Population based cancer incidence rates were abstracted from National Cancer Institute, State Cancer Profiles for all available counties in the United States for which data were available. This is a national county-level database of cancer data that are collected by state public health surveillance systems. All-site cancer is defined as any type of cancer that is captured in the state registry data, though non-melanoma skin cancer is not included. All-site age-adjusted cancer incidence rates were abstracted separately for males and females. County-level annual age-adjusted all-site cancer incidence rates for years 2006–2010 were available for 2687 of 3142 (85.5%) counties in the U.S. Counties for which there are fewer than 16 reported cases in a specific area-sex-race category are suppressed to ensure confidentiality and stability of rate estimates; this accounted for 14 counties in our study. Two states, Kansas and Virginia, do not provide data because of state legislation and regulations which prohibit the release of county level data to outside entities. Data from Michigan does not include cases diagnosed in other states because data exchange agreements prohibit the release of data to third parties. Finally, state data is not available for three states, Minnesota, Ohio, and Washington. The age-adjusted average annual incidence rate for all counties was 453.7 per 100,000 persons. We selected 2006–2010 as it is subsequent in time to the EQI exposure data which was constructed to represent the years 2000–2005. We also gathered data for the three leading causes of cancer for males (lung, prostate, and colorectal) and females (lung, breast, and colorectal). The EQI was used as an exposure metric as an indicator of cumulative environmental exposures at the county-level representing the period 2000 to 2005. A complete description of the datasets used in the EQI are provided in Lobdell et al. and methods used for index construction are described by Messer et al. The EQI was developed for the period 2000– 2005 because it was the time period for which the most recent data were available when index construction was initiated. The EQI includes variables representing each of the environmental domains. The air domain includes 87 variables representing criteria and hazardous air pollutants. The water domain includes 80 variables representing overall water quality, general water contamination, recreational water quality, drinking water quality, atmospheric deposition, drought, and chemical contamination. The land domain includes 26 variables representing agriculture, pesticides, contaminants, facilities, and radon. The built domain includes 14 variables representing roads, highway/road safety, public transit behavior, business environment, and subsidized housing environment. The sociodemographic environment includes 12 variables representing socioeconomics and crime. This dataset is not publicly accessible because: EPA cannot release personally identifiable information regarding living individuals, according to the Privacy Act and the Freedom of Information Act (FOIA). This dataset contains information about human research subjects. Because there is potential to identify individual participants and disclose personal information, either alone or in combination with other datasets, individual level data are not appropriate to post for public access. Restricted access may be granted to authorized persons by contacting the party listed. It can be accessed through the following means: Human health data are not available publicly. EQI data are available at: https://edg.epa.gov/data/Public/ORD/NHEERL/EQI. Format: Data are stored as csv files. This dataset is associated with the following publication: Jagai, J., L. Messer, K. Rappazzo , C. Gray, S. Grabich , and D. Lobdell. County-level environmental quality and associations with cancer incidence#. Cancer. John Wiley & Sons Incorporated, New York, NY, USA, 123(15): 2901-2908, (2017).

Number and rate of new cancer cases diagnosed annually from 1992 to the most recent diagnosis year available. Included are all invasive cancers and in situ bladder cancer with cases defined using the Surveillance, Epidemiology and End Results (SEER) Groups for Primary Site based on the World Health Organization International Classification of Diseases for Oncology, Third Edition (ICD-O-3). Random rounding of case counts to the nearest multiple of 5 is used to prevent inappropriate disclosure of health-related information.

Rapid Cancer Registration Data (RCRD) provides a quick, indicative source of cancer data. It is provided to support the planning and provision of cancer services. The data is based on a rapid processing of cancer registration data sources, in particular on Cancer Outcomes and Services Dataset (COSD) information. In comparison, National Cancer Registration Data (NCRD) relies on additional data sources, enhanced follow-up with trusts and expert processing by cancer registration officers. The Rapid Cancer Registration Data (RCRD) may be useful for service improvement projects including healthcare planning and prioritisation. However, it is poorly suited for epidemiological research due to limitations in the data quality and completeness.

What is Lung Cancer Dataset?

