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An Explanatory Analytics Model For Identifying Factors Indi - 2022 - Decision An
An Explanatory Analytics Model For Identifying Factors Indi - 2022 - Decision An
∗ Corresponding author.
E-mail addresses: moamini@okstate.edu (M. Amini), ali.bagheri@okstate.edu (A. Bagheri), dursun.delen@okstate.edu, dursun.delen@istinye.edu.tr
(D. Delen).
URL: http://spears.okstate.edu/delen (D. Delen).
https://doi.org/10.1016/j.dajour.2022.100058
Received 5 April 2022; Received in revised form 21 April 2022; Accepted 25 April 2022
Available online 3 May 2022
2772-6622/© 2022 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license
(http://creativecommons.org/licenses/by-nc-nd/4.0/).
M. Amini, A. Bagheri and D. Delen Decision Analytics Journal 3 (2022) 100058
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M. Amini, A. Bagheri and D. Delen Decision Analytics Journal 3 (2022) 100058
The primary objective of this study was to leverage predictive 3.2. Prediction models
models and explainable AI techniques to discover the impactful factors
for a patient’s lung transplant’s prolonged survival. We recognized two In the first phase of our analysis, we were to build the most accurate
post-operative variables that could be used towards finding candidate model for classifying patients with respect to their survival time after
outcomes. These variables are pstatus, a binary variable that represents the transplant. The model would then be used as an input for the
whether the patient has survived at the last follow-up time (0 if living), explanation phase.
and ptime, a continuous variable, that denotes the time frame from To select the predictive models, we speculated that tree-based mod-
transplant until last follow-up or death. See Fig. 2 for ptime distribution els, such as gradient boosted trees (GBT) and Random Forests (RF),
in the dataset for lung transplants when the patient is dead (pstatus = would outperform others because most of the variables were either
1). categorical or binary. However, former studies proved the strength
We excluded organ transplantations of non-adult patients (less than of number-based models such as logistic regression (LR), K nearest
18 years of age) and the patients whose death was not related to the neighbors (KNN), support vector machines (SVM), and artificial neural
lung (using the variable COD, defined as the cause of death). Following networks (ANN). As a result, we tried models from both groups. We
UNOS recommendations, to avoid overestimating patients with short also included a decision tree (DT) to evaluate and foolproof the results
survival time, we also cut off the records with transplant dates within of tree-based models. We found no fallible split in trees or any sign of
14 months of the data acquisition. Next, we removed patients with cheating variables.
missing ptime because we could not determine their survival time. To enhance the predictive performance measures, we fine-tuned
the hyperparameters of the models. For example, in the case of RF
Abiding by the cleaning steps in [30], we then omitted the intra-
(our winning model), we tried numerous split criteria (information
and postoperative factors since our research was to address the factors
gain, information gain ratio, and Gini index) for the decision trees. We
before the operation. Next, we cleaned all invalid and duplicated
increased the number of trees gradually to achieve the best performing
records. We eliminated variables that would not have any predictive
configuration.
power (e.g., IDs and codes) and variables with little change in the entire
In addition, to use the data efficiently and prevent our models
dataset (e.g., constants for more than 95% of the data). To address
from overfitting the training dataset or choosing a specific test set, we
missing values, we first distinguished various missing patterns in the
conducted k-fold cross-validation (with 𝑘 = 10) for all the predictive
dataset using the variable definitions and handled them accordingly
models. This way, we improved the generalization capabilities of the
via removal, imputation, or recoding. We ended up having 37,580 models.
patient records and 171 variables in the dataset. Unlike previous stud-
ies [22,31,32] we removed only variables with many missing (more
3.3. Explanation models
than 70%), thereby providing a more comprehensive approach while
using state-of-the-art ML and explainable AI techniques.
In general, the need for model explanation is two-fold. First, we
From Fig. 3, 27% of patients survive one year or less, whereas 14% need to comprehend what variables are used for classification judgment
survive ten years or more. The data is derived based on the reported in the black box of advanced algorithms to certify their legitimacy. A
deaths. However, the number of patients that outlive ten years needs machine may solely learn the characteristics of the dataset and produce
to be adjusted, whereas living patients should also be considered in accurate predictions that have nothing to do with desired patterns
this category. This approach has been previously used in [25]. This in the data. In this case, the explanation phase tells us whether the
way, we carried about a quarter of the data in the long survival variables used are both meaningful and relevant. Second, to be effective
category (i.e., >= 10 years). Fig. 4 shows the frequency and cumulative for practitioners and end-users, we need an explanation model to return
percentage of the adjusted long survival category compared with other the most prominent variables and their importance, especially when
categories. For identifying factors indicative of long- versus short-term working with a feature-rich dataset [33]. So, in the second phase of
survival after LTx, we finally chose two categories of short term (<= our study, we were required to explain the predictions drawn from the
1 year) and long term (>= 10 years) for our classification. These time previous step.
