to give you an example of how to paraphrase source content
  • You can use AI text spinners to give you an example of how to express an idea
  • You can use AI text editors to correct punctuation, grammar, and word choice errors in your writing
  • You can use AI translation tools to help you determine how to express a term or idea in English

This text is adapted from a LibGuide created by Daniel Xiao, Research Impact Librarian at Texas A&M University Libraries and from the Canvas module of Prof. Debra Hunter from San Jose State University.

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Common Types of Prompts Used in GPT-Based Systems

Action Prompts - To perform a specific task:  Can you write/explain/summarize/provide/analyze/compose / re-write /translate ... Give me a table summarizing some of the key differences between Web of Science and Scopus. Expand the idea based on the following descriptors .....

WH Prompts - (what, when, where, who, which, whose, why, how...) What are the leading causes/factors/impacts/definitions/benefits of/challenges, barriers, issues with...? What would be a good image to use for a talk about quantum computing? 

Prompts to Set a Specific Context - Generating responses to specific situations or hypothetical scenarios. Summarize the article [citation] in one short paragraph...Create a list of five ChatGPT features that can be used to promote...  I am doing a literature review on the use of AI in education: "We aim to examine the effectiveness of AI-driven educational interventions, identifying challenges, and uncovering the implications for educators and learners alike." Please list 15 sources that might be used in this review. 

Prompts That Pose Multiple Queries - Please discuss the current state of genetic engineering research. What are some recent breakthroughs, and what ethical considerations have been raised concerning these advancements?

Act As an Expert Prompt Specify a role for ChatGPT to take a question. This is also known as system message prompting.

 User: I am going to conduct a systematic review on gaming and mathematics related to K-12 education. First question: "Which databases should I use?" Second question: "What are the relevant subject terms, descriptors and key words?" 

Find Similar Articles or Titles Prompts -  Find similar articles like this one [then paste in the abstract].

Summarize/Synthesize Prompts - Given the following article, please discuss its key findings. Reference: How Large Language Models are Transforming Machine-Paraphrased Plagiarism at https://arxiv.org/abs/2210.03568 

This text is adapted from a LibGuide created by Daniel Xiao, Research Impact Librarian at Texas A&M University Libraries and from the Canvas module of Prof. Debra Hunter from San Jose State University.

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Things to Consider When Writing a Prompt

Context: A good prompt might explain the roles of both AI and the user in the task, outline your output requirements, and/or specify the anticipated results. With a given role the AI model knows how it should 'act' and what kind of output it should give you. 

User: I am a graduate student working on a project to develop a machine learning model capable of optimizing chemical reactions to improve yield, reaction speed, and scale.  The goal of the project is to develop the model for optimization and to validate the optimized conditions in the wet lab. Please provide a step-by-step guide to how I might develop a machine learning model to optimize chemical reactions.

Instructions: Include explicit instructions for the desired behavior, for instance, ask the model to plan step by step, outline, search, summarize, or synthesize (find commonalities in multiple sources of information).

User: Please find some academic papers on the various ways that AI is affecting the job market. Compile a list of pro and con viewpoints like:  AI leads to job reduction, and AI has the potential to generate new employment opportunities.

Examples: Providing example inputs can help the model understand the desired patterns or format for its responses. Example inputs may include the use of examples, demonstrations of the expected behavior, a set of relevant keywords or descriptors, the abstract of a related article, or a reference text. 

User: I found this paper very helpful. Reference: AI Impact On The Labor Force at Https://arxiv.org/abs/2302.xxxx. Please find four more studies like this one. 

Outcome Indicators: Direct the model to generate a response for a given style, tone, format or scenario.

User: Help me structure my graduate literature review on the use of AI in video gaming by suggesting a structure that begins with an introduction, ends with a conclusion and has four main sections that review the literature.  The abstracts of the articles that I am using are as follows: (abstracts are copied and pasted here). 

Testing, Fine-tuning, and Effectiveness: Prompt creation often involves the testing and refining of prompts, and the effectiveness of prompt techniques may differ depending on the particular task, model, and the user's prompt engineering experience.

This text is adapted from a LibGuide created by Daniel Xiao, Research Impact Librarian at Texas A&M University Libraries and from the Canvas module of Prof. Debra Hunter from San Jose State University.

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Users of AI generative tools should keep the following in mind:

1. Attribution. All ideas that are not originally one's own have a source and that source must be attributed. Please be aware that generative AI tends to invent sources. You have a two-fold obligation. (1) you need to document the process, and (2) you need to find and attribute the original source of the idea, identify the location within the source, and provide a working link to the location. If you quote the AI itself, label it as “synthesized communication” and reference it like the conventions for a “personal communication”. Note that such a “synthesized communication" is not a valid source for facts, only for the conversation itself.

 

Citing sources from AI-assisted software

APA editorial style (https://apastyle.apa.org/blog/how-to-cite-chatgpt)

  1. For the in-text citations: (OpenAI, 2023)
  2. For the referenceOpenAI. (2023). ChatGPT (Sep 14 version) [Large language model]. https://chat.openai.com/chat

 

IEEE editorial style 

IEEE has developed guidelines on citing ChatGPT use in their style. They recommend using their "Software" category.

Template: Author firstname initial. Lastname. Title of Software. Date Repository or Archive. (version or year). Publisher Name. Accessed: Date (when applicable). [Type of Medium]. Global Persistent Identifier. Available: site/path/file

Example: ChatGPT. (GPT-4). OpenAI. Accessed: Sep. 26, 2023. [Online]. Available: https://chat.openai.com/chat

Example (Prompt included):

ChatGPT. (GPT-4). "Solid State Physics Explained." OpenAI. Accessed: Sep. 26, 2023. [Online]. Prompt: "What is solid state physics? Explain it to someone with no physics background." Available: https://chat.openai.com/chat

 

2. Facticity. Besides inventing sources, generative AI may invent facts as well. Verification is your responsibility: submitting factually wrong material is an academic offence, and whether the source of the error is you or the AI makes no difference. You need to check the facts, the quotes, the arguments, the logic, and document what you did to validate your material.