The effectiveness of the cancer prediction system helps people to know their cancer risk at a low cost and it also helps the people to take the appropriate decision based on their cancer risk status. The data is collected from the website online lung cancer prediction system.

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Acknowledgments

When we use this dataset in our research, we credit the authors as :

• License : CC BY 4.0.

• Hong, Z.Q. and Yang, J.Y. "Optimal Discriminant Plane for a Small Number of Samples and Design Method of Classifier on the Plane", Pattern Recognition, Vol. 24, No. 4, pp. 317-324, 1991 and it is published t to reuse in google research dataset

The main idea for uploading this dataset is to practice data analysis with my students, as I am working in college and want my student to train our studying ideas in a big dataset, It may be not up to date and I mention the collecting years, but it is a good resource of data to practice

Age standardized rate of cancer incidence, by selected sites of cancer and sex, three-year average, census metropolitan areas.

Dataset Card for Lung Cancer

  Dataset Summary

The effectiveness of cancer prediction system helps the people to know their cancer risk with low cost and it also helps the people to take the appropriate decision based on their cancer risk status. The data is collected from the website online lung cancer prediction system .

  Supported Tasks and Leaderboards

[More Information Needed]

  Languages

[More Information Needed]

  Dataset Structure… See the full description on the dataset page: https://huggingface.co/datasets/virtual10/lungs_cancer.

