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Research results refer to the findings and conclusions derived from a systematic investigation or study conducted to answer a specific question or hypothesis. These results are typically presented in a written report or paper and can include various forms of data such as numerical data, qualitative data, statistics, charts, graphs, and visual aids.
The results section of the research paper presents the findings of the study. It is the part of the paper where the researcher reports the data collected during the study and analyzes it to draw conclusions.
In the results section, the researcher should describe the data that was collected, the statistical analysis performed, and the findings of the study. It is important to be objective and not interpret the data in this section. Instead, the researcher should report the data as accurately and objectively as possible.
The structure of the research results section can vary depending on the type of research conducted, but in general, it should contain the following components:
The following is an outline of the key components typically included in the Results section:
I. Introduction
II. Descriptive statistics
III. Inferential statistics
IV. Effect sizes and confidence intervals
V. Subgroup analyses
VI. Limitations and assumptions
VII. Conclusions
An Example of a Research Results Section could be:
II. Participants
III. Results
IV. Discussion
V. Conclusion
Example of Research Results in Research Paper :
Our study aimed to compare the performance of three different machine learning algorithms (Random Forest, Support Vector Machine, and Neural Network) in predicting customer churn in a telecommunications company. We collected a dataset of 10,000 customer records, with 20 predictor variables and a binary churn outcome variable.
Our analysis revealed that all three algorithms performed well in predicting customer churn, with an overall accuracy of 85%. However, the Random Forest algorithm showed the highest accuracy (88%), followed by the Support Vector Machine (86%) and the Neural Network (84%).
Furthermore, we found that the most important predictor variables for customer churn were monthly charges, contract type, and tenure. Random Forest identified monthly charges as the most important variable, while Support Vector Machine and Neural Network identified contract type as the most important.
Overall, our results suggest that machine learning algorithms can be effective in predicting customer churn in a telecommunications company, and that Random Forest is the most accurate algorithm for this task.
Example 3 :
Title : The Impact of Social Media on Body Image and Self-Esteem
Abstract : This study aimed to investigate the relationship between social media use, body image, and self-esteem among young adults. A total of 200 participants were recruited from a university and completed self-report measures of social media use, body image satisfaction, and self-esteem.
Results: The results showed that social media use was significantly associated with body image dissatisfaction and lower self-esteem. Specifically, participants who reported spending more time on social media platforms had lower levels of body image satisfaction and self-esteem compared to those who reported less social media use. Moreover, the study found that comparing oneself to others on social media was a significant predictor of body image dissatisfaction and lower self-esteem.
Conclusion : These results suggest that social media use can have negative effects on body image satisfaction and self-esteem among young adults. It is important for individuals to be mindful of their social media use and to recognize the potential negative impact it can have on their mental health. Furthermore, interventions aimed at promoting positive body image and self-esteem should take into account the role of social media in shaping these attitudes and behaviors.
Research results are important for several reasons, including:
Here are some general guidelines on how to write results in a research paper:
Here are situations When to Write Research Results”
The purposes of Research Results are as follows:
Some Advantages of Research Results are as follows:
Researcher, Academic Writer, Web developer
A research report is a concise document that summarizes the findings, methods, and conclusions of a research study or investigation. There are various types of research reports available for different purposes.
It typically includes details on the research question, methodology, data analysis, and results, providing a structured and informative account of the research process and outcomes.
Limitations, key highlights.
1. technical or scientific reports.
Technical and scientific reports communicate research findings to experts and professionals in a particular field.
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Characteristics:
Popular reports are designed for a general audience and aim to inform, educate, or entertain on a wide range of topics.
Survey reports include data collected through surveys and focus on presenting insights and opinions on specific issues or questions.
Market research reports provide insights into consumer behavior, market trends, and industry analysis.
Case study reports focus on an in-depth examination of a single entity, often to explore complex, real-life situations.
Analytical research reports involve a deep analysis of data to uncover patterns, trends, or relationships.
Literature review reports provide an overview of existing research on a specific topic, highlighting gaps and trends.
Experimental research reports involve controlled experiments to test hypotheses and determine if the results support or reject the hypothesis.
Descriptive research reports aim to provide a comprehensive picture of a phenomenon, group, or situation. They seek to answer the “what” and “how” questions.
Exploratory research reports are conducted when there is little prior knowledge about a subject. They aim to identify key variables and research questions.
Explanatory research reports seek to understand the relationships between variables and explain why certain phenomena occur.
Policy or white papers aim to inform policymakers, stakeholders, and the public about specific issues and recommend actions.
These are some common components you must know while writing different types of research reports.
1. Title Page:
2. Abstract: Add a concise summary of the research, including the research question or objective, methodology, key findings, and implications. Typically, it should be no more than 150-250 words.
3. Table of Contents: Include a list of sections and subsections with page numbers.
4. List of Figures and Tables: If your research includes numerical data, add all the statistics and tables along with their corresponding page numbers. It is similar to a table of contents for quantitative data.
5. List of Abbreviations and Symbols: Include any abbreviations or symbols you have used in the report and their meanings.
6. Introduction:
7. Literature Review:
8. Methodology:
9. Results:
10. Discussion:
11. Conclusion:
12. References: Include a list of all the sources cited in your report in a standardized citation style (e.g., APA, MLA, Chicago).
Let us see an example of a research report.
Research Report: The Impact of Artificial Intelligence on the Labor Market
This research study explores the profound changes occurring in the labor market due to the increasing adoption of artificial intelligence (AI) technologies. The study examines the potential benefits and challenges AI poses for the workforce, job displacement, and the skills required in the future job market.
Introduction, literature review, methodology.
The introduction section provides an overview of the research topic. It explains the significance of studying the impact of AI on the labor market, outlines the research questions, and previews the structure of the report.
The literature review section reviews existing research on the effects of AI on employment and the labor market. It discusses the different perspectives on whether AI will create new jobs or lead to job displacement. It also explores the skills and education required for the future workforce.
This section explains the research methods used, such as data collection methods, sources, and analytical techniques. It outlines how data on AI adoption, job displacement, and future job projections were gathered and analyzed.
The results section presents the key findings of the study. It includes data on the extent of AI adoption across industries, job displacement rates, and projections for AI-related occupations.
The discussion section interprets the results in the context of the research questions. It analyzes the potential benefits and challenges AI poses for the labor market, discusses policy implications, and explores the role of education and training in preparing the workforce for the AI era.
In conclusion, this research highlights the transformative impact of artificial intelligence on the labor market. While AI brings opportunities for innovation and efficiency, it also presents challenges related to job displacement and workforce adaptation. Preparing for this evolving job landscape is crucial for individuals and policymakers.
Given below are various types of research reports writing that researchers and organizations use to present findings, progress, and other information.
Outlines a plan for a project or research for approval or funding. | Research proposal submitted to study the impact of climate change on local ecosystems. | |
Generated at regular intervals to provide project updates. | Weekly sales reports summarizing product sales figures. | |
Detailed, structured reports often used in academic, scientific, or business settings. | Formal business report analyzing a company’s financial performance for the year. | |
Less structured reports for quick internal communication. | Email summarizing key takeaways from a team meeting. | |
Concise documents offering a brief overview of a specific topic. | A one-page summary of customer feedback from a product launch. | |
Comprehensive reports with in-depth analysis and information. | 100-page research report on the effects of a new drug on a medical condition. | |
Focus on data analysis and provide insights or recommendations. | Market research report analyzing consumer behavior trends and recommending marketing strategies. | |
Convey information without providing analysis or recommendations. | Report detailing the steps of a manufacturing process for new employees. | |
Flow within the organizational hierarchy, moving up or down. | Report from a department manager to the company’s vice president on department performance. | |
Sent between individuals or departments at the same organizational level. | Report from one project manager to another project manager in a different department. | |
Created and distributed within an organization for internal purposes. | Internal audit report examining the company’s financial records for compliance. | |
Prepared for external audiences, such as clients, investors, or regulators. | A publicly traded company publishes an annual report for shareholders and the general public. |
Here is why the different types of research reports are important.
Listed below are some limitations of different types of research reports.
Different types of research reports are important for sharing knowledge, making smart choices, and moving forward in different areas of study. It’s vital for both researchers and those who use research to grasp the different kinds of reports, what goes into them, and why they matter.
Q1. Are research reports the same as research papers? Answer: Research reports and research papers share similarities but have distinct purposes and structures. Research papers are often more academic and can vary in structure, while research reports are typically more structured and cater to a broader audience.
Q2. How do I choose the right type of research report for my study? Answer: The choice of research report type depends on your research goals, audience, and the nature of your study. Consider whether you are conducting scientific research, market analysis, academic research, or policy analysis, and select the format that aligns with your objectives.
Q3. Can research reports be used as references in other research reports? Answer: Yes, research reports can be cited and used as references in other research reports as long as they are credible sources. Citing previous research reports adds depth and credibility to your work.
This article lists all the types of research reports available for research methodologies. We have also included its format, example, and several report-writing methods. For similar articles, you can check the following articles,
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A report is a nonfiction account that presents and/or summarizes the facts about a particular event, topic, or issue. The idea is that people who are unfamiliar with the subject can find everything they need to know from a good report.
Reports make it easy to catch someone up to speed on a subject, but actually writing a report is anything but easy. So to help you understand what to do, below we present a little report of our own, all about report writing and report format best practices.
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What is a report?
What is the structure of a report, what should be included in a report, how to write a report in 7 steps, what is a report .
In technical terms, the definition of a report is pretty vague: any account, spoken or written, of the matters concerning a particular topic. This could refer to anything from a courtroom testimony to a grade schooler’s book report .
Really, when people talk about “reports,” they’re usually referring to official documents outlining the facts of a topic, typically written by an expert on the subject or someone assigned to investigate it. There are different types of reports, explained in the next section, but they mostly fit this description.
What kind of information is shared in reports? Although all facts are welcome, reports, in particular, tend to feature these types of content:
Reports are closely related to essay writing , although there are some clear distinctions. While both rely on facts, essays add the personal opinions and arguments of the authors. Reports typically stick only to the facts, although they may include some of the author’s interpretation of these facts, most likely in the conclusion.
Moreover, reports are heavily organized, commonly with tables of contents and copious headings and subheadings. This makes it easier for readers to scan reports for the information they’re looking for. Essays, on the other hand, are meant to be read start to finish, not browsed for specific insights.
There are a few different types of reports, depending on the purpose and to whom you present your report. Here’s a quick list of the common types of reports:
Reports can be further divided into categories based on how they are written. For example, a report could be formal or informal, short or long, and internal or external. In business, a vertical report shares information with people on different levels of the hierarchy (i.e., people who work above you and below you), while a lateral report is for people on the author’s same level, but in different departments.
There are as many types of reports as there are writing styles, but in this guide, we focus on academic reports, which tend to be formal and informational.
>>Read More: What Is Academic Writing?
The report format depends on the type of report and the requirements of the assignment. While reports can use their own unique structure, most follow this basic template:
If you’re familiar with how to write a research paper , you’ll notice that report writing follows the same introduction-body-conclusion structure, sometimes adding an executive summary. Reports usually have their own additional requirements as well, such as title pages and tables of content, which we explain in the next section.
There are no firm requirements for what’s included in a report. Every school, company, laboratory, task manager, and teacher can make their own format, depending on their unique needs. In general, though, be on the lookout for these particular requirements—they tend to crop up a lot:
As always, refer to the assignment for the specific guidelines on each of these. The people who read the report should tell you which style guides or formatting they require.
Now let’s get into the specifics of how to write a report. Follow the seven steps on report writing below to take you from an idea to a completed paper.
Before you start writing, you need to pick the topic of your report. Often, the topic is assigned for you, as with most business reports, or predetermined by the nature of your work, as with scientific reports. If that’s the case, you can ignore this step and move on.
If you’re in charge of choosing your own topic, as with a lot of academic reports, then this is one of the most important steps in the whole writing process. Try to pick a topic that fits these two criteria:
Of course, don’t forget the instructions of the assignment, including length, so keep those in the back of your head when deciding.
With business and scientific reports, the research is usually your own or provided by the company—although there’s still plenty of digging for external sources in both.
For academic papers, you’re largely on your own for research, unless you’re required to use class materials. That’s one of the reasons why choosing the right topic is so crucial; you won’t go far if the topic you picked doesn’t have enough available research.
The key is to search only for reputable sources: official documents, other reports, research papers, case studies, books from respected authors, etc. Feel free to use research cited in other similar reports. You can often find a lot of information online through search engines, but a quick trip to the library can also help in a pinch.
Before you go any further, write a thesis statement to help you conceptualize the main theme of your report. Just like the topic sentence of a paragraph, the thesis statement summarizes the main point of your writing, in this case, the report.
Once you’ve collected enough research, you should notice some trends and patterns in the information. If these patterns all infer or lead up to a bigger, overarching point, that’s your thesis statement.
For example, if you were writing a report on the wages of fast-food employees, your thesis might be something like, “Although wages used to be commensurate with living expenses, after years of stagnation they are no longer adequate.” From there, the rest of your report will elaborate on that thesis, with ample evidence and supporting arguments.
It’s good to include your thesis statement in both the executive summary and introduction of your report, but you still want to figure it out early so you know which direction to go when you work on your outline next.
Writing an outline is recommended for all kinds of writing, but it’s especially useful for reports given their emphasis on organization. Because reports are often separated by headings and subheadings, a solid outline makes sure you stay on track while writing without missing anything.
Really, you should start thinking about your outline during the research phase, when you start to notice patterns and trends. If you’re stuck, try making a list of all the key points, details, and evidence you want to mention. See if you can fit them into general and specific categories, which you can turn into headings and subheadings respectively.
Actually writing the rough draft , or first draft, is usually the most time-consuming step. Here’s where you take all the information from your research and put it into words. To avoid getting overwhelmed, simply follow your outline step by step to make sure you don’t accidentally leave out anything.
