<span style="font-variant: small-caps">EpiInfer</span>: A Non-Markovian Method and System to Forecast Infection Rates in Epidemics
Consider an evolving epidemic in which each person is either (S) susceptible and healthy; (E) exposed, contagious but asymptomatic; (I) infected, symptomatic, and quarantined; or (R) recovered, healthy, and susceptible. The inference problem, given (i) who is showing symptoms (I) and who is not (S,...
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-07-01
|
| Series: | Algorithms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4893/18/7/450 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849714294696968192 |
|---|---|
| author | Jovan Kascelan Ruoxi Yang Dennis Shasha |
| author_facet | Jovan Kascelan Ruoxi Yang Dennis Shasha |
| author_sort | Jovan Kascelan |
| collection | DOAJ |
| description | Consider an evolving epidemic in which each person is either (S) susceptible and healthy; (E) exposed, contagious but asymptomatic; (I) infected, symptomatic, and quarantined; or (R) recovered, healthy, and susceptible. The inference problem, given (i) who is showing symptoms (I) and who is not (S, E, R) and (ii) the distribution of meetings among people each day, is to predict the number of infected people (state I) in future days (e.g., 1 through 20 days out into the future) for the purpose of planning resources (e.g., needles, medicine, staffing) and policy responses (e.g., masking). Each prediction horizon has different uses. For example, staffing may require forecasts of only a few days, while logistics (i.e., which supplies to order) may require a two- or three-week horizon. Our algorithm and system <span style="font-variant: small-caps;">EpiInfer</span> is a non-Markovian approach to forecasting infection rates. It is non-Markovian because it looks at infection rates over the past several days in order to make predictions about the future. In addition, it makes use of the following information: (i) the distribution of the number of meetings per person and (ii) the transition probabilities between states and uses those estimates to forecast future infection rates. In both simulated and real data, <span style="font-variant: small-caps;">EpiInfer</span> performs better than the standard (in epidemiology) differential equation approaches as well as general-purpose neural network approaches. Compared to ARIMA, <span style="font-variant: small-caps;">EpiInfer</span> is better starting with 6-day forecasts, while ARIMA is better for shorter forecast horizons. In fact, our operational recommendation would be to use ARIMA (1,1,1) for short predictions (5 days or less) and then <span style="font-variant: small-caps;">EpiInfer</span> thereafter. Doing so would reduce relative Root Mean Squared Error (RMSE) over any state of the art method by up to a factor of 4. Predictions of this accuracy could be useful for people, supply, and policy planning. |
| format | Article |
| id | doaj-art-4ada4d6facdc42469e374d13d93edca9 |
| institution | DOAJ |
| issn | 1999-4893 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Algorithms |
| spelling | doaj-art-4ada4d6facdc42469e374d13d93edca92025-08-20T03:13:44ZengMDPI AGAlgorithms1999-48932025-07-0118745010.3390/a18070450<span style="font-variant: small-caps">EpiInfer</span>: A Non-Markovian Method and System to Forecast Infection Rates in EpidemicsJovan Kascelan0Ruoxi Yang1Dennis Shasha2Department of Computer Science, New York University Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab EmiratesDepartment of Biostatistics, School of Global Public Health, New York University, New York, NY 10012, USAComputer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USAConsider an evolving epidemic in which each person is either (S) susceptible and healthy; (E) exposed, contagious but asymptomatic; (I) infected, symptomatic, and quarantined; or (R) recovered, healthy, and susceptible. The inference problem, given (i) who is showing symptoms (I) and who is not (S, E, R) and (ii) the distribution of meetings among people each day, is to predict the number of infected people (state I) in future days (e.g., 1 through 20 days out into the future) for the purpose of planning resources (e.g., needles, medicine, staffing) and policy responses (e.g., masking). Each prediction horizon has different uses. For example, staffing may require forecasts of only a few days, while logistics (i.e., which supplies to order) may require a two- or three-week horizon. Our algorithm and system <span style="font-variant: small-caps;">EpiInfer</span> is a non-Markovian approach to forecasting infection rates. It is non-Markovian because it looks at infection rates over the past several days in order to make predictions about the future. In addition, it makes use of the following information: (i) the distribution of the number of meetings per person and (ii) the transition probabilities between states and uses those estimates to forecast future infection rates. In both simulated and real data, <span style="font-variant: small-caps;">EpiInfer</span> performs better than the standard (in epidemiology) differential equation approaches as well as general-purpose neural network approaches. Compared to ARIMA, <span style="font-variant: small-caps;">EpiInfer</span> is better starting with 6-day forecasts, while ARIMA is better for shorter forecast horizons. In fact, our operational recommendation would be to use ARIMA (1,1,1) for short predictions (5 days or less) and then <span style="font-variant: small-caps;">EpiInfer</span> thereafter. Doing so would reduce relative Root Mean Squared Error (RMSE) over any state of the art method by up to a factor of 4. Predictions of this accuracy could be useful for people, supply, and policy planning.https://www.mdpi.com/1999-4893/18/7/450epidemic modelingcompartmental modelsSEIRSforecastingcontact networksparameter estimation |
| spellingShingle | Jovan Kascelan Ruoxi Yang Dennis Shasha <span style="font-variant: small-caps">EpiInfer</span>: A Non-Markovian Method and System to Forecast Infection Rates in Epidemics Algorithms epidemic modeling compartmental models SEIRS forecasting contact networks parameter estimation |
| title | <span style="font-variant: small-caps">EpiInfer</span>: A Non-Markovian Method and System to Forecast Infection Rates in Epidemics |
| title_full | <span style="font-variant: small-caps">EpiInfer</span>: A Non-Markovian Method and System to Forecast Infection Rates in Epidemics |
| title_fullStr | <span style="font-variant: small-caps">EpiInfer</span>: A Non-Markovian Method and System to Forecast Infection Rates in Epidemics |
| title_full_unstemmed | <span style="font-variant: small-caps">EpiInfer</span>: A Non-Markovian Method and System to Forecast Infection Rates in Epidemics |
| title_short | <span style="font-variant: small-caps">EpiInfer</span>: A Non-Markovian Method and System to Forecast Infection Rates in Epidemics |
| title_sort | span style font variant small caps epiinfer span a non markovian method and system to forecast infection rates in epidemics |
| topic | epidemic modeling compartmental models SEIRS forecasting contact networks parameter estimation |
| url | https://www.mdpi.com/1999-4893/18/7/450 |
| work_keys_str_mv | AT jovankascelan spanstylefontvariantsmallcapsepiinferspananonmarkovianmethodandsystemtoforecastinfectionratesinepidemics AT ruoxiyang spanstylefontvariantsmallcapsepiinferspananonmarkovianmethodandsystemtoforecastinfectionratesinepidemics AT dennisshasha spanstylefontvariantsmallcapsepiinferspananonmarkovianmethodandsystemtoforecastinfectionratesinepidemics |