SUMMARYThis analysis, designed and executed by Ribble Rivers Trust, identifies areas across England with the greatest levels of cancer (in persons of all ages). Please read the below information to gain a full understanding of what the data shows and how it should be interpreted.ANALYSIS METHODOLOGYThe analysis was carried out using Quality and Outcomes Framework (QOF) data, derived from NHS Digital, relating to cancer (in persons of all ages).This information was recorded at the GP practice level. However, GP catchment areas are not mutually exclusive: they overlap, with some areas covered by 30+ GP practices. Therefore, to increase the clarity and usability of the data, the GP-level statistics were converted into statistics based on Middle Layer Super Output Area (MSOA) census boundaries.The percentage of each MSOA’s population (all ages) with cancer was estimated. This was achieved by calculating a weighted average based on:The percentage of the MSOA area that was covered by each GP practice’s catchment areaOf the GPs that covered part of that MSOA: the percentage of registered patients that have that illness The estimated percentage of each MSOA’s population with cancer was then combined with Office for National Statistics Mid-Year Population Estimates (2019) data for MSOAs, to estimate the number of people in each MSOA with cancer, within the relevant age range.Each MSOA was assigned a relative score between 1 and 0 (1 = worst, 0 = best) based on:A) the PERCENTAGE of the population within that MSOA who are estimated to have cancerB) the NUMBER of people within that MSOA who are estimated to have cancerAn average of scores A & B was taken, and converted to a relative score between 1 and 0 (1= worst, 0 = best). The closer to 1 the score, the greater both the number and percentage of the population in the MSOA that are estimated to have cancer, compared to other MSOAs. In other words, those are areas where it’s estimated a large number of people suffer from cancer, and where those people make up a large percentage of the population, indicating there is a real issue with cancer within the population and the investment of resources to address that issue could have the greatest benefits.LIMITATIONS1. GP data for the financial year 1st April 2018 – 31st March 2019 was used in preference to data for the financial year 1st April 2019 – 31st March 2020, as the onset of the COVID19 pandemic during the latter year could have affected the reporting of medical statistics by GPs. However, for 53 GPs (out of 7670) that did not submit data in 2018/19, data from 2019/20 was used instead. Note also that some GPs (997 out of 7670) did not submit data in either year. This dataset should be viewed in conjunction with the ‘Health and wellbeing statistics (GP-level, England): Missing data and potential outliers’ dataset, to determine areas where data from 2019/20 was used, where one or more GPs did not submit data in either year, or where there were large discrepancies between the 2018/19 and 2019/20 data (differences in statistics that were > mean +/- 1 St.Dev.), which suggests erroneous data in one of those years (it was not feasible for this study to investigate this further), and thus where data should be interpreted with caution. Note also that there are some rural areas (with little or no population) that do not officially fall into any GP catchment area (although this will not affect the results of this analysis if there are no people living in those areas).2. Although all of the obesity/inactivity-related illnesses listed can be caused or exacerbated by inactivity and obesity, it was not possible to distinguish from the data the cause of the illnesses in patients: obesity and inactivity are highly unlikely to be the cause of all cases of each illness. By combining the data with data relating to levels of obesity and inactivity in adults and children (see the ‘Levels of obesity, inactivity and associated illnesses: Summary (England)’ dataset), we can identify where obesity/inactivity could be a contributing factor, and where interventions to reduce obesity and increase activity could be most beneficial for the health of the local population.3. It was not feasible to incorporate ultra-fine-scale geographic distribution of populations that are registered with each GP practice or who live within each MSOA. Populations might be concentrated in certain areas of a GP practice’s catchment area or MSOA and relatively sparse in other areas. Therefore, the dataset should be used to identify general areas where there are high levels of cancer, rather than interpreting the boundaries between areas as ‘hard’ boundaries that mark definite divisions between areas with differing levels of cancer.TO BE VIEWED IN COMBINATION WITH:This dataset should be viewed alongside the following datasets, which highlight areas of missing data and potential outliers in the data:Health and wellbeing statistics (GP-level, England): Missing data and potential outliersLevels of obesity, inactivity and associated illnesses (England): Missing dataDOWNLOADING THIS DATATo access this data on your desktop GIS, download the ‘Levels of obesity, inactivity and associated illnesses: Summary (England)’ dataset.DATA SOURCESThis dataset was produced using:Quality and Outcomes Framework data: Copyright © 2020, Health and Social Care Information Centre. The Health and Social Care Information Centre is a non-departmental body created by statute, also known as NHS Digital.GP Catchment Outlines. Copyright © 2020, Health and Social Care Information Centre. The Health and Social Care Information Centre is a non-departmental body created by statute, also known as NHS Digital. Data was cleaned by Ribble Rivers Trust before use.MSOA boundaries: © Office for National Statistics licensed under the Open Government Licence v3.0. Contains OS data © Crown copyright and database right 2021.Population data: Mid-2019 (June 30) Population Estimates for Middle Layer Super Output Areas in England and Wales. © Office for National Statistics licensed under the Open Government Licence v3.0. © Crown Copyright 2020.COPYRIGHT NOTICEThe reproduction of this data must be accompanied by the following statement:© Ribble Rivers Trust 2021. Analysis carried out using data that is: Copyright © 2020, Health and Social Care Information Centre. The Health and Social Care Information Centre is a non-departmental body created by statute, also known as NHS Digital; © Office for National Statistics licensed under the Open Government Licence v3.0. Contains OS data © Crown copyright and database right 2021. © Crown Copyright 2020.CaBA HEALTH & WELLBEING EVIDENCE BASEThis dataset forms part of the wider CaBA Health and Wellbeing Evidence Base.

One-year and five-year net survival for adults (15-99) in England diagnosed with one of 29 common cancers, by age and sex.

Cancer Mortality & Incidence Rates: (Country LVL)

Investigating Cancer Trends over time

By Data Exercises [source]

About this dataset

This dataset is a comprehensive collection of data from county-level cancer mortality and incidence rates in the United States between 2000-2014. This data provides an unprecedented level of detail into cancer cases, deaths, and trends at a local level. The included columns include County, FIPS, age-adjusted death rate, average death rate per year, recent trend (2) in death rates, recent 5-year trend (2) in death rates and average annual count for each county. This dataset can be used to provide deep insight into the patterns and effects of cancer on communities as well as help inform policy decisions related to mitigating risk factors or increasing preventive measures such as screenings. With this comprehensive set of records from across the United States over 15 years, you will be able to make informed decisions regarding individual patient care or policy development within your own community!

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How to use the dataset

This dataset provides comprehensive US county-level cancer mortality and incidence rates from 2000 to 2014. It includes the mortality and incidence rate for each county, as well as whether the county met the objective of 45.5 deaths per 100,000 people. It also provides information on recent trends in death rates and average annual counts of cases over the five year period studied.