Don’t be afraid to make mistakes; that’s the number one rule for writing a rough draft. Expecting your first draft to be perfect adds a lot of pressure. Instead, write in a natural and relaxed way, and worry about the specific details like word choice and correcting mistakes later. That’s what the last two steps are for, anyway.
Once your rough draft is finished, it’s time to go back and start fixing the mistakes you ignored the first time around. (Before you dive right back in, though, it helps to sleep on it to start editing fresh, or at least take a small break to unwind from writing the rough draft.)
We recommend first rereading your report for any major issues, such as cutting or moving around entire sentences and paragraphs. Sometimes you’ll find your data doesn’t line up, or that you misinterpreted a key piece of evidence. This is the right time to fix the “big picture” mistakes and rewrite any longer sections as needed.
If you’re unfamiliar with what to look for when editing, you can read our previous guide with some more advanced self-editing tips .
Last, it pays to go over your report one final time, just to optimize your wording and check for grammatical or spelling mistakes. In the previous step you checked for “big picture” mistakes, but here you’re looking for specific, even nitpicky problems.
A writing assistant like Grammarly flags those issues for you. Grammarly’s free version points out any spelling and grammatical mistakes while you write, with suggestions to improve your writing that you can apply with just one click. The Premium version offers even more advanced features, such as tone adjustments and word choice recommendations for taking your writing to the next level.
Understanding research reports, financial analyst research reports, research report impact, conflicts of interest.
James Chen, CMT is an expert trader, investment adviser, and global market strategist.
A research report is a document prepared by an analyst or strategist who is a part of the investment research team in a stock brokerage or investment bank . A research report may focus on a specific stock or industry sector, a currency, commodity or fixed-income instrument, or on a geographic region or country. Research reports generally, but not always, have actionable recommendations such as investment ideas that investors can act upon.
Research reports are produced by a variety of sources, ranging from market research firms to in-house departments at large organizations. When applied to the investment industry, the term usually refers to sell-side research, or investment research produced by brokerage houses.
Such research is disseminated to the institutional and retail clients of the brokerage that produces it. Research produced by the buy-side, which includes pension funds, mutual funds, and portfolio managers , is usually for internal use only and is not distributed to external parties.
Financial analysts may produce research reports for the purpose of supporting a particular recommendation, such as whether to buy or sell a particular security or whether a client should consider a particular financial product. For example, an analyst may create a report in regards to a new offering being proposed by a company. The report could include relevant metrics regarding the company itself, such as the number of years they have been in operation as well as the names of key stakeholders , along with statistics regarding the current state of the market in which the company participates. Information regarding overall profitability and the intended use of the funds can also be included.
Enthusiasts of the Efficient Market Hypothesis (EMH) might insist that the value of professional analysts' research reports is suspect and that investors likely place too much confidence in the conclusions such analysts make. While a definitive conclusion about this topic is difficult to make because comparisons are not exact, some research papers do exist which claim empirical evidence supporting the value of such reports.
One such paper studied the market for India-based investments and analysts who cover them. The paper was published in the March 2014 edition of the International Research Journal of Business and Management. Its authors concluded that analyst recommendations do have an impact and are beneficial to investors at least in short-term decisions.
While some analysts are functionally unaffiliated, others may be directly or indirectly affiliated with the companies for which they produce reports. Unaffiliated analysts traditionally perform independent research to determine an appropriate recommendation and may have a limited concern regarding the outcome.
Affiliated analysts may feel best served by ensuring any research reports portray clients in a favorable light. Additionally, if an analyst is also an investor in the company on which the report is based, he may have a personal incentive to avoid topics that may result in a lowered valuation of the securities in which he has invested.
The purpose of a field report in the social sciences is to describe the deliberate observation of people, places, and/or events and to analyze what has been observed in order to identify and categorize common themes in relation to the research problem underpinning the study. The content represents the researcher's interpretation of meaning found in data that has been gathered during one or more observational events.
Flick, Uwe. The SAGE Handbook of Qualitative Data Collection . London: SAGE Publications, 2018; Lofland, John, David Snow, Leon Anderson, and Lyn H. Lofland. Analyzing Social Settings: A Guide to Qualitative Observation and Analysis. Long Grove, IL: Waveland Press, 2022; Baker, Lynda. "Observation: A Complex Research Method." Library Trends 55 (Summer 2006): 171-189.; Kellehear, Allan. The Unobtrusive Researcher: A Guide to Methods . New York: Routledge, 2020.
How to Begin
Field reports are most often assigned in disciplines of the applied social sciences [e.g., social work, anthropology, gerontology, criminal justice, education, law, the health care services] where it is important to build a bridge of relevancy between the theoretical concepts learned in the classroom and the practice of actually doing the work you are being taught to do. Field reports are also common in certain science disciplines [e.g., geology] but these reports are organized differently and serve a different purpose than what is described below.
Professors will assign a field report with the intention of improving your understanding of key theoretical concepts by applying methods of careful and structured observation of, and reflection about, people, places, or phenomena existing in their natural settings. Field reports facilitate the development of data collection techniques and observation skills and they help you to understand how theory applies to real world situations. Field reports are also an opportunity to obtain evidence through methods of observing professional practice that contribute to or challenge existing theories.
We are all observers of people, their interactions, places, and events; however, your responsibility when writing a field report is to conduct research based on data generated by the act of designing a specific study, deliberate observation, synthesis of key findings, and interpretation of their meaning.
When writing a field report you need to:
Techniques to Record Your Observations Although there is no limit to the type of data gathering techniques you can use, these are the most frequently used methods:
Note Taking This is the most common and easiest method of recording your observations. Tips for taking notes include: organizing some shorthand symbols beforehand so that recording basic or repeated actions does not impede your ability to observe, using many small paragraphs, which reflect changes in activities, who is talking, etc., and, leaving space on the page so you can write down additional thoughts and ideas about what’s being observed, any theoretical insights, and notes to yourself that are set aside for further investigation. See drop-down tab for additional information about note-taking.
Photography With the advent of smart phones, an almost unlimited number of high quality photographs can be taken of the objects, events, and people observed during a field study. Photographs can help capture an important moment in time as well as document details about the space where your observation takes place. Taking a photograph can save you time in documenting the details of a space that would otherwise require extensive note taking. However, be aware that flash photography could undermine your ability to observe unobtrusively so assess the lighting in your observation space; if it's too dark, you may need to rely on taking notes. Also, you should reject the idea that photographs represent some sort of "window into the world" because this assumption creates the risk of over-interpreting what they show. As with any product of data gathering, you are the sole instrument of interpretation and meaning-making, not the object itself. Video and Audio Recordings Video or audio recording your observations has the positive effect of giving you an unfiltered record of the observation event. It also facilitates repeated analysis of your observations. This can be particularly helpful as you gather additional information or insights during your research. However, these techniques have the negative effect of increasing how intrusive you are as an observer and will often not be practical or even allowed under certain circumstances [e.g., interaction between a doctor and a patient] and in certain organizational settings [e.g., a courtroom]. Illustrations/Drawings This does not refer to an artistic endeavor but, rather, refers to the possible need, for example, to draw a map of the observation setting or illustrating objects in relation to people's behavior. This can also take the form of rough tables, charts, or graphs documenting the frequency and type of activities observed. These can be subsequently placed in a more readable format when you write your field report. To save time, draft a table [i.e., columns and rows] on a separate piece of paper before an observation if you know you will be entering data in that way.
NOTE: You may consider using a laptop or other electronic device to record your notes as you observe, but keep in mind the possibility that the clicking of keys while you type or noises from your device can be obtrusive, whereas writing your notes on paper is relatively quiet and unobtrusive. Always assess your presence in the setting where you're gathering the data so as to minimize your impact on the subject or phenomenon being studied.
ANOTHER NOTE: Techniques of deliberate observation and data gathering are not innate skills; they are skills that must be learned and practiced in order to achieve proficiency. Before your first observation, practice the technique you plan to use in a setting similar to your study site [e.g., take notes about how people choose to enter checkout lines at a grocery store if your research involves examining the choice patterns of unrelated people forced to queue in busy social settings]. When the act of data gathering counts, you'll be glad you practiced beforehand.
YET ANOTHER NOTE: An issue rarely discussed in the literature about conducting field research is whether you should move around the study site while observing or remaining situated in one place. Moving around can be intrusive, but it facilitates observing people's behavior from multiple vectors. However, if you remain in one place throughout the observation [or during each observation], you will eventually blend into the background and diminish the chance of unintentionally influencing people's behavior. If the site has a complex set of interactions or interdependent activities [e.g., a play ground], consider moving around; if the study site is relatively fixed [e.g., a classroom], then consider staying in one place while observing.
Examples of Things to Document While Observing
Brief notes about all of these examples contextualize your observations; however, your observation notes will be guided primarily by your theoretical framework, keeping in mind that your observations will feed into and potentially modify or alter these frameworks.
Sampling Techniques
Sampling refers to the process used to select a portion of the population for study . Qualitative research, of which observation is one method of data gathering, is generally based on non-probability and purposive sampling rather than probability or random approaches characteristic of quantitatively-driven studies. Sampling in observational research is flexible and often continues until no new themes emerge from the data, a point referred to as data saturation.
All sampling decisions are made for the explicit purpose of obtaining the richest possible source of information to answer the research questions. Decisions about sampling assumes you know what you want to observe, what behaviors are important to record, and what research problem you are addressing before you begin the study. These questions determine what sampling technique you should use, so be sure you have adequately answered them before selecting a sampling method.
Ways to sample when conducting an observation include:
Alderks, Peter. Data Collection. Psychology 330 Course Documents. Animal Behavior Lab. University of Washington; Emerson, Robert M. Contemporary Field Research: Perspectives and Formulations . 2nd ed. Prospect Heights, IL: Waveland Press, 2001; Emerson, Robert M. et al. “Participant Observation and Fieldnotes.” In Handbook of Ethnography . Paul Atkinson et al., eds. (Thousand Oaks, CA: Sage, 2001), 352-368; Emerson, Robert M. et al. Writing Ethnographic Fieldnotes . 2nd ed. Chicago, IL: University of Chicago Press, 2011; Ethnography, Observational Research, and Narrative Inquiry. Writing@CSU. Colorado State University; Hazel, Spencer. "The Paradox from Within: Research Participants Doing-Being-Observed." Qualitative Research 16 (August 2016): 446-457; Pace, Tonio. Writing Field Reports. Scribd Online Library; Presser, Jon and Dona Schwartz. “Photographs within the Sociological Research Process.” In Image-based Research: A Sourcebook for Qualitative Researchers . Jon Prosser, editor (London: Falmer Press, 1998), pp. 115-130; Pyrczak, Fred and Randall R. Bruce. Writing Empirical Research Reports: A Basic Guide for Students of the Social and Behavioral Sciences . 5th ed. Glendale, CA: Pyrczak Publishing, 2005; Report Writing. UniLearning. University of Wollongong, Australia; Wolfinger, Nicholas H. "On Writing Fieldnotes: Collection Strategies and Background Expectancies.” Qualitative Research 2 (April 2002): 85-95; Writing Reports. Anonymous. The Higher Education Academy.
How you choose to format your field report is determined by the research problem, the theoretical framework that is driving your analysis, the observations that you make, and/or specific guidelines established by your professor. Since field reports do not have a standard format, it is worthwhile to determine from your professor what the preferred structure and organization should be before you begin to write. Note that field reports should be written in the past tense. With this in mind, most field reports in the social sciences include the following elements:
I. Introduction The introduction should describe the research problem, the specific objectives of your research, and the important theories or concepts underpinning your field study. The introduction should describe the nature of the organization or setting where you are conducting the observation, what type of observations you have conducted, what your focus was, when you observed, and the methods you used for collecting the data. Collectively, this descriptive information should support reasons why you chose the observation site and the people or events within it. You should also include a review of pertinent literature related to the research problem, particularly if similar methods were used in prior studies. Conclude your introduction with a statement about how the rest of the paper is organized.
II. Description of Activities
Your readers only knowledge and understanding of what happened will come from the description section of your report because they were not witnesses to the situation, people, or events that you are writing about. Given this, it is crucial that you provide sufficient details to place the analysis that will follow into proper context; don't make the mistake of providing a description without context. The description section of a field report is similar to a well written piece of journalism. Therefore, a useful approach to systematically describing the varying aspects of an observed situation is to answer the "Five W’s of Investigative Reporting." As Dubbels notes [p. 19], these are:
III. Interpretation and Analysis
Always place the analysis and interpretations of your field observations within the larger context of the theoretical assumptions and issues you described in the introduction. Part of your responsibility in analyzing the data is to determine which observations are worthy of comment and interpretation, and which observations are more general in nature. It is your theoretical framework that allows you to make these decisions. You need to demonstrate to the reader that you are conducting the field work through the eyes of an informed viewer and from the perspective of a casual observer.
Here are some questions to ask yourself when analyzing your observations:
NOTE: Only base your interpretations on what you have actually observed. Do not speculate or manipulate your observational data to fit into your study's theoretical framework.
IV. Conclusion and Recommendations
The conclusion should briefly recap of the entire study, reiterating the importance or significance of your observations. Avoid including any new information. You should also state any recommendations you may have based on the results of your study. Be sure to describe any unanticipated problems you encountered and note the limitations of your study. The conclusion should not be more than two or three paragraphs.
V. Appendix
This is where you would place information that is not essential to explaining your findings, but that supports your analysis [especially repetitive or lengthy information], that validates your conclusions, or that contextualizes a related point that helps the reader understand the overall report. Examples of information that could be included in an appendix are figures/tables/charts/graphs of results, statistics, pictures, maps, drawings, or, if applicable, transcripts of interviews. There is no limit to what can be included in the appendix or its format [e.g., a DVD recording of the observation site], provided that it is relevant to the study's purpose and reference is made to it in the report. If information is placed in more than one appendix ["appendices"], the order in which they are organized is dictated by the order they were first mentioned in the text of the report.
VI. References
List all sources that you consulted and obtained information from while writing your field report. Note that field reports generally do not include further readings or an extended bibliography. However, consult with your professor concerning what your list of sources should be included and be sure to write them in the preferred citation style of your discipline or is preferred by your professor [i.e., APA, Chicago, MLA, etc.].
Alderks, Peter. Data Collection. Psychology 330 Course Documents. Animal Behavior Lab. University of Washington; Dubbels, Brock R. Exploring the Cognitive, Social, Cultural, and Psychological Aspects of Gaming and Simulations . Hershey, PA: IGI Global, 2018; Emerson, Robert M. Contemporary Field Research: Perspectives and Formulations . 2nd ed. Prospect Heights, IL: Waveland Press, 2001; Emerson, Robert M. et al. “Participant Observation and Fieldnotes.” In Handbook of Ethnography . Paul Atkinson et al., eds. (Thousand Oaks, CA: Sage, 2001), 352-368; Emerson, Robert M. et al. Writing Ethnographic Fieldnotes . 2nd ed. Chicago, IL: University of Chicago Press, 2011; Ethnography, Observational Research, and Narrative Inquiry. Writing@CSU. Colorado State University; Pace, Tonio. Writing Field Reports. Scribd Online Library; Pyrczak, Fred and Randall R. Bruce. Writing Empirical Research Reports: A Basic Guide for Students of the Social and Behavioral Sciences . 5th ed. Glendale, CA: Pyrczak Publishing, 2005; Report Writing. UniLearning. University of Wollongong, Australia; Wolfinger, Nicholas H. "On Writing Fieldnotes: Collection Strategies and Background Expectancies.” Qualitative Research 2 (April 2002): 85-95; Writing Reports. Anonymous. The Higher Education Academy.
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Published on October 30, 2022 by Jack Caulfield . Revised on April 13, 2023.
The content of the conclusion varies depending on whether your paper presents the results of original empirical research or constructs an argument through engagement with sources .
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Step 1: restate the problem, step 2: sum up the paper, step 3: discuss the implications, research paper conclusion examples, frequently asked questions about research paper conclusions.
The first task of your conclusion is to remind the reader of your research problem . You will have discussed this problem in depth throughout the body, but now the point is to zoom back out from the details to the bigger picture.
While you are restating a problem you’ve already introduced, you should avoid phrasing it identically to how it appeared in the introduction . Ideally, you’ll find a novel way to circle back to the problem from the more detailed ideas discussed in the body.
For example, an argumentative paper advocating new measures to reduce the environmental impact of agriculture might restate its problem as follows:
Meanwhile, an empirical paper studying the relationship of Instagram use with body image issues might present its problem like this:
Avoid starting your conclusion with phrases like “In conclusion” or “To conclude,” as this can come across as too obvious and make your writing seem unsophisticated. The content and placement of your conclusion should make its function clear without the need for additional signposting.
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Having zoomed back in on the problem, it’s time to summarize how the body of the paper went about addressing it, and what conclusions this approach led to.
Depending on the nature of your research paper, this might mean restating your thesis and arguments, or summarizing your overall findings.
In an argumentative paper, you will have presented a thesis statement in your introduction, expressing the overall claim your paper argues for. In the conclusion, you should restate the thesis and show how it has been developed through the body of the paper.
Briefly summarize the key arguments made in the body, showing how each of them contributes to proving your thesis. You may also mention any counterarguments you addressed, emphasizing why your thesis holds up against them, particularly if your argument is a controversial one.
Don’t go into the details of your evidence or present new ideas; focus on outlining in broad strokes the argument you have made.
In an empirical paper, this is the time to summarize your key findings. Don’t go into great detail here (you will have presented your in-depth results and discussion already), but do clearly express the answers to the research questions you investigated.
Describe your main findings, even if they weren’t necessarily the ones you expected or hoped for, and explain the overall conclusion they led you to.
Having summed up your key arguments or findings, the conclusion ends by considering the broader implications of your research. This means expressing the key takeaways, practical or theoretical, from your paper—often in the form of a call for action or suggestions for future research.
An argumentative paper generally ends with a strong closing statement. In the case of a practical argument, make a call for action: What actions do you think should be taken by the people or organizations concerned in response to your argument?
If your topic is more theoretical and unsuitable for a call for action, your closing statement should express the significance of your argument—for example, in proposing a new understanding of a topic or laying the groundwork for future research.
In a more empirical paper, you can close by either making recommendations for practice (for example, in clinical or policy papers), or suggesting directions for future research.
Whatever the scope of your own research, there will always be room for further investigation of related topics, and you’ll often discover new questions and problems during the research process .
Finish your paper on a forward-looking note by suggesting how you or other researchers might build on this topic in the future and address any limitations of the current paper.
Full examples of research paper conclusions are shown in the tabs below: one for an argumentative paper, the other for an empirical paper.
While the role of cattle in climate change is by now common knowledge, countries like the Netherlands continually fail to confront this issue with the urgency it deserves. The evidence is clear: To create a truly futureproof agricultural sector, Dutch farmers must be incentivized to transition from livestock farming to sustainable vegetable farming. As well as dramatically lowering emissions, plant-based agriculture, if approached in the right way, can produce more food with less land, providing opportunities for nature regeneration areas that will themselves contribute to climate targets. Although this approach would have economic ramifications, from a long-term perspective, it would represent a significant step towards a more sustainable and resilient national economy. Transitioning to sustainable vegetable farming will make the Netherlands greener and healthier, setting an example for other European governments. Farmers, policymakers, and consumers must focus on the future, not just on their own short-term interests, and work to implement this transition now.
As social media becomes increasingly central to young people’s everyday lives, it is important to understand how different platforms affect their developing self-conception. By testing the effect of daily Instagram use among teenage girls, this study established that highly visual social media does indeed have a significant effect on body image concerns, with a strong correlation between the amount of time spent on the platform and participants’ self-reported dissatisfaction with their appearance. However, the strength of this effect was moderated by pre-test self-esteem ratings: Participants with higher self-esteem were less likely to experience an increase in body image concerns after using Instagram. This suggests that, while Instagram does impact body image, it is also important to consider the wider social and psychological context in which this usage occurs: Teenagers who are already predisposed to self-esteem issues may be at greater risk of experiencing negative effects. Future research into Instagram and other highly visual social media should focus on establishing a clearer picture of how self-esteem and related constructs influence young people’s experiences of these platforms. Furthermore, while this experiment measured Instagram usage in terms of time spent on the platform, observational studies are required to gain more insight into different patterns of usage—to investigate, for instance, whether active posting is associated with different effects than passive consumption of social media content.
If you’re unsure about the conclusion, it can be helpful to ask a friend or fellow student to read your conclusion and summarize the main takeaways.
You can also get an expert to proofread and feedback your paper with a paper editing service .
The conclusion of a research paper has several key elements you should make sure to include:
No, it’s not appropriate to present new arguments or evidence in the conclusion . While you might be tempted to save a striking argument for last, research papers follow a more formal structure than this.
All your findings and arguments should be presented in the body of the text (more specifically in the results and discussion sections if you are following a scientific structure). The conclusion is meant to summarize and reflect on the evidence and arguments you have already presented, not introduce new ones.
If you want to cite this source, you can copy and paste the citation or click the “Cite this Scribbr article” button to automatically add the citation to our free Citation Generator.
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Reporting by Jayshree.P. Upadhyay; Additional reporting by Ira Dugal, Neha Arora and Jahnavi Nidumolu; Editing by Jacqueline Wong, William Mallard, David Goodman and Toby Chopra
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U.S. Republican Senator Lindsey Graham called Ukraine's shock cross-border operation into Russia's Kursk region "brilliant" and "bold" in a visit to Kyiv on Monday, and he urged the Biden administration to provide Ukraine with the weapons it needs.
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A research report is one big argument how and why you came up with your conclusions. To make it a convincing argument, a typical guiding structure has developed. In the different chapters, distinct issues need to be addressed to explain to the reader why your conclusions are valid. The governing principle for writing the report is full disclosure: to explain everything and ensure replicability by another researcher.
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Field, A. (2016). An adventure in statistics. The reality enigma . SAGE.
Field, A. (2020). Discovering statistics using IBM SPSS statistics (5th ed.). SAGE.
Früh, M., Keimer, I., & Blankenagel, M. (2019). The impact of Balanced Scorecard excellence on shareholder returns. IFZ Working Paper No. 0003/2019. Retrieved June 09, 2021, from https://zenodo.org/record/2571603#.YMDUafkzZaQ .
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Hunziker, S., Blankenagel, M. (2021). Writing up a Research Report. In: Research Design in Business and Management. Springer Gabler, Wiesbaden. https://doi.org/10.1007/978-3-658-34357-6_4
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The Stanford Doerr School of Sustainability has selected eight interconnected Solution Areas to focus its research efforts over the next decade. This new research plan amplifies the school’s ability to translate Stanford research into large-scale solutions and inform key decision makers in policy and business.
Selected based on extensive faculty input and assessment of where Stanford can make the most meaningful impact, the eight areas are: climate; water; energy; food; risk, resilience, and adaptation; nature; cities; and platforms and tools for monitoring and decision making.
“Solution Areas identify and leverage the critical junctions between the most pressing global sustainability challenges and the areas where Stanford has the talent and expertise to find solutions,” said Dean Arun Majumdar. “This collaborative all-campus approach expands and strengthens our commitment to using all the power we have – the knowledge, the education, the talent, the innovation, the resources, the influence – to build a thriving planet for future generations.”
In each Solution Area, the school plans to build two types of research initiatives. One type, called Integrative Projects, will be managed by the school’s institutes, including the Stanford Woods Institute for the Environment , the Precourt Institute for Energy , and a planned Sustainable Societies Institute.
Integrative Projects will be organized around decade-long research themes and dedicated to creating solutions through interdisciplinary collaboration, engagement with partners beyond Stanford, identifying significant knowledge gaps, and understanding systems.
According to Chris Field , the Perry L. McCarty Director of the Stanford Woods Institute for the Environment and a professor in the Stanford Doerr School of Sustainability and the School of Humanities and Sciences , the new commitment to these areas “will provide both resources and coordination that expand Stanford faculty’s capacity to deliver sustainability solutions at scale.”
A second type of research initiative, called Flagship Destinations, is managed by Stanford’s Sustainability Accelerator . Flagship Destinations are targets for the pace and scale of work to address challenges facing Earth, climate, and society. For example, the school’s first Flagship Destination, announced in 2023 , calls for enabling the removal of billions of tons of planet-warming gases annually from Earth’s atmosphere by the middle of this century. By working backward from sustainability targets in consultation with faculty and external experts, this initiative seeks to rapidly translate Stanford research into policy and technology solutions. Additional Flagship Destinations will be announced later this week.
Whereas Integrative Projects are designed to produce knowledge and evidence that can eventually lead to solutions, Flagship Destination projects are intended to help verify and demonstrate that well-studied solutions can succeed at large scale so they can be launched out of Stanford and implemented for the benefit of humanity and our planet. Scalable solutions nurtured and launched through these projects could take the form of policy frameworks, open-source platforms, nonprofit organizations, new for-profit companies, and ongoing collaborations all committed to addressing pressing sustainability challenges.
“By working together in these Solution Areas across disciplines and with collaborators beyond the university, we maximize our ability to have positive impacts on the timeframe and scale needed for the planet and humanity,” said Scott Fendorf , senior associate dean for integrative initiatives and the Terry Huffington Professor in the Stanford Doerr School of Sustainability.
Workshops will be held with faculty and external experts to develop research strategies for each Solution Area on a rolling basis. Strategy workshops, opportunities to provide input on future Integrative Projects, and requests for proposals (open to all Stanford faculty) will be announced in the coming months.
Related message from leadership: Read a letter to faculty about the new Solution Areas from Dean Majumdar with Precourt Institute for Energy director William Chueh; Stanford Woods Institute for the Environment director Chris Field; Accelerator faculty director Yi Cui and executive director Charlotte Pera; and Integrative Initiatives associate dean Jenna Davis and senior associate dean Scott Fendorf.
Shares of Indian conglomerate Adani Group’s listed firms slumped Monday, after a report by U.S. short seller Hindenburg Group accused the head of India’s market regulator of a conflict of interest that allegedly prevented a proper investigation into Hindenburg’s earlier claims of fraud and stock manipulation by the billionaire-owned conglomerate.
Adani Group chairperson and founder Gautam Adani's fortune slipped again on Monday after ... [+] Hindenburg's latest report.
Shares of the conglomerate’s flagship firm Adani Enterprises dropped more than 5% to $35.9 (Rs 3,013) after Indian stock markets opened on Monday, before recovering to $37.42 (Rs 3,145).
Adani Power’s shares dropped more than 10% to $7.37 (Rs 619), but soon recovered to $8.04 (Rs 675)—down 2.9% from Friday’s closing.
Shares of the group’s other key listed firms—Adani Energy, Adani Green, Adani Total Gas and Adani Ports—were also hit on Monday, falling between 1-4%.
In a report published Saturday, New York-based short seller Hindenburg Research alleged Madhabi Puri Buch, the chair of the Securities and Exchange Board of India (SEBI), and her husband, Dhaval Buch, invested in offshore funds linked to Adani in Bermuda and Mauritius.
Adani’s brother Vinod Adani allegedly used these funds to purchase and trade “large positions in shares of the Adani Group,” the report alleged.
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According to our estimates , Gautam Adani’s net worth is $83.8 billion, down $1.5 billion due to Monday’s selloff. Despite this, he remains both India’s and Asia’s second richest person behind Mukesh Ambani.
Buch and her husband made the investments in 2015—two years before she joined SEBI, the report said, citing “whistleblower documents.” The Adani Group has dismissed Hindenburg’s allegations calling them “malicious, mischievous and manipulative selections of publicly available information to arrive at pre-determined conclusions for personal profiteering with wanton disregard for facts and the law.”