This dataset can be extremely useful to researchers looking to study trends in cancer death rates across counties. By using this data, researchers will be able to gain valuable insight into how different counties are performing in terms of providing treatment and prevention services for cancer patients and whether preventative measures and healthcare access are having an effect on reducing cancer mortality rates over time. This data can also be used to inform policy makers about counties needing more target prevention efforts or additional resources for providing better healthcare access within at risk communities.

When using this dataset, it is important to pay close attention to any qualitative columns such as “Recent Trend” or “Recent 5-Year Trend (2)” that may provide insights into long term changes that may not be readily apparent when using quantitative variables such as age-adjusted death rate or average deaths per year over shorter periods of time like one year or five years respectively. Additionally, when studying differences between different counties it is important to take note of any standard FIPS code differences that may indicate that data was collected by a different source with a difference methodology than what was used in other areas studied

Research Ideas

• Using this dataset, we can identify patterns in cancer mortality and incidence rates that are statistically significant to create treatment regimens or preventive measures specifically targeting those areas.
• This data can be useful for policymakers to target areas with elevated cancer mortality and incidence rates so they can allocate financial resources to these areas more efficiently.
• This dataset can be used to investigate which factors (such as pollution levels, access to medical care, genetic make up) may have an influence on the cancer mortality and incidence rates in different US counties

Acknowledgements

If you use this dataset in your research, please credit the original authors. Data Source

License

License: Dataset copyright by authors - You are free to: - Share - copy and redistribute the material in any medium or format for any purpose, even commercially. - Adapt - remix, transform, and build upon the material for any purpose, even commercially. - You must: - Give appropriate credit - Provide a link to the license, and indicate if changes were made. - ShareAlike - You must distribute your contributions under the same license as the original. - Keep intact - all notices that refer to this license, including copyright notices.

Columns

File: death .csv | Column name | Description | |:-------------------------------------------|:-------------------------------------------------------------------...

Age-standardised rate of mortality from oral cancer (ICD-10 codes C00-C14) in persons of all ages and sexes per 100,000 population.RationaleOver the last decade in the UK (between 2003-2005 and 2012-2014), oral cancer mortality rates have increased by 20% for males and 19% for females1Five year survival rates are 56%. Most oral cancers are triggered by tobacco and alcohol, which together account for 75% of cases2. Cigarette smoking is associated with an increased risk of the more common forms of oral cancer. The risk among cigarette smokers is estimated to be 10 times that for non-smokers. More intense use of tobacco increases the risk, while ceasing to smoke for 10 years or more reduces it to almost the same as that of non-smokers3. Oral cancer mortality rates can be used in conjunction with registration data to inform service planning as well as comparing survival rates across areas of England to assess the impact of public health prevention policies such as smoking cessation.References:(1) Cancer Research Campaign. Cancer Statistics: Oral – UK. London: CRC, 2000.(2) Blot WJ, McLaughlin JK, Winn DM et al. Smoking and drinking in relation to oral and pharyngeal cancer. Cancer Res 1988; 48: 3282-7. (3) La Vecchia C, Tavani A, Franceschi S et al. Epidemiology and prevention of oral cancer. Oral Oncology 1997; 33: 302-12.Definition of numeratorAll cancer mortality for lip, oral cavity and pharynx (ICD-10 C00-C14) in the respective calendar years aggregated into quinary age bands (0-4, 5-9,…, 85-89, 90+). This does not include secondary cancers or recurrences. Data are reported according to the calendar year in which the cancer was diagnosed.Counts of deaths for years up to and including 2019 have been adjusted where needed to take account of the MUSE ICD-10 coding change introduced in 2020. Detailed guidance on the MUSE implementation is available at: https://www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/deaths/articles/causeofdeathcodinginmortalitystatisticssoftwarechanges/january2020Counts of deaths for years up to and including 2013 have been double adjusted by applying comparability ratios from both the IRIS coding change and the MUSE coding change where needed to take account of both the MUSE ICD-10 coding change and the IRIS ICD-10 coding change introduced in 2014. The detailed guidance on the IRIS implementation is available at: https://www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/deaths/bulletins/impactoftheimplementationofirissoftwareforicd10causeofdeathcodingonmortalitystatisticsenglandandwales/2014-08-08Counts of deaths for years up to and including 2010 have been triple adjusted by applying comparability ratios from the 2011 coding change, the IRIS coding change and the MUSE coding change where needed to take account of the MUSE ICD-10 coding change, the IRIS ICD-10 coding change and the ICD-10 coding change introduced in 2011. The detailed guidance on the 2011 implementation is available at https://webarchive.nationalarchives.gov.uk/ukgwa/20160108084125/http://www.ons.gov.uk/ons/guide-method/classifications/international-standard-classifications/icd-10-for-mortality/comparability-ratios/index.htmlDefinition of denominatorPopulation-years (aggregated populations for the three years) for people of all ages, aggregated into quinary age bands (0-4, 5-9, …, 85-89, 90+)