Hindenburg disclosed a short position against the Adani Group’s listed firms in January 2023 and published a report accusing the conglomerate of engaging in “brazen stock manipulation and accounting fraud scheme over the course of decades.” The report caused Adani’s fortune to tank sharply, dropping from a high of $126 billion in January 2023 to less than $50 billion later in the year. The company vehemently denied these allegations and its billionaire founder labeled them a “malicious” attack on his company and India’s economic growth. The controversy spiraled into a political issue in India due to Adani’s decades-long close relationship with Indian Prime Minister Narendra Modi. Earlier this year, the Supreme Court rejected a request for an independent probe into Hindenburg’s allegations and the short seller was hit with a show cause notice by SEBI for violating Indian securities laws.
Buch responded to Hindenburg’s allegations in a statement on Sunday: “The investment in the fund referred to in the Hindenburg report was made in 2015” when the Buchs were “both private citizens living in Singapore and almost 2 years before Madhabi joined SEBI.” The two consulting companies set up by Buch when she was in Singapore “became immediately dormant on her appointment with SEBI” and were “explicitly part of her disclosures.” The Buchs criticized Hindenburg, claiming the short seller had been served a “show cause notice for a variety of violations in India” and in response “they have chosen to attack the credibility of the SEBI and attempt character assassination of the SEBI Chairperson.” In response, Hindenburg tweeted : “Buch’s response now publicly confirms her investment in an obscure Bermuda/Mauritius fund structure, alongside money allegedly siphoned by Vinod Adani. She also confirmed the fund was run by a childhood friend of her husband, who at the time was an Adani director.”
India’s opposition parties criticized the government and have called for Buch’s resignation. Rahul Gandhi, the leader of the opposition in Parliament, responded to Hindenburg’s report: “This is an explosive allegation because it alleges the umpire herself is compromised. The savings of millions of Indians…are at risk, it is therefore imperative that this matter is investigated… If investors lose their hard-earned money, who will be held accountable—PM Modi, the SEBI Chairperson, or Gautam Adani?”
Indian Billionaire Adani Attacks 'Malicious' Hindenburg Report—And Invokes Nationalism Again (Forbes)
Adani Group Shares Slide After Hindenburg Alleges ‘Largest Con In Corporate History’ (Forbes)
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Indian billionaire gautam adani loses another $2.4b after fresh hindenburg allegations.
Adani Group, the Indian conglomerate rocked by a Hindenburg Research report last year , faced another heavy share selloff on Monday after the shortseller accused the head of India’s market regulator of having links to offshore funds also used by the group.
About $2.4 billion, or 1%, had been wiped off the market value of Adani companies by the end of the trading day, although that was a substantial recovery from earlier losses of more than $13 billion.
The battle between Hindenburg Research and the Gautam Adani’s Adani Group began 18 months ago when the US shortseller alleged Adani improperly used tax havens, accusations the group denied again on Sunday, saying its overseas holding structure was fully transparent.
Citing whistleblower documents, Hindenburg said on Saturday that Madhabi Puri Buch, chair of the Securities and Exchange Board of India (SEBI) since 2022, has a conflict of interest in the Adani matter due to previous investments.
Buch said the report’s allegations were baseless and in a separate statement the regulator said allegations made by Hindenburg Research against the Adani Group have been duly investigated.
Shares in the group’s flagship firm Adani Enterprises closed out Monday 1.1% lower, while Adani Ports, Adani Total Gas, Adani Power, Adani Wilmar and Adani Energy Solutions were down between 0.6% and 4.2%. Only Adani Green bucked the trend, closing 1% higher.
“The allegations are coming for the second time. Lot of investigations have happened over the last year and a half. This is a temporary, knee-jerk reaction. Things will get back to normalcy,” said Sunny Agrawal, head of fundamental equity research at SBICAPS Securities.
Investments from Abu Dhabi-based International Holding and US boutique investment firm GQG Partners have helped restore some investor confidence since Hindenburg’s first report in January 2023, with Adani Group’s share value losses narrowing to about $32.5 billion from $150 billion in the immediate aftermath.
Buch termed Hindenburg’s allegations an attempt at “character assassination” following the regulator’s enforcement action and “show cause” notice to the shortseller for violating Indian rules.
A show cause notice signals an intention to take disciplinary action if satisfactory explanations are not provided.
Adani Enterprises is looking to launch a $1 billion share sale by mid-September, having shelved a record $2.5 billion offer in the wake of Hindenburg’s first set of allegations.
Adani Energy raised $1 billion from US investors and sovereign wealth funds earlier this month.
“We will likely see a short to medium term sentiment impact on Adani stocks, especially as retail investors are pressurized by the allegations made against SEBI,” said Kranthi Bathini, Director, Equity Strategy, WealthMills Securities.
As the latest allegations gained political traction, ruling Bharatiya Janata Party lawmaker Ravi Shankar Prasad said: “Instead of giving a response to the SEBI show cause notice, Hindenburg has issued this report, which is a baseless attack.”
“The SEBI and the family (of Buch) have responded, we don’t have anything to add to that,” he told reporters.
However, opposition leader Rahul Gandhi said on X: “The integrity of SEBI, the securities regulator entrusted with safeguarding the wealth of small retail investors, has been gravely compromised by the allegations against its chairperson.”
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Nature Communications volume 15 , Article number: 6601 ( 2024 ) Cite this article
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Understanding protein function is pivotal in comprehending the intricate mechanisms that underlie many crucial biological activities, with far-reaching implications in the fields of medicine, biotechnology, and drug development. However, more than 200 million proteins remain uncharacterized, and computational efforts heavily rely on protein structural information to predict annotations of varying quality. Here, we present a method that utilizes statistics-informed graph networks to predict protein functions solely from its sequence. Our method inherently characterizes evolutionary signatures, allowing for a quantitative assessment of the significance of residues that carry out specific functions. PhiGnet not only demonstrates superior performance compared to alternative approaches but also narrows the sequence-function gap, even in the absence of structural information. Our findings indicate that applying deep learning to evolutionary data can highlight functional sites at the residue level, providing valuable support for interpreting both existing properties and new functionalities of proteins in research and biomedicine.
Introduction.
Proteins bind to other molecules to facilitate nearly all essential biological activities. Consequently, understanding protein function is of paramount importance for comprehending health, disease, evolution, and the functioning of living organisms at the molecular level 1 , 2 , 3 . The primary sequence of a protein contains all the essential information required to fold up into a particular three-dimensional shape, thereby determining its activities within cells 4 , 5 . The evolutionary information in massive protein sequences that are gleaned from extensive genome sequencing efforts has significantly contributed to recent advances in protein structure prediction 6 , 7 , 8 , 9 . This evolutionary data, especially the couplings between pairwise residues, has also been utilized to characterize protein functional sites 10 , 11 . The evolutionary couplings have been utilized to pinpoint functional sites in proteins, capturing interactions between residues that contribute to specific functions 5 , 12 . Indeed, the analysis of evolutionary information has allowed the identification of allosteric mechanisms in proteins 13 , 14 , disease variants 15 , and metamorphism in proteins that undergo reversible switches between distinct folds, often accompanied by different functions 16 .
To date, more than 356 million proteins in the UniProt database 17 (6/2023) have been sequenced and the vast majority (~80%) of these have no known functional annotations (e.g., enzyme commission numbers and gene ontology terms). Classical methods for annotating protein functions have been constrained by the extensive sizes of sequences, and the majority of function annotations are assigned at the protein level rather than the residue level 18 , 19 . As an alternative to these classical methods, computational approaches have been utilized to assign function annotations to proteins 20 , 21 , 22 , 23 , 24 . Notably, deep learning methods have attained remarkable accuracy in predicting protein 3D structures, surpassing the capabilities of classical approaches such as ab initio methods and homology modeling. These methods involve millions of parameters and operate without making any assumptions about the relationship between input and output data samples (e.g., AlphaFold 8 and RoseTTAFold 9 ). Unlike the classical approaches, deep learning-based methods learn a large amount of parameters directly through the training of neural networks on extensive datasets. This enables them to generate accurate mappings from input data to expected outputs. Yet accurately assigning function annotations to proteins remains challenging, especially in comparison to experimental determinations. While there is abundant data available–whether from a single amino acid sequence, alignments of numerous homologous sequences, or protein structural information–to train deep learning-based methods, achieving accurate protein function prediction remains a persistent challenge 20 , 21 , 22 , 23 , 24 , 25 . Integrating physics-based knowledge from provided datasets, physics-informed deep learning methods have driven recent advances across diverse fields 26 . As a promising alternative to classical and pure deep learning techniques, they enhance the capacity of machine learning to construct interpretable methods for scientific problems. Despite decades of dedicated effort, assigning a function to a protein is more arduous than predicting its 3D structure 21 , 27 , 28 , 29 , 30 . The state-of-the-art approaches that utilize structural information have encountered less success in accurately assigning protein functions 21 . This is largely attributed to the scarcity of experimentally determined protein structures in comparison to the abundance of available sequences. Moreover, computationally predicted structures vary in their confidence scores and may not always be reliable for estimating protein function annotations, leading to variable accuracy in function annotation 21 , 30 . Furthermore, assessing the significance of residues using a scoring function that reliably measures their contributions to function remains challenging, as a quantitative characterization of residue roles is not yet fully comprehended.
To address these challenges, we hypothesized that the information encapsulated in coevolving residues can be leveraged to annotate functions at the residue level. Here, we devised a statistics-informed learning approach, termed PhiGnet, to facilitate the functional annotation of proteins and the identification of functional sites. Our method capitalizes on the knowledge derived from evolutionary data to drive two stacked graph convolutional networks. Empowered by the acquired knowledge and designed network architecture, the present method can accurately assign function annotations to proteins and, importantly, quantify the significance of each individual residue with respect to specific functions.
In this study, we developed the PhiGnet method using statistics-informed graph networks to annotate protein functions and to identify functional sites across species based on their sequences (Fig. 1 ). To assimilate knowledge from the evolutionary couplings (EVCs, relationships between pairwise residues at two co-variant sites) and the residue communities (RCs, hierarchical interactions among residues) 12 , we devised the method with a dual-channel architecture, adopting stacked graph convolutional networks (GCNs) (Fig. 1 a). This method specializes in assigning functional annotations, including Enzyme Commission (EC) numbers and Gene Ontology (GO) terms (biological process, BP, cellular component, CC, and molecular function, MF), to proteins. When provided with a protein sequence, we derive its embedding using the pre-trained ESM-1b model 31 . Subsequently, we input the embedding as graph nodes, accompanied by EVCs and RCs (graph edges), into the six graph convolutional layers of the dual stacked GCNs. These layers, working in conjunction with a block of two fully connected (FC) layers, meticulously process the information from the two GCNs, ultimately generating a tensor of probabilities for assessing the viability of assigning functional annotations to the protein. In addition, an activation score, derived using the gradient-weighted class activation maps (Grad-CAMs) approach 32 , is used to assess the significance of each individual residue in a specific function. The score allows PhiGnet to pinpoint functional sites at the level of individual residues (bottom, Fig. 1 c, see Methods).
a PhiGnet predicts protein function from sequence alone. Given a sequence, PhiGnet learns the pre-embedding, EVCs, and RCs using stacked GCNs to infer protein function annotations. b RCs of the Serine-aspartate repeat-containing protein D (SdrD, PDB ID: 4JDZ). The two communities (community I and community II) with coupling strengths in bars are highlighted in red and blue. Each bar in either community I or II illustrates the strength of coupling that a residue has with others, while the conservation scores of these residues are depicted in the bars on the right. On the tertiary structure of SdrD (right), the residues within the community I (red) bind to the calcium ions (sphere in yellow) are shown in sticks, while the residues within the community II (blue) adopt cartoon in blue. c Function annotations of the MgIA protein at the residue level. The activation score (bottom) computed by PhiGnet is to measure the importance of each residue, where the higher the score is, the more likely it is to adopt a functional role in biological activity. Compared to functional sites in BioLip (marked with Y in black), the score indicates that co-evolved residues may be more important than those at conserved positions (top). The scores are mapped to color the MgIA 3D structure (PDB ID: 6IZW) from lower (blue) to higher (red), GDP is shown with sphere in yellow, SO 4 in stick in cyan, and Mg 2+ ion in a sphere with orange. Source data are provided as a Source Data file.
As an example, we computed RCs for the Serine-aspartate repeat-containing protein D (SdrD) that promotes bacterial survival in human blood by inhibiting innate immune-mediated bacterial killing 33 , 34 . Two RCs are mapped on a fully β sheet fold that binds to three Ca 2+ ions ( 1 Ca 2+ is enclosed in a loop, 2 Ca 2+ is more solvent exposed and closer to 3 Ca 2+ , which is coordinated by an asparagine (N564) and an aspartic acid (D665), Fig. 1 b). Within the community I, most residues (in red sticks) that are identified from EVCs bind to the three Ca 2+ ions, contributing together to stabilize the SdrD fold. This suggests that EVCs contain the essential information for deducing the functional role of residues, even when they are sparsely distributed across RCs. Empowered by EVCs and RCs, we implemented the present PhiGnet to assess the functional significance of residues. We carried out PhiGnet to calculate the activation scores for the functional sites of the mutual gliding-motility (MgIA) protein (annotated with EC 3.6.5.2) (Fig. 1 c). The resulting activation scores show that the residues with high scores ( ⩾ 0.5) are in agreement with or close to that of semi-manually curated BioLip database 35 . Moreover, these residues are located at the most conserved positions (top left, Fig. 1 c). Upon mapping these scores onto the 3D structure of MgIA, the activation scores highlight residues (red) that constitute a pocket that binds the guanosine di-nucleotide (GDP) and play a role in facilitating nucleotide exchange 36 . Together, this suggests that residues at functional sites are conserved through natural evolution, and that PhiGnet is capable of capturing such information, improving the method for predicting protein function at the residue level, even in the absence of structural data.
Many proteins perform their biological functions through essential residues that are sparsely distributed across different structural levels (e.g., primary, secondary, and tertiary) and are linked to functional sites (such as enzyme active sites, ligand-binding sites, or protein-protein interaction sites). Given the functional contributions of amino acids can significantly differ from one function to another, a key feature of PhiGnet is its ability to quantitatively estimate the importance of individual amino acids for a specific function, enabling us to identify residues that are pertinent to distinct biological activities.
Are the computational predictions as accurate as experimentally determined function annotations? To address this question, we carried out quantitative examinations of the contribution of each amino acid to a protein function using the activation score. We evaluated the predictive performance of PhiGnet and assessed the importance of residues (their contributions to protein function) in nine proteins: the c2-domain of cytosolic phospholipase A 2 α (cPLA 2 α ), Tyrosine-protein kinase BTK (TpK-BTK), Ribokinase, alpha-lactalbumin ( α LA), MCM1 transcriptional regular (MCM1-TR), the Fos-Jun heterodimer (FosJun), the thymidylate kinase (TmpK), Ecl18kI, and helicobacter pylori uridylate kinase (HPUK). These proteins vary in size from approximately 60 to 320 residues, harbor different folds, and perform diverse functions, including ligand binding, ion interaction, and DNA binding. We calculated the activation score for each residue in the nine proteins, comparing them to residues identified through either experimental or semi-manual annotations. Our method demonstrated promising accuracy (with an average ⩾ 75%) in predicting significant sites at the residue level, in a good agreement with actual ligand-/ion-/DNA-binding sites (Fig. 2 ). The activation score per residue, mapped onto their 3D structures, exhibits significant enrichment for functional relevance at the binding interfaces. PhiGnet accurately identifies functionally significant residues with high activation scores for the proteins (Fig. 2 , Supplementary Figs. S1 and S2) .
a The activation score of each residue is predicted using PhiGnet and compared to the biologically relevant ligand-protein binding sites from the BioLiP database. b The activation scores are mapped to the tertiary structures of nine proteins, including (left to right, top to bottom) the c2-domain of cytosolic phospholipase A 2 α (cPLA 2 α , PDB ID: 6IEJ) 37 , Tyrosine-protein kinase BTK (TpK-BTK, PDB ID: 6W8I), Ribokinase (PDB ID: 6XK2), alpha-lactalbumin ( α LA, PDB ID: 1HFX) 38 , MCM1 transcriptional regular (MCM1-TR, PDB ID: 1MNM) 60 , the Fos-Jun heterodimer (FosJun, PDB ID: 1FOS) 61 , the thymidylate kinase (TmpK, PDB ID: 3TMK) 62 , Ecl18kI (PDB ID: 2GB7) 39 , and helicobacter pylori uridylate kinase (HPUK, PDB ID: 4A7W) 63 . Source data are provided as a Source Data file.
Across the proteins cPLA 2 α , Ribokinase, α LA, TmpK, and Ecl18kI, PhiGnet predicted near-perfect functional sites compared to the experimental identifications. For instance, for cPLA 2 α , our method accurately identified residues, Asp40, Asp43, Asp93, Ala94 and Asn95, that bind to 1 Ca 2+ and residues, Asp40, Asp43, Asn65 and Thr41, that bind to 4 Ca 2+ , as well as a residue Asn65 supports 3 Ca 2+ for stabilizing fold 37 . Moreover, our method predicted a high score (0.6) for the residue Tyr96, which plays a crucial role in lipid headgroup recognition through cation- π interaction with the phosphatidylcholine trimethylammonium group 37 . We also applied PhiGnet to α LA, which contains a single, tightly bound calcium ion that is cradled in the EF-hand motif to stabilize the protein against denaturation 38 . In the α LA protein, the important motif is computationally characterized by a constellation of residues: Lys79, Asp82, Asp84, Asp87, and Asp88. In Ecl18kI, the major groove contacts the bases of the recognition sequence through the three consecutive residues Arg186, Glu187 and Arg188. Specifically, Arg186 and Arg188 form bidentate hydrogen bonds to the outer and inner guanines, respectively. The side chain oxygen atoms of Glu187 each accept one hydrogen bond from the two neighboring cytosines of the recognition sequence. Moreover, the sequence-specific minor groove contacts are exclusively mediated by Glu114 39 . To evaluate the importance of each residue in Ecl18kI, we computed the activation scores for each residue. These scores confirmed the agreement between the residues captured by PhiGnet and those identified through experimental data. For the proteins MCM1-TR and FosJun, our method captured residues with top activation scores that bind to DNAs, although not all of the residues at functional sites were characterized by high probabilities. Meanwhile, the activation scores failed to highlight function-relevant sites for a few residues. For instance, few residues with scores >0.5 were not located at the functional sites in Ribokinase, α LA, and HPUK. This discrepancy could be attributed to the noise present in EVCs. Together, the activation scores can indicate essential ligand-/ion-contacting residues, suggesting that learning from diverse levels of evolutionary knowledge can identify binding interfaces at the residue level. Such capability would be valuable in discerning interfaces both inter- and intra-proteins, even in the absence of structural information. Moreover, the predictions suggest that learning from evolutionary knowledge enables us to understand residues arranged in highly ordered patterns, relevant to diverse binding activities. On the other hand, biases originating from the evolutionary data could obscure the activation scores for accessing the functional significance of residues. Collectively, the activation scores can underscore essential ligand-/ion-contacting residues, indicating that learning from diverse levels of evolutionary knowledge can effectively identify binding interfaces at the residue level. Conversely, noise originating from the evolutionary data could influence the activation scores, potentially leading to biases in the identification of functional sites.
To assess the predictive performance of PhiGnet, we implemented the method to infer function annotations (EC numbers and GO terms) for proteins in the two benchmark test sets (see Methods). We proceeded to compare our method against state-of-the-art methods, including alignment-based methods (BLAST 18 , FunFams 40 , and Pannzer 41 ), deep learning-based methods (DeepGO 25 , DeepFRI 21 , DeepGOWeb 42 , ProteInfer 43 , SPROF-GO 44 , ATGO+ 45 , and CLEAN 46 ). Two essential metrics, including the protein-centric F m a x -score and the area under the precision-recall curve (AUPR), were utilized for the comparisons. Our method demonstrated predictive capabilities for assigning function annotations to proteins across the two test sets. It achieved an average AUPR of 0.70 and 0.89, as well as F m a x scores of 0.80 and 0.88, for GO terms and EC numbers, respectively (Fig. 3 ). Moreover, it consistently maintained strong performance, with average AUPR scores of 0.64, 0.65, and 0.80, alongside corresponding F m a x values of 0.82, 0.75, and 0.81, for the three branches of GO terms – CC, BP, and MF (Fig. 3 d). Overall, PhiGnet significantly outperformed all supervised and unsupervised approaches across the benchmark datasets. For example, in the benchmark of EC numbers, we compared the predictions of various methods, including BLAST, FunFams, DeepGO, DeepFRI, Pannzer, ProteInfer, and CLEAN, against experimentally determined function annotations across the test proteins. Our method yielded F m a x score of 0.88 and AUPR of 0.89, surpassing the performance of other approaches (Fig. 3 a, b, Supplementary Fig. S3) . All the compared methods exhibited various performances, as illustrated in the precision-recall curves. DeepFRI, Pannzer, and ProteInfer achieved a similar F m a x score, approximately 0.68, outperforming BLAST and DeepGO. In terms of AUPR, FunFams, DeepFRI, and CLEAN yielded similar performances, which were better than those of ProteInfer and Pannzer. PhiGnet achieved F m a x of 0.88 and AUPR of 0.89, respectively, outperforming the CNN-based DeepGO (F m a x of 0.37 and AUPR of 0.21), structure-based DeepFRI (F m a x of 0.69 and AUPR of 0.70), and the contrastive learning-based CLEAN (F m a x of 0.76 and AUPR of 0.70) (Fig. 3 a, b, Supplementary Fig. S3) . These results suggest that PhiGnet has the ability to achieve accurate assignment of EC numbers to proteins. In the benchmark of GO terms, we compared our method against nine state-of-the-art methods, utilizing the same metrics to evaluate their performance. Across predictions of CC, BP, MF ontologies, PhiGnet achieved F m a x of 0.82, 0.75, 0.81 and AUPR of 0.64, 0.65, 0.80, respectively, which are significantly better than those of the compared methods. Notably, although ensemble-networks-based ProteInfer outperformed the remaining approaches over MF and BP ontologies, and the alignment-free SPROF-GO and structure-based DeepFRI excelled over CC ontology, PhiGnet’s performance remained superior (Fig. 3 d, e, Supplementary Figs. S4 – S7 , and Table S1) . Comparing predictive performances on the GO terms, we found that PhiGnet achieved first place in both accuracy and robustness, significantly better than the eight methods above and another prediction from a web server, DeepGOWeb (Fig. 3 d–f).
a Precision-recall curves illustrate the performance of different methods in predicting EC numbers for proteins. b Protein-centric F m a x scores and function-centric AUPR scores are computed across all test proteins to predict EC numbers, where the scores are presented as mean values with standard deviations of 10 bootstrap iterations. c Evaluation of robustness in predicting EC numbers as sequence identity increases, where the F m a x scores of each method at different sequence identities are depicted as boxplots of 50 bootstrap iterations, with the median values at the center and the interquartile range shown by the upper and lower edges of the boxes. d Precision-recall performance across GO terms in different ontologies. e Left, violin plots showing AUPR with the median values at the center of the distribution of 10 bootstrap iterations, and right, F m a x scores for the different methods in predicting CC, BP, and MF. f Computed Matthews correlation coefficient between predicted scores and ground-truth values for both EC numbers and GO terms using different methods. Source data are provided as a Source Data file.
Moreover, we demonstrated the robustness of PhiGnet for generalization to test proteins with varying thresholds of sequence identity compared to the proteins in the training set. At various maximum sequence identity levels (30%, 40%, 50%, 70%, and 95%), PhiGnet exhibited improved predictive performance as sequence identity increased (Fig. 3 c, Supplementary Fig. S5) . PhiGnet has been ranked among the top two robust methods for the test set of EC numbers, demonstrating consistently predictive performance with F m a x values of 0.61 and 0.72 at sequence identity levels of 30% and 40%, respectively. When compared to the domain-based method FunFams (F m a x of 0.67 and 0.74), PhiGnet slightly underperformed at sequence identity thresholds of 30% and 40%. However, PhiGnet achieved comparable or better performance when sequence identity exceeded 50%. Similarly, the performance of DeepFRI, FunFams, ProteInfer, and CLEAN also improved as sequence identity increased. Pannzer exhibited a similar trend when sequence identity was below 50%, but its performance remained nearly constant with a slight decrease in F m a x . In contrast, both BLAST and DeepGO showed slight improvements as the proteins in the test set increased sequence identity to those in the training set. The robustly predictive performance of PhiGnet has also been demonstrated by predicting the three branches of GO terms, maintaining high accuracy even at low sequence identity (Supplementary Fig. S5) . In predictions of both EC numbers and GO terms, we also calculated the Matthew’s correlation coefficient (MCC) between the predicted scores and ground truth to quantitatively compare the performance of various methods. PhiGnet achieved an average MCC of 0.76, which is higher than the average MCCs of the other ten state-of-the-art methods (Fig. 3 f).
The evolutionary data plays an important role in PhiGnet for predicting protein function annotations and identifying functional sites. First, we performed ablation experiments to test how EVCs/RCs contribute to PhiGnet. We trained PhiGnet using either EVCs or RCs alone and assessed its performance in terms of F m a x -score and AUPR over predictions of EC numbers/GO terms. To accomplish this, we chose a threshold (0.2) for both EVCs and RCs based on the similar performances in predicting EC numbers/GO terms (Supplementary Fig. S8) , aiming to mitigate potential noise arising from coevolution or weak couplings between pairwise residues. We first test whether the information in EVCs, which preserve evolutionary couplings at sites of co-variation, is sufficient to infer functional annotations. The second experiment tests the necessity of information in RCs that independently capture high-order couplings. Similarly, we built a model using RCs alone to computationally assign functional labels to proteins, and this model produced slightly better predictions (Supplementary Figs. S9 and S10) . The two experiments indicate that both models demonstrate the capability to accurately assign functional annotations to proteins. Moreover, PhiGnet, utilizing either EVCs or RCs, demonstrates a robust capacity to learn general sequence-function relationships, often better than or as good as other approaches, even test proteins exhibiting low sequence identity in presence of the training set (Fig. 3 c, Supplementary Figs. S9c and S10c) . Through precision and robustness comparisons, we have demonstrated that the evolutionary signatures (EVCs and RCs) constitute crucial attributes capable of enhancing deep learning-based methods for protein function annotations.
Secondly, we asked whether the residues, particularly within RCs that are often relevant to the specific function, can be quantified for functional sites. To address this, we further investigated the capability of PhiGnet to characterize meaningful features from the identified function-relevant residues within the residue communities. The activation scores were computed for the residues to underscore their contributions to the protein function. Notably, the predicted residues concurred with those at the functional sites identified through experimental determinations, better identifications than those in RCs (Fig. 4 ). In the human cytidine deaminase (hCDA) protein 47 , compared to residues within RCs that were identified as functionally relevant, PhiGnet quantitatively characterized their importance in the binding between hCDA and Zn 2+ /BRD through more accurate predictions of active sites: Cys65, Cys99, and Cys102, which coordinate with the zinc ion, as indicated by the activation scores (Fig. 4 a). In the Peroxide operon regulator (PerR), we also observed that PhiGnet narrowed down the number of residues located within RCs 48 and effectively distinguished non-Zn 2+ -binding residues from the binding ones, compared to RCs. Specifically, Cys96, Cys99 and Cys136, Cys139 exhibited much higher activation scores. These residues collectively coordinate the zinc ion, locking the three β -strands together to form the arrangement of the dimeric β -sheet, in contrast to the non-binding residues (Fig. 4 b). In light of these results, we conclude that the evolutionary information, particularly that contained in RCs, is sufficient to specify a protein’s function and to quantitatively characterize the residues at the functional sites. Moreover, the results argue that RCs contain evolutionary knowledge at a higher-ordered level than the information in EVCs at a lower-ordered level. Meanwhile, information contained in RCs plays an important role in enhancing PhiGnet’s ability to identify functionally relevant sites at the residue level.