Mortality Rates for Lake County, Illinois. Explanation of field attributes: Average Age of Death – The average age at which a people in the given zip code die. Cancer Deaths – Cancer deaths refers to individuals who have died of cancer as the underlying cause. This is a rate per 100,000. Heart Disease Related Deaths – Heart Disease Related Deaths refers to individuals who have died of heart disease as the underlying cause. This is a rate per 100,000. COPD Related Deaths – COPD Related Deaths refers to individuals who have died of chronic obstructive pulmonary disease (COPD) as the underlying cause. This is a rate per 100,000.

All individuals diagnosed with cancer from 2000 to 2007 were identified in the Cancer Register of Southern Sweden, but only individuals who were also identified in the Population Register of Scania were included in this cohort. Age- and gender-matched controls were identified in the Population Register of Scania. The controls were reconciled with the cancer registry in southern Sweden so that they had no prior diagnosis of cancer and with the Population Register of Scania that they were alive at time of diagnosis to the matched case. Also spouses to cancer patients were used as controls.

For each individual, healthcare costs were monitored related to the date of diagnosis. Costs for outpatient care, inpatient care, number of days in hospital and medications were included. Costs were also calculated for the controls.

Other information available about the individuals in the cohort are age, sex, domicile, type of tumor and medication.

Purpose:

To study the health cost per individual in relation to mortality and comorbidity.

Dataset includes the study controls (individuals matched by age and sex ) Also spouses to cancer patients were included in the control group.

This is historical data. The update frequency has been set to "Static Data" and is here for historic value. Updated on 8/14/2024 Cancer Mortality Rate - This indicator shows the age-adjusted mortality rate from cancer (per 100,000 population). Maryland’s age adjusted cancer mortality rate is higher than the US cancer mortality rate. Cancer impacts people across all population groups, however wide racial disparities exist. Link to Data Details

This paper demonstrates the flexibility of a general approach for the analysis of discrete time competing risks data that can accommodate complex data structures, different time scales for different causes, and nonstandard sampling schemes. The data may involve a single data source where all individuals contribute to analyses of both cause-specific hazard functions, overlapping datasets where some individuals contribute to the analysis of the cause-specific hazard function of only one cause while other individuals contribute to analyses of both cause-specific hazard functions, or separate data sources where each individual contributes to the analysis of the cause-specific hazard function of only a single cause. The approach is modularized into estimation and prediction. For the estimation step, the parameters and the variance-covariance matrix can be estimated using widely available software. The prediction step utilizes a generic program with plug-in estimates from the estimation step. The approach is illustrated with three prognostic models for stage IV male oral cancer using different data structures. The first model uses only men with stage IV oral cancer from population-based registry data. The second model strategically extends the cohort to improve the efficiency of the estimates. The third model improves the accuracy for those with a lower risk of other causes of death, by bringing in an independent data source collected under a complex sampling design with additional other-cause covariates. These analyses represent novel extensions of existing methodology, broadly applicable for the development of prognostic models capturing both the cancer and non-cancer aspects of a patient's health.

Annual percent change and average annual percent change in age-standardized cancer incidence rates since 1984 to the most recent diagnosis year. The table includes a selection of commonly diagnosed invasive cancers, as well as in situ bladder cancer. Cases are defined using the Surveillance, Epidemiology and End Results (SEER) Groups for Primary Site based on the World Health Organization International Classification of Diseases for Oncology, Third Edition (ICD-O-3) from 1992 to the most recent data year and on the International Classification of Diseases, ninth revision (ICD-9) from 1984 to 1991.