Mappings of RCs and activation scores of ( a ) the human cytidine deaminase protein (hCDA, PDB ID: 1MQ0-A, GO term 0008270), and ( b ) the Peroxide operon regulator (PDB ID: 2FE3-A, GO term 0046872). The residues within each RC are shown in the chord plotting with coupling strength and degree of conservation in bars. The activation scores (dotted lines) of each protein are compared to the BioLip identifications (marked with Y in black), and residues with high scores (in red) are also compared to those within RCs on their 3D structures. The 1-beta-ribofuranosyl-1,3-diazepinone (BRD) and Zn 2+ ions are shown with spheres in yellow (orange for the Zn 2+ ion in hCDA). Source data are provided as a Source Data file.
To assess whether the different performances of the methods under evaluation, and the superiority of PhiGnet were inherent to the algorithms or due to different training sets, we re-executed two alignment-based methods (BLAST and FunFams) and conducted retraining on four deep learning-based methods (DeepGO, ATGO+, SPROF-GO, and PhiGnet). Other methods were excluded primarily due to the unavailability of trainable source codes or because such method required unavailable structural information) against an identical dataset. We used the third Critical Assessment of Protein Function Annotation (CAFA3) dataset consisting of 66,841 proteins 49 . To address homology issues, proteins sharing over 30% sequence identity with the test proteins were excluded from the training dataset 45 . The remaining proteins were utilized to construct databases for BLAST and FunFams. 95% of them were randomly selected for training DeepGO, ATGO+, SPROF-GO, and PhiGnet, with the remaining 5% reserved for validation to fine-tune the methods’ parameters. Moreover, we conducted comparisons among the different methods using the CAFA3 test proteins either with less than 60% sequence identity to those in the training dataset or without redundancy removal (Supplementary Fig. S12) .
A comparison among the six different methods implemented on the CAFA3 dataset reveals that PhiGnet exhibits the best performance across both \({{{{\rm{F}}}}}_{\max }\) and AUPR metrics (Table 1 , Supplementary Fig. S12 ). PhiGnet achieved the highest \({{{{\rm{F}}}}}_{\max }\) scores across all three categories: BP (0.531), CC (0.584), and MF (0.606), indicating its superior capability in predicting functional annotations across diverse biological processes, cellular components, and molecular functions compared to methods such as BLAST, DeepGO, FunFams, and ATGO+. Furthermore, PhiGnet outperformed other methods with AUPR scores of 0.425 for BP, 0.590 for CC, and 0.571 for MF, demonstrating its effectiveness in accurately identifying true positive annotations while minimizing false positives across various functional categories. Although methods like BLAST, DeepGO, FunFams, and ATGO+ exhibited respectable performance in specific categories, none consistently achieved high scores across both \({{{{\rm{F}}}}}_{\max }\) and AUPR metrics as PhiGnet did. Overall, the comparison underscores PhiGnet as one of the state-of-the-art methods on the CAFA3 dataset, demonstrating that its increased performance is independent of the training dataset used.
Can PhiGnet annotate uncharacterized proteins? We carried out our predictions for the independent hold-out set of 6229 proteins (Supplementary Fig. S13 ). We followed the same procedures to collect EVCs, RCs, and sequence embeddings for all the proteins. They were utilized to feed into the fine-tuned PhiGnet in order to compute a probability tensor for assigning functional annotations to the proteins. Among the collected proteins, our method’s overall performance was superior to that of state-of-the-art methods. Given that these proteins were independently collected, our computational predictions can be valuable in assigning functional annotations to new proteins (Supplementary Figs. S14 , S15 , and Table S2 ). For example, across the T. forsythia NanH (PDB ID: 7QXO) and human Sar1b (PDB ID: 8E0A), the activation scores successfully indicate the functional sites that bind to Oseltamivir and guanosine tetraphosphate (Supplementary Fig. S16) . Our analysis shows that PhiGnet’s high confidence prediction is in a good agreement with experimental annotations, suggesting that it would contribute to computational efforts for assigning function annotations to proteins with unknown labels. This applies even when dealing with experimental annotations of lower confidence scores, and can benefit experimental investigations of different biological activities. Moreover, by leveraging evolutionary information, PhiGnet provides function annotations as well as residue-level activation scores for over 2.5 million individual sequences within the UniProt database. The activation score assigned to each individual residue offers a quantitative measure of its significance in a specific activity, proving beneficial for screening experiments aimed at identifying functionally important sites.
It has been long appreciated that investigating evolutionary information across species can further our understanding of protein function and of the consequences of pathological mutations, even at the residue level. By leveraging deep learning methods on continuously expanding sequencing data, we can extract valuable knowledge to accurately annotate protein functions. This can greatly benefit both biological and clinical research, as well as facilitate drug discovery.
We have demonstrated that a statistics-informed learning method trained solely on evolutionary data achieves state-of-the-art performance in predicting protein function annotations at the residue level. The approach presented here requires no inputs other than the protein sequence and learns its characterized embedding using the statistics-informed graph convolutional networks. We show that EVCs and RCs have crucial effects on the predictions of protein function annotations and on the identifications of residues at functionally relevant sites. Our method produces high-accuracy annotations and identifies functional sites at the residue level. Therefore, this approach is well-suited for gaining a better understanding of the biological activities of unannotated or poorly studied proteins, as well as for quantitatively investigating the effects of disease-related variants.
When evaluating the performance of the methods presented (see Fig. 3 ), it becomes evident that PhiGnet outperforms its counterparts due to its distinctive amalgamation of two key factors. Firstly, it integrates insights derived from both evolutionary coupling analysis and spectrum analysis, resulting in a more comprehensive grasp of the intricate relationship between protein sequences and their functions. In contrast, other methods, such as FunFams and Pannzer, predominantly rely on homology-based approaches. Although homology-based methods have their merits, they might not capture the subtle nuances and intricate connections between proteins that are unveiled by the evolutionary coupling data. Conversely, while DeepFRI, DeepGO, SPROF-GO, and ATGO+ depend on structural data and homologous information, they may not harness the same depth of evolutionary data as PhiGnet. Moreover, the spectrum analysis applied to evolutionary data delves into the high-order patterns within protein sequences, which also contributes to PhiGnet’s superior performance. Secondly, although DeepFRI, DeepGO, SPROF-GO, ATGO+, and CLEAN are effective in leveraging pre-trained models for protein function prediction, PhiGnet distinguishes itself by enhancing the pre-trained model with evolutionary insights. This augmentation enables PhiGnet to offer a more holistic perspective on protein functions. By combining the ESM-1b model with evolutionary knowledge, PhiGnet achieves a deeper and more comprehensive understanding of the intricate relationship between protein sequences and their functions. This unique combination gives PhiGnet a competitive edge in accurately assigning EC numbers or GO terms to proteins, as it taps into a broader array of evolutionary features that many other methods do not fully explore.
In conclusion, the better performance of PhiGnet can be attributed to its utilization of the evolutionary data and high-order patterns of the data from protein sequences, allowing for a deeper and more accurate understanding of protein functions. PhiGnet leverages physically-inferred knowledge (EVCs and RCs) and performs significantly better predictions across both benchmark test sets of EC numbers and GO terms. This underscores PhiGnet’s capacity to effectively assimilate enriched evolutionary knowledge, where protein function has evolved and been encoded, to delineate the intricate relationship between protein sequences and their functions. Moreover, PhiGnet achieved higher accuracy in F m a x compared to the other approaches, even when dealing with proteins in the test set with low sequence identity to those in the training set. These comparisons lead us to conclude that PhiGnet demonstrates the capability for generalization in predicting protein function annotations across both EC numbers and GO terms.
The primary success of our approach lies in the utilization of statistics-informed graph convolutional neural networks to facilitate hierarchical learning over evolutionary data from massive sequence datasets. This approach surpasses existing supervised and unsupervised methods significantly and may be used to guide future biological and clinical experiments. We are aware that machine learning-based methods are highly dependent on the datasets that are used to tune their parameters. To mitigate bias arising from the datasets, it is important to curate proteins for training, maintain diversity in sequences, and evaluate the methods on various proteins to assess their generalization capabilities. Limitations of our method might include biases/noise arising in protein families with less diverse sequences. Incorporating (co-)evolutionary information into PhiGnet can impact the accurate identification of residue communities, particularly if the information is derived from a highly conserved protein family. While integrating physically extracted knowledge into our method yields a significant improvement compared to other approaches, there are still significant challenges in interpreting the learning mechanisms within PhiGnet. For instance, a protein might have more than one active or functionally relevant sites. The activation score does not allow to discern active site a given residue is part of.
We anticipate that evolutionary information will enable statistics-informed learning approaches to effectively characterize protein function at the residue level, including predicting disease variants, allosteric regulation, binding affinity, and specificity from sequence alone, as well as incorporating structural information for specific applications. The synergy between evolutionary data and machine learning will pave the way for accurately determining and engineering the biophysical properties of proteins, with implications spanning clinical decisions, industrial applications, and environmental biotechnology.
In the present study, we collected protein chains from the Protein Data Bank (PDB) 50 using the protocols 21 to construct datasets (until 10/2021). The collected protein chains were clustered at 95% sequence identity. From each cluster, we selected a representative protein possessing at least one annotated function. Two benchmark datasets were created, comprising 41,896 and 20,215 protein chains (with a maximum of 1024 residues each), annotated with GO terms and EC numbers, respectively. In the benchmark of EC numbers, we extracted unique annotations from the third-/fourth-level of the proteins, forming a total of six primary catalytic reaction classes: oxidoreductase, transferase, hydrolase, lyase, isomerase, and ligase. For the benchmark of GO terms, the three categories, BP, CC, and MF, are utilized to evaluate and compare the performance of various methods in this study. In the present study, we divided each dataset into three subsets, including training, validation, and test sets, with ratios of 8:1:1, respectively. The protein sequences in the test set (Supplementary Fig. S17) are of varying degrees (30%, 40%, 50%, 70%, and 95%) of sequence identity against that in the training set.
To create an independent hold-out set, we collected 13,584 proteins that are released after 1/2022 from the RCSB PDB database 50 (released between 1/2022 and 12/2022). Subsequently, we then searched these proteins against the SIFT database 51 (as of December 2022) to filter out proteins lacking experimentally determined functional annotations. As a result, we obtained 6229 proteins of less than 1024 residues as an independent hold-out test set. We implemented the trained PhiGnet to assign function annotations to these recently released proteins, and the predictions are evaluated against the annotations in the SIFT database.
To calculate evolutionary couplings, we collected an MSA for the target protein by searching its sequence against the UniClust30 database (up to February 2022) 52 using the hhblits tool 53 (version 3.3.0) with default parameters. Afterward, we performed trimming on each MSA using in-house scripts to eliminate sequences of low quality (for instance, sequences with over 80% gaps were removed). The distributions of MSA quality were obtained for both the training and test sets (Supplementary Fig. S18) . For each of the trimmed MSAs, we utilized our in-house scripts based on leri 12 to compute EVCs between pairwise residues. Subsequently, we derived RCs that capture functional signatures from these couplings. Both evolutionary couplings and residue communities were used as graph edges within PhiGnet in predicting protein functions. The computed EVCs may contain noise arising from the coevolution of residues across different sequences 54 . As a result, we implemented a normalization process on all computed EVCs, using a threshold of 0.2 to enhance their quality. Likewise, the scores within the RCs were also normalized to fall within the [0, 1] range and were subjected to filtering using a threshold of 0.2. These actions were informed by the experimental design’s focus on hyper-parameter optimization through grid search (Supplementary Fig. S8 ).
To allow evolutionary diversity of natural sequences, we leveraged the pre-trained model ESM-1b transformer 31 as physically embedded knowledge (across 250 million protein sequences) to improve the prediction ability of PhiGnet. The ESM-1b transformer is pre-trained on UniRef50 representative sequences and a specialized embedding of protein sequences to represent biological information at multiple levels, e.g., evolutionary homology. In this study, we derived the embedding of the provided protein sequence from the ESM-1b transformer’s output. This embedding was then integrated with EVCs and RCs to feed into PhiGnet. The integrated strategy offers insights into remote protein homology, leveraging informative relationships within the embedding representations of homologous proteins. This allows for generalization to previously unseen proteins in the training set.
We encoded each protein sequence using a sequence-level embedding from the ESM-1b model. Each amino acid is represented by a one-hot feature vector and embedded as an input representation for PhiGnet. The ESM-1b embedding captures the unique amino acid at each specific site along the sequence, enabling the stacked GCN layers to acquire higher-level features from either EVCs or RCs using distinct convolutional filters.
PhiGnet adopts dual channels consisting of stacked GCNs. In one channel, a stack of GCNs gathers information from the sequence embedding using evolutionarily coupled residues as graph nodes. In the other channel, the graph layers learn information about functionally significant residues using RCs as nodes. The PhiGnet architecture is composed of six GCN layers and two fully connected layers with dropout. Initially, a protein sequence of interest is used to compute EVCs, RCs, and the ESM-1b embedding information 31 . The first layer of each channel loads tensors of L × 1,280 from sequence embedding, and a tensor of EVCs/RCs is used as the adjacency matrix throughout all the three stacked graph layers (Fig. 1 a). In the two channels, EVCs are to describe the linkage between pairwise residues, while RCs are used to characterize hierarchical interactions for the other three stacked graph layers (Supplementary Fig. S19 ). They motivate PhiGnet to learn knowledge of residues that significantly contribute to protein function. The final fully connected layer incorporates a fixed-number SoftMax layer to compute the prediction probability for assigning function annotations to the protein.