Among many types of cancers, to date, lung cancer remains one of the deadliest cancers around the world. Many researchers, scientists, doctors, and people from other fields continuously contribute to this subject regarding early prediction and diagnosis. One of the significant problems in prediction is the black-box nature of machine learning models. Though the detection rate is comparatively satisfactory, people have yet to learn how a model came to that decision, causing trust issues among patients and healthcare workers. This work uses multiple machine learning models on a numerical dataset of lung cancer-relevant parameters and compares performance and accuracy. After comparison, each model has been explained using different methods. The main contribution of this research is to give logical explanations of why the model reached a particular decision to achieve trust. This research has also been compared with a previous study that worked with a similar dataset and took expert opinions regarding their proposed model. We also showed that our research achieved better results than their proposed model and specialist opinion using hyperparameter tuning, having an improved accuracy of almost 100% in all four models.

Welcome to the the CSAW-M dataset homepageThis page includes the files and metadata related to the CSAW-M, a curated dataset of mammograms with expert assessments of the masking of cancer. CSAW-M is collected from over 10,000 individuals and annotated with potential masking. In contrast to the previous approaches which measure breast image density as a proxy, our dataset directly provides annotations of masking potential assessments from five specialists. We trained deep learning models on CSAW-M to estimate the masking level, and showed that the estimated masking is significantly more predictive of screening participants diagnosed with interval and large invasive cancers — without being explicitly trained for these tasks — than its breast density counterparts. Please find the paper corresponding to our work here and the GitHub repo here.CSAW-M Research Use LicensePlease read carefully all the terms and conditions of the CSAW-M Research Use License. How to access the dataset:If you want to get access to the data, please use the "Request access to files" option above (currently, non-Swedish researchers need to have a general figshare account to be able to to request access). We will ask you to agree to our terms of conditions and provide us with some information about what you will use the data for. We will then receive the request and process it, after which you would be able to download all the files.If you use this Work, please cite our paper:@article{sorkhei2021csaw, title={CSAW-M: An Ordinal Classification Dataset for Benchmarking Mammographic Masking of Cancer}, author={Sorkhei, Moein and Liu, Yue and Azizpour, Hossein and Azavedo, Edward and Dembrower, Karin and Ntoula, Dimitra and Zouzos, Athanasios and Strand, Fredrik and Smith, Kevin}, year={2021} }

The Cancer Mapping data consists of counts of newly diagnosed cancer among New York State residents and is in response to legislation regarding "Cancer incidence and environmental facility maps" signed into law in 2010 (Public Health Law §2401-B). The law specifies the publication of maps showing cancer counts for small geographic areas along with certain facilities regulated by the State Department of Environmental Conservation. The official web site is called Environmental Facilities and Cancer Mapping.

The dataset is ONLY for the cancer-related data fields on the Environmental Facilities and Cancer Mapping web site. This dataset includes observed counts for 23 separate anatomical sites at the level of census block group. Block groups are small geographic areas typically averaging 1,000 to 1,500 people. To protect confidentiality, each area contains a minimum of 6 total cancers among males and 6 total cancers among females.

For more information, check out http://www.health.ny.gov/statistics/cancer/registry/about.htm .

Links to code and bioRxiv pre-print:

1. Multi-lens Neural Machine (MLNM) Code

2. An AI-assisted Tool For Efficient Prostate Cancer Diagnosis (bioRxiv Pre-print)

Digitized hematoxylin and eosin (H&E)-stained whole-slide-images (WSIs) of 40 prostatectomy and 59 core needle biopsy specimens were collected from 99 prostate cancer patients at Tan Tock Seng Hospital, Singapore. There were 99 WSIs in total such that each specimen had one WSI. H&E-stained slides were scanned at 40× magnification (specimen-level pixel size 0·25μm × 0·25μm) using Aperio AT2 Slide Scanner (Leica Biosystems). Institutional board review from the hospital were obtained for this study, and all the data were de-identified.