In PhiGnet, we embed the given sequence of L amino acids using the ESM-1b transformer as a tensor T e s m ( T e s m ∈ R L × D , D is the dimension of the tensor). The sequence embedding is the input of the two channels in GCN to represent graphs at different levels, and we employ two adjacency matrices (EVCs and RCs) to describe the linkages between residues at two different levels. In each GCN layer of PhiGnet, we employed an undirected connected graph G = { V , E , A }, consisting of a set of nodes V with L residues, a set of edges E defined by the adjacency matrix A (a matrix of EVCs or RCs is used in the present study). If residue i is correlated with residue j as defined by the entry A ( i , j ) = 1; otherwise, there is no edge between residues i and j , A ( i , j ) = 0. The degree of the matrix A is denoted as a diagonal matrix D , where \({{{\bf{D}}}}(i,\, i)={\sum }_{j=1}^{n}{{{\bf{A}}}}(i,\, \, j)\) . Each GCN layer involves two phases of aggregation, where each node gathers and aggregates features of its neighbor nodes to update the local features, and combination, where the updated features are further merged to extract high-level abstraction through a local multilayer perceptron network. The layer-wise forward propagation of GCN is defined as follows,
where H ( k ) and W ( k ) are the representation of residues and weights of the k th layer, respectively, and σ ( ⋅ ) non-linear activation functions. In the present study, we implemented a normalized form over GCN and essentially arrive at the propagation rule 55 :
with \(\hat{{{{\bf{A}}}}}={{{\bf{A}}}}+{{{\bf{I}}}}\) , where I is an identity matrix and \(\hat{{{{\bf{D}}}}}\) is the diagonal node degree matrix of \(\hat{{{{\bf{A}}}}}\) .
There are three blocks of GCN layer that are used in each channel of PhiGnet, and the number of hidden units in each GCN layer is set to 512. Information extracted by different channels, using either EVCs or RCs, can promote PhiGnet to learn features at two levels (Supplementary Figs. S9 – S11) . The outputs of the GCNs are concatenated into a tensor of dimensions L × D , where L represents the number of nodes in the graphs. To consolidate the information across the L dimension, we apply a SumPooling layer, reducing L to 1 while preserving the other dimension. This aggregated tensor of size 1 × D is forwarded to the FC layers for predicting protein functions.
The present PhiGnet allows us to directly learn information from a sequence alone (without using any structural knowledge) to significantly explore functional sites at the residue level. To achieve an optimized model, we have to tune and choose values of the hyper-parameters in our method, e.g., thresholds for filtering EVCs/RCs (Supplementary Fig. S8 ). This tuning of parameters is crucial to guarantee both the stability and performance of PhiGnet.
With the pre-defined hyper-parameters, we implemented a cross-entropy loss function to balance the abilities of learning and generalization. The loss function is defined as follows,
where N is the number of data samples, and F is the number of function classes in EC numbers/GO terms. y i j is to label the ground truth to 1 if the i th sample is in the j th function class, otherwise, it is 0. Similarly, \({\hat{y}}_{ij}\) is a label for the prediction.
PhiGnet was trained with batch size of 64 for maximum 500 epochs using early-stopping criterion over the defined cross-entropy loss (Eq. ( 3 )). During training, we leveraged the Adam optimizer 56 with a learning rate of 2 × 10 −4 , β 1 = 0.9, β 2 = 0.999, ϵ = 1 × 10 −6 , and L 2 weight decay of 2 × 10 −5 . To avoid over-fitting, we implemented a dropout of 0.3 for the second fully connected layer. Accordingly, we achieved fine-trained models of PhiGnet that are leveraged to predict the probability of assigning EC numbers/GO terms to a given protein by learning from sequence embedding under constraints of evolutionary couplings and couplings intra residue communities.
To quantitatively evaluate the importance of residues, we implemented the gradient-weighted class activation map method (that localizes the most important regions in images relevant for making correct classification decisions in computer vision) 32 for a specific function annotation to compute scores that are assigned to each residue in a protein. In the grad-CAM method, the gradient information of a given layer is used to compute localization map \({{{{\bf{M}}}}}^{c}\in {{\mathbb{R}}}^{u\times v}\) with width u and height v , and it is used to characterize the importance of every single element of the input for a specific class c . Given a feature map F k , the activation value \({{{{\mathcal{S}}}}}^{c}\) for scoring the class c is computed to measure the importance of neurons, \({\alpha }_{k}^{c}\) , as follows,
where ReLU( ⋅ ) is a non-linear activation function, holding a positive effect for function class c , and L is the number of elements in the input.
In the present method, we evaluated the importance of the i th amino acid in the feature map F k obtained from the layer concatenated from the two channels in PhiGnet, and the gradient \(\frac{\partial {{{{\bf{Y}}}}}^{c}}{\partial {{{{\bf{F}}}}}_{i}^{k}}\) is calculated by the derivative of the function annotation c with predicted score Y c , with respect to the feature map \({{{{\bf{F}}}}}_{i}^{k}\) in sequence of length L .
In the present study, we compared our method to eight methods, including BLAST 18 , FunFams 40 , DeepGO 25 , DeepFRI 21 , ProteInfer 43 ATGO 45 , SPROF-GO 44 , and CLEAN 46 in details. Moreover, our method was compared to predictions collected from two web-servers, DeepGOWeb 42 and Pannzer 41 , over predictions of either GO terms in different ontologies or EC numbers using the collected data sets.
BLAST is a sequence searching tool based on the local sequence alignment algorithm 18 . Implementing BLAST, we transferred function annotations to proteins within the test set from all the annotated sequences in the training dataset following the same procedure as presented in refs. 20 , 21 . The probability assigning annotation(s) to each protein was computed by sequence identity in percentage between the sequences in the test and training sets. More specifically, if a protein in the test set hits against proteins in the training set with a maximum sequence identity of 75%, it was assigned function annotation(s) by transferring all the annotations from training proteins with a score of 0.75. In practice, we filtered out sequences from the training set using default parameters to keep within limits of assigning annotation(s) from homologous sequences 21 .
FunFams is a domain-based approach that leverages CATH super-families to transfer function annotation from a protein to another 40 . Given a protein, its sequence is searched against the CATH using the HMMER tool 57 , and its function annotation (EC numbers and GO terms) is copied from the FunFams with the highest HMM score. We obtained EC numbers and GO terms for the test proteins in this study by following the procedure present at https://github.com/UCLOrengoGroup/cath-tools-genomescan . More specifically, each protein is assigned a score (measuring either GO terms or EC numbers) that is computed from the frequency of proteins from the sequence alignment collected by FunFams from the CATH database.
DeepGO is a supervised deep learning method using convolutional neural networks (CNN) to predict GO terms initially 25 . DeepGO learns features from both protein sequences and a cross-species protein-protein interaction network using a CNN layer with 32 filters. In DeepGO, each protein sequence is encoded as a one-hot embedding and fed into the CNN model to compute sequence representation, combined with the embedding of protein-protein network. With a fully-connected layer of a sigmoid activation function, DeepGO generates a probability as confidence to assign a function annotation the query sequence. For fair comparison, we locally adopted DeepGO with default settings to predict both EC numbers and GO terms for the test set of proteins.
DeepFRI was constructed based on an architecture of graph convolutional networks to learn both protein sequence using a pre-trained LSTM model and its structural information 21 . DeepFRI leverages the pre-trained LSTM model to extract the feature of sequence, and such feature is learned by the graph convolutional networks using residue contacts that are derived from protein tertiary structure as representations for connections of residues, e.g., the i th and j th residues are contacted if the distance between the two C α atoms of the residues is less than a threshold of 10 Å; otherwise, they are not contacted. We locally implemented DeepFRI with its default configurations and collected the protein structures for the test set from the RCSB PDB database 50 . The residue contacts within each protein were computed under the threshold from its structure and used as structural information for DeepFRI to predict EC numbers/GO terms.
DeepGOWeb is developed based on DeepGOPlus 58 , an extended variant of the DeepGO method, and it utilizes many convolutional filters of different kernel sizes to learn protein sequence representations. As an improved method, it further embeds homology-based predictions from DIAMOND 59 to improve predictive accuracy. We collected the DeepGOWeb predictions over our test set of proteins from its webs-server with default parameters. We submitted our test protein sequences to the DeepGOWeb web-server and collected the predictions over the test sequences to compute both protein-centric F m a x score and term-centric AUPR for comparison.
Pannzer is a weighted K-nearest neighbor predictor for assigning function annotations to proteins 41 . Pannzer searches a query sequence against the UniProt database to collect the sequence neighborhood, and the annotations are transferred to the query protein from its homologous neighbors. We collect the Pannzer predictions of EC numbers and GO terms on our test set using its web-server.
ProteInfer is a method based on a single convolutional neural network scan for all known domains in parallel 43 . Proteinfer has 1100 filters to learn the mapping between protein sequences and functional annotations. The method was trained on the well-curated portion of Swiss-Prot data. The finely-tuned ProteInfer maps an amino acid sequence through five residual convolutional layers to create embeddings. These embeddings are then extracted using a fully connected layer featuring an element-wise sigmoid activation function, which facilitates the prediction of per-label probabilities.
SPROF-GO is a sequence-based alignment-free protein function predictor that embeds protein sequences using a pre-trained protein language model 44 . The sequence embedding is acquired through two parallel multi-layer perceptron networks, each designed for different latent representations. Additionally, another multi-layer perceptron is to map these representations to protein function label(s) (GO terms). The final predicted annotations are derived from the network model’s predictions and homology information with the training dataset, established using DIAMOND 59 .
ATGO adopts a triplet neural-network architecture using embeddings from the pre-trained ESM-1b model 31 to predict protein annotations (GO terms) 45 . In ATGO, the embeddings are generated from the last three layers and fused by a fully connected neural network. The triplet neural-network maps the fused representation to predict the confidence scores of protein GO terms. The ATGO+ method is a combination of the ATGO method and a sequence homology-based method, resulting in superior performance compared to ATGO.
CLEAN has been developed based on the contrastive learning for predictive assignments of EC numbers to enzymes 46 . The CLEAN method learns embedded representations of enzymes, in which proteins of the same EC numbers are close to each in Euclidean distances; otherwise, they are far from each other. The positive and negative samples are defined by the distances to the anchor sequence. Positive samples are closer to the anchor sequence, while negative samples are farther away from the anchor sequence. All sequences are embedded using the pre-trained ESM-1b model 31 and are then fed into a supervised contrastive learning neural network. Both the maximum separation and P value methods are employed to prioritize confident predictions of EC numbers in the final inferred results.
We evaluate the different methods using two metrics: protein-centric maximum F-score (F m a x ) that measures the precision of labeling EC numbers/GO terms to a protein and term-centric area under precision-recall (AUPR) curve that measures the precision of labeling proteins to different EC numbers/GO terms. The F-score is the harmonic mean of the precision p ( t ) and recall r ( t ), while F m a x represents the maximum F-score achieved. F m a x and AUPR were defined as follows,
where p and r are precision that measures the predictive accuracy and recall that is to measure successfully retrieved information, respectively.
No statistical method was used to predetermine sample size.
Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.
All relevant data supporting the key findings of this study are available within the article and its Supplementary Information files. All crystal structures of proteins used in this study are available at Protein Data Bank ( https://www.rcsb.org ) under accession codes: 4JDZ [ https://doi.org/10.2210/pdb4JDZ/pdb ], 6IZW [ https://doi.org/10.2210/pdb6IZW/pdb ], 6IEJ [ https://doi.org/10.2210/pdb6IEJ/pdb ], 6W8I [ https://doi.org/10.2210/pdb6W8I/pdb ], 6XK2 [ https://doi.org/10.2210/pdb6XK2/pdb ], 1HFX [ https://doi.org/10.2210/pdb1HFX/pdb ], 1MNM [ https://doi.org/10.2210/pdb1MNM/pdb ], 1FOS [ https://doi.org/10.2210/pdb1FOS/pdb ], 3TMK [ https://doi.org/10.2210/pdb3TMK/pdb ], 2GB7 [ https://doi.org/10.2210/pdb2GB7/pdb ], 4A7W [ https://doi.org/10.2210/pdb4A7W/pdb ], 1MQ0 [ https://doi.org/10.2210/pdb1MQ0/pdb ], 2FE3 [ https://doi.org/10.2210/pdb2FE3/pdb ], 7QXO [ https://doi.org/10.2210/pdb7QXO/pdb ], and 8E0A [ https://doi.org/10.2210/pdb8E0A/pdb ]. The data is available for download at https://doi.org/10.5281/zenodo.12496869 . Source data are provided with this paper.
The PhiGnet Python code and pre-trained model are available at: https://doi.org/10.5281/zenodo.12496869 .
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This work was funded by Wellcome Trust (214291/Z/18/Z, to B.K.). We thank members of the Kornmann laboratory and AmoAi for many valuable discussions. Y.J.J. and Q.Q.Q. are supported by AmoAi.
These authors contributed equally: Yaan J. Jang, Qi-Qi Qin.
Department of Biochemistry, University of Oxford, Oxford, UK
Yaan J. Jang & Benoît Kornmann
AmoAi Technologies, Oxford, UK
Yaan J. Jang, Qi-Qi Qin & Si-Yu Huang
School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, China
Qi-Qi Qin & Xue-Ming Ding
Oxford Martin School, University of Oxford, Oxford, UK
Si-Yu Huang
School of Systems Science, Beijing Normal University, Beijing, China
Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
Arun T. John Peter
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Y.J.J. led the research, conceived the end-to-end approach, designed experiments, financed the experiments, and wrote the manuscript. Q.Q.Q. collected the data, implemented the method, contributed with principal analysis and wrote the first draft. S.Y.H. conducted principal analysis over predictions. X.M.D. conducted data analysis. A.T.J.P. supported with principal analysis and wrote the manuscript. B.K. led the research, funding acquisition, contributed technical advice, and wrote the manuscript. All authors read the final manuscript.