Prostate glandular structures in core needle biopsy slides were manually annotated and classified using the ASAP annotation tool (ASAP). A senior pathologist reviewed 10% of the annotations in each slide, ensuring that some reference annotations were provided to the researcher at different regions of the core. It is to be noted that partial glands appearing at the edges of the biopsy cores were not annotated.

Patches of size 512 × 512 pixels were cropped from whole slide images at resolutions 5×, 10×, 20×, and 40× with an annotated gland centered at each patch. This dataset contains these cropped images.

This dataset is used to train two AI models for Gland Segmentation (99 patients) and Gland Classification (46 patients). Tables 1 and 2 illustrate both gland segmentation and gland classification datasets. We have put the two corresponding sub-datasets as two zip files as follows:

1. gland_segmentation_dataset.zip
2. gland_classification_dataset.zip

Table 1: The number of slides and patches in training, validation, and test sets for gland segmentation task. There is one H&E stained WSI for each prostatectomy or core needle biopsy specimen.

	#Slides
	Train	Valid	Test	Total
Prostatectomy	17	8	15	40
Biopsy	26	13	20	59
Total	43	21	35	99
	#Patches
	Train	Valid	Test	Total
Prostatectomy	7795	3753	7224	18772
Biopsy	5559	4028	5981	15568
Total	13354	7781	13205	34340

Table 2: The number of slides and patches in training, validation, and test sets for gland classification task. There is one H&E stained WSI for each prostatectomy or core needle biopsy specimen. The gland classification datasets are the subsets of the gland segmentation datasets. GS: Gleason Score. B: Benign. M: Malignant.

	#Slides (GS 3+3:3+4:4+3)
	Train	Valid	Test	Total
Biopsy	10:9:1	3:7:0	6:10:0	19:26:1
	#Patches (B:M)
	Train	Valid	Test	Total
Biopsy	1557:2277	1216:1341	1543:2718	4316:6336

NB: Gland classification folder (gland_classification_dataset.zip) may contain extra patches, labels of which could not be identified from H&E slides. They were not used in the machine learning study.

Background

Sarcomas are uncommon cancers that can affect any part of the body. There are many different types of sarcoma and subtypes can be grouped into soft tissue or bone sarcomas. About 15 people are diagnosed every day in the UK. 3 in every 200 people with cancer in the UK have sarcoma.

A highly granular dataset with a confirmed sarcoma event including hospital presentation, serial physiology, demography, treatment prescribed and administered, prescribed and administered drugs. The infographic includes data from 27/12/2004 to 31/12/2021 but data is available from the past 10 years+.

PIONEER geography: The West Midlands (WM) has a population of 5.9 million & includes a diverse ethnic & socio-economic mix.

EHR. UHB is one of the largest NHS Trusts in England, providing direct acute services & specialist care across four hospital sites, with 2.2 million patient episodes per year, 2750 beds & an expanded 250 ITU bed capacity during COVID. UHB runs a fully electronic healthcare record (EHR) (PICS; Birmingham Systems), a shared primary & secondary care record (Your Care Connected) & a patient portal “My Health”.

Scope: All hospitalised patients from 2004 onwards, curated to focus on Sarcoma. Longitudinal & individually linked, so that the preceding & subsequent health journey can be mapped & healthcare utilisation prior to & after admission understood. The dataset includes highly granular patient demographics & co-morbidities taken from ICD-10 & SNOMED-CT codes. Serial, structured data pertaining to acute care process (timings, staff grades, specialty review, wards and triage). Along with presenting complaints, outpatients admissions, microbiology results, referrals, procedures, therapies, all physiology readings (pulse, blood pressure, respiratory rate, oxygen saturations and others), and all blood results (urea, albumin, platelets, white blood cells and others). Includes all prescribed & administered treatments and all outcomes. Linked images are also available (radiographs, CT scans, MRI).

Available supplementary data: Matched controls; ambulance, OMOP data, synthetic data.

Available supplementary support: Analytics, Model build, validation & refinement; A.I.; Data partner support for ETL (extract, transform & load) process, Clinical expertise, Patient & end-user access, Purchaser access, Regulatory requirements, Data-driven trials, “fast screen” services.