Correspondence to Yaan J. Jang or Benoît Kornmann .
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Y.J.J. is a founder of AmoAi Technologies, UK. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interests.
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Jang, Y.J., Qin, QQ., Huang, SY. et al. Accurate prediction of protein function using statistics-informed graph networks. Nat Commun 15 , 6601 (2024). https://doi.org/10.1038/s41467-024-50955-0
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U.s. department of commerce announces preliminary terms with sk hynix to advance u.s. ai supply chain security, office of public affairs.
Biden-Harris Administration’s Bipartisan CHIPS and Science Act Attracts All Five Major Leading-Edge Logic and Memory Companies to Produce Chips on U.S. Soil
Today, the Biden-Harris Administration announced that the U.S. Department of Commerce and SK hynix have signed a non-binding preliminary memorandum of terms (PMT) to provide up to $450 million in proposed federal incentives under the CHIPS and Science Act to establish a high-bandwidth memory (HBM) advanced packaging fabrication and research and development (R&D) facility. President Biden signed the bipartisan CHIPS and Science Act to usher in a new era of semiconductor manufacturing in the United States, bringing with it a revitalized domestic supply chain, good-paying jobs, and investments in the industries of the future. The proposed CHIPS investment builds upon SK hynix’s investment of approximately $3.87 billion in West Lafayette, Indiana, to build a memory packaging plant for artificial intelligence (AI) products and an advanced packaging R&D facility, creating approximately 1,000 new jobs and filling a critical gap in the U.S. semiconductor supply chain.
“The Biden-Harris Administration’s CHIPS and Science Act is a once-in-a-generation opportunity to supercharge America’s global technology leadership and create quality jobs in the process. Today’s historic announcement with SK hynix would further solidify America’s AI hardware supply chain in a way no other country on earth can match, with every major player in advanced semiconductor manufacturing and packaging building or expanding on our shores,” said U.S. Secretary of Commerce Gina Raimondo. “Because of President Biden and Vice President Harris’ leadership, we are creating hundreds of new jobs in Indiana and ensuring the Hoosier state and Purdue University will play a crucial role in advancing America’s national security and supply chains.”
“President Biden and Vice President Harris are bringing the most advanced semiconductor manufacturing back to the United States,” said Arati Prabhakar, Assistant to the President for Science and Technology and Director of the White House Office of Science and Technology Policy. “Advanced packaging is more and more critical for AI and other leading-edge systems, but it requires extremely precise manufacturing processes. With this incentive from the CHIPS and Science Act, SK hynix will make a major contribution to the complex computing systems that our nation relies on. At the same time, we are making the R&D investments to win the future, too.”
The West Lafayette plant builds on SK Group’s previously announced multi-billion commitment to invest in American manufacturing, including EV batteries and biotechnology, which was announced during a meeting with President Biden in July 2022. Through the proposed CHIPS investment in SK hynix, the world’s leading producer of HBM, the Biden-Harris Administration would take a meaningful step in advancing the security of the U.S. AI supply chain. With this announcement, the United States will have preliminary agreements with all five of the world’s leading-edge logic, memory, and advanced packaging providers. No other economy in the world has more than two of these companies producing leading-edge chips on its shores.
SK hynix’s West Lafayette facility, located at the Purdue University Research Park, will be home to an advanced semiconductor packaging line that will mass-produce next generation HBM. These high-performance memory chips are crucial components of graphics processing units (GPUs) that train AI systems due to their increased processing power. This next generation chip would be mass-produced at the West Lafayette facility and will boast a more advanced performance than the company’s latest HBM, which processes up to 1.18 terabytes of data – the equivalent of 230 full HD movies – per second. Mass production at the facility is expected to begin in the second half of 2028.
“The Biden-Harris Administration is dedicated to inventing and commercializing semiconductor technology in the United States and to promoting domestic semiconductor manufacturing. With President Biden and Vice President Harris’ proposed investment in SK hynix, we could advance our commitment to accomplishing both,” said Under Secretary of Commerce for Standards and Technology and National Institute of Standards and Technology Director Laurie E. Locascio . “With proposed investments in companies like SK hynix, the United States has the opportunity to be the only country in the world where every company capable of producing leading-edge chips will have both a high-volume manufacturing presence and a significant research and development presence.”
As a result of this proposed investment, the Biden-Harris Administration would establish a research hub in Indiana because of SK hynix’s partnership with Purdue University, which hosts the largest facility of its kind at a U.S. university, while bringing next generation HBM and advanced packaging R&D to the United States. The next generation HBM that will be researched and developed, mass-produced, and packaged in this ecosystem with Purdue University will play an important role in the U.S. semiconductor ecosystem and advancing U.S. technological leadership.
“We deeply appreciate the U.S. Department of Commerce’s support and are excited to collaborate in seeing this transformational project fully realized,” said SK hynix CEO Kwak Noh-Jung. “We are moving forward with the construction of the Indiana production base, working with the State of Indiana, Purdue University and our U.S. business partners to ultimately supply leading-edge AI memory products from West Lafayette. We look forward to establishing a new hub for AI technology, creating skilled jobs for Indiana and helping build a more robust, resilient supply chain for the global semiconductor industry.”
SK hynix will collaborate with Purdue University on plans for future R&D projects, which include working on advanced packaging and heterogeneous integration with Purdue’s Birck Nanotechnology Center and other research institutes and industry partners. SK hynix plans to collaborate on projects for memory-centric solutions and architecture for generative AI – specifically memory design and in/near memory computing. As part of its workforce development efforts, SK hynix plans to work with Purdue University and Ivy Tech Community College to develop training programs and interdisciplinary degree curricula that will cultivate a high-tech workforce and build a reliable pipeline of new talent. Additionally, SK hynix plans to support the work of the Purdue Research Foundation and other local non-profits and charities by building partnerships that provide community development, growth opportunities, and leadership training.
The company has indicated that it plans to claim the Department of the Treasury’s Investment Tax Credit, which is expected to be up to 25% of qualified capital expenditures. In addition to the proposed direct funding of up to $450 million, the CHIPS Program Office would make up to $500 million of proposed loans – which is part of the $75 billion in loan authority provided by the CHIPS and Science Act – available to SK hynix under the non-binding PMT.
As explained in its first Notice of Funding Opportunity , the Department may offer applicants a PMT on a non-binding basis after satisfactory completion of the merit review of a full application. The PMT outlines key terms for a potential CHIPS incentives award, including the amount and form of the award. The award amounts are subject to due diligence and negotiation of award documents and are conditional on the achievement of certain milestones. After the PMT is signed, the Department begins a comprehensive due diligence process on the proposed projects and continues negotiating or refining certain terms with the applicant. The terms contained in any final award documents may differ from the terms of the PMT being announced today.
About CHIPS for America
Nearly two years after the passage of CHIPS and Science Act, the Biden-Harris Administration is moving full speed ahead in order to help protect our economic and national security and restore American leadership in an industry that we started decades ago. By allocating over $30 billion in proposed funding to build factories domestically and proposing to invest billions more in research and innovation, we are unlocking over $300 billion in public and private investment and creating more than 100,000 jobs, including tens of thousands of good-paying jobs that don't require a college degree. Our efforts are a meaningful step towards ensuring that the United States produces more of the world’s most advanced technologies – from AI to defense systems and everyday items like cars and medical devices. With a focus on expanding capacity, enhancing capabilities, maintaining competitiveness, and driving commercialization, CHIPS for America is working towards driving our future, securing our supply chains, and cementing America’s place at the forefront of technology.
CHIPS for America is part of President Biden’s economic plan to invest in America, stimulate private sector investment, create good-paying jobs, make more in the United States, and revitalize communities left behind. CHIPS for America includes the CHIPS Program Office, responsible for manufacturing incentives, and the CHIPS Research and Development Office, responsible for R&D programs, that both sit within the National Institute of Standards and Technology (NIST) at the Department of Commerce. Visit https://www.chips.gov to learn more.
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A research report is a collection of contextual data, gathered through organized research, that provides new insights into a particular challenge (which, for this article, is business-related). Research reports are a time-tested method for distilling large amounts of data into a narrow band of focus. Their effectiveness often hinges on whether ...
A research report is a well-crafted document that outlines the processes, data, and findings of a systematic investigation. It is an important document that serves as a first-hand account of the research process, and it is typically considered an objective and accurate source of information.
Thesis is a type of research report. A thesis is a long-form research document that presents the findings and conclusions of an original research study conducted by a student as part of a graduate or postgraduate program. It is typically written by a student pursuing a higher degree, such as a Master's or Doctoral degree, although it can also ...
An outline of the research questions and hypotheses; the assumptions or propositions that your research will test. Literature Review. Not all research reports have a separate literature review section. In shorter research reports, the review is usually part of the Introduction. A literature review is a critical survey of recent relevant ...
Research reports are recorded data prepared by researchers or statisticians after analyzing the information gathered by conducting organized research, typically in the form of surveys or qualitative methods. A research report is a reliable source to recount details about a conducted research. It is most often considered to be a true testimony ...
There are three main forms of reports: factual, instructional and persuasive; each has a different purpose and will require different arguments and evidence to achieve that purpose. It will help you write good reports if you know what you are trying to achieve before you start your report. Factual. Instructional. Persuasive.
THE RESEARCH REPORT. This chapter gives attention to two primary topics, both of which present information about research reports. The first part deals with the many valuable things that can be found in research reports beyond the obvious—the results. In the second part we discuss what a research report is and what it is not.
What are the implications of the findings? The research report contains four main areas: Introduction - What is the issue? What is known? What is not known? What are you trying to find out? This sections ends with the purpose and specific aims of the study. Methods - The recipe for the study. If someone wanted to perform the same study ...
This review is divided into sections for easy reference. There are five MAJOR parts of a Research Report: 1. Introduction 2. Review of Literature 3. Methods 4. Results 5. Discussion. As a general guide, the Introduction, Review of Literature, and Methods should be about 1/3 of your paper, Discussion 1/3, then Results 1/3.
A research report is one big argument about how and why you came up with your conclusions. To make it a convincing argument, a typical guiding structure has developed. In the different chapters, there are distinct issues that need to be addressed to explain to the reader why your conclusions are valid. The governing principle for writing the ...
Use the section headings (outlined above) to assist with your rough plan. Write a thesis statement that clarifies the overall purpose of your report. Jot down anything you already know about the topic in the relevant sections. 3 Do the Research. Steps 1 and 2 will guide your research for this report.
When reporting the methods used in a sample -based study, the usual convention is to. discuss the following topics in the order shown: Chapter 13 Writing a Research Report 8. • Sample (number in ...
A research report is a document that conveys the outcomes of a study or investigation. Its purpose is to communicate the research's findings, conclusions, and implications to a particular audience. This report aims to offer a comprehensive and unbiased overview of the research process, methodology, and results.
A research report is an end product of research. As earlier said that report writing provides useful information in arriving at rational decisions that may reform the business and society. The findings, conclusions, suggestions and recommendations are useful to academicians, scholars and policymakers.
A research report is a well-crafted document that outlines the processes, data, and findings of a systematic investigation. ... The framework furthermore serves at least the following functions ...
Table of contents. Step 1: Introduce your topic. Step 2: Describe the background. Step 3: Establish your research problem. Step 4: Specify your objective (s) Step 5: Map out your paper. Research paper introduction examples. Frequently asked questions about the research paper introduction.
Research Results. Research results refer to the findings and conclusions derived from a systematic investigation or study conducted to answer a specific question or hypothesis. These results are typically presented in a written report or paper and can include various forms of data such as numerical data, qualitative data, statistics, charts, graphs, and visual aids.
Comprehensive reports with in-depth analysis and information. 100-page research report on the effects of a new drug on a medical condition. Analytical. Focus on data analysis and provide insights or recommendations. Market research report analyzing consumer behavior trends and recommending marketing strategies.
1 Choose a topic based on the assignment. Before you start writing, you need to pick the topic of your report. Often, the topic is assigned for you, as with most business reports, or predetermined by the nature of your work, as with scientific reports. If that's the case, you can ignore this step and move on.
Research Report: A research report is a document prepared by an analyst or strategist who is a part of the investment research team in a stock brokerage or investment bank . A research report may ...
Note that field reports should be written in the past tense. With this in mind, most field reports in the social sciences include the following elements: I. Introduction The introduction should describe the research problem, the specific objectives of your research, and the important theories or concepts underpinning your field study.
Table of contents. Step 1: Restate the problem. Step 2: Sum up the paper. Step 3: Discuss the implications. Research paper conclusion examples. Frequently asked questions about research paper conclusions.
The initial 12 risk factors were linked with 40% of cases, but the new report suggests addressing the 14 risk factors could help eliminate or delay 45% of dementia cases, said Livingston, a ...
U.S. based short-seller Hindenburg Research alleged on Saturday that the head of India's market regulator, Madhabi Puri Buch, previously held investments in offshore funds also used by the Adani ...
Provide details only in the body of your report. So, this is the foundation on which you build the logical next step to reach a conclusion that answers your research question. Try to keep the structure of the introduction simple. An effective way is to start with a rather general statement about the topic.
This new research plan amplifies the school's ability to translate Stanford research into large-scale solutions and inform key decision makers in policy and business.
Short seller Hindenburg Research published a report alleging a conflict of interest by the head of India's market regulator and claimed this prevented a proper investigation into Adani.
Adani Group, the Indian conglomerate rocked by a Hindenburg Research report last year, faced another heavy share selloff on Monday after the shortseller accused the head of India's market ...
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol. 20 , 1-23 (2019).
Today, the Biden-Harris Administration announced that the U.S. Department of Commerce and SK hynix have signed a non-binding preliminary memorandum of terms (PMT) to provide up to $450 million in proposed federal incentives under the CHIPS and Science Act to establish a high-bandwidth memory (HBM) advanced packaging fabrication and research and ...