thresholds were commonly suggested by LTx scholars for short- and Recently, many scholars in data analytics research have dedicated
long-term survival [15,16]. These categories involved 13,080 patients their research to the explanation aspect. Consequently, a variety of
(9,864 records after cleaning). approaches, such as LIME [33], DeepLIFT [34], Layer-Wise Relevance
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M. Amini, A. Bagheri and D. Delen Decision Analytics Journal 3 (2022) 100058
Fig. 4. Yearly ptime distribution after LTx with adjusted >= 10 category.
Propagation [35], Shapley regression values [36], Shapley sampling In this phase of our study, we employed SHAP to shed light on the
values [37], and Quantitative Input Influence [38] have been developed black box of our best performing predictive model and interpret which
(for detailed discussion and review on explanation methods see [24, factors play a critical role in prediction.
39]).
In this vein, Lundberg and Lee [40] proposed a unified framework 4. Results
for interpreting black-box predictions by assigning each feature an
importance value, called the ‘SHapley Additive exPlanations’ (SHAP) Our analysis included two phases to understand the critical fac-
value. SHAP values are defined as the sequential impact of each fea- tors of short- versus long-term survival in LTx, i.e., predictive models
ture’s value on the model’s output, averaged over all possible orders by and model explanation. We explain the results of these phases in the
which features are added to the model. Due to the complexity of the following sections.
problem, SHAP values can only be approximated. However, Lundberg
et al. [41] suggested computing precise values for a prediction when 4.1. Predictive models
working with tree-based machine learning algorithms for instance.
Given an instance x and the feature set 𝐹 , SHAP algorithm computes The objective of this phase was to discover a model with the
the marginal contribution of the feature 𝑖 in the performance of the most robust predictions. As we mentioned before, due to the superior
provided prediction model compared to all subsets of 𝐹 conditioning capability of tree-based models in handling categorical variables, we
on (with or without) feature 𝑖 (Eq. (1)). surmised that such models would be a better fit. However, the literature
∑ 𝑃𝑆 (𝑥) − 𝑃𝑆−𝑖 (𝑥) brought a few number-based methods to our consideration. We tuned
𝑆𝐻𝐴𝑃𝑖 (𝑥) = ( ) , (1) the hyperparameters and tested models in both categories to keep
𝑆⊆𝐹 ,𝑖∈𝑆 |𝐹 |
|𝑆| an open mind and approach. Table 1 represents the performance of
|𝑆|
these algorithms. Although LR, among the number-based algorithms,
where, 𝑆 is any subset of features, 𝑃𝑆 (𝑥) denotes predicted outcome by has comparable performance to tree-based models, we still can see the
a model trained with subset 𝑆 for instance 𝑥, and | ⋅ | indicates the size superiority of tree-based models, most significantly RF.
of a set. We compared four evaluation metrics of performance to conclude
The strength of these SHAP values is that they are locally accurate, our best model. These metrics are accuracy, sensitivity, specificity, and
that is, for each instance, prediction is an aggregation of an additive set area under ROC curve (AUC). A model must excel in all these metrics in
of marginal contributions. In our study, the short versus long survival classification problems, where only one decent metric (e.g., specificity
of each patient with a LTx is collectively determined by a set of of SVM) cannot be a determining criterion. It is evident from the results
values for each feature that helps us understand that instance prediction that RF is the best model where it outperforms all others in almost all
accurately. metrics.
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M. Amini, A. Bagheri and D. Delen Decision Analytics Journal 3 (2022) 100058
Table 1
Predictive models’ performance.
4.2. Model explanation survival. Doricic et al. [47] used serum creatinine (END_CREAT) and
other clinical factors to predict the long-term mortality after LTx. Singer
We utilized the SHAP algorithm [41] to achieve the explanation et al. [48] investigated the impact of pretransplant ventilation support
phase objectives in the final step. First, to ensure that the predictive (VENT_SUPPORT_AFTER_LIST) on short- and long-term survival after
models relied on meaningful and relevant patterns and features; next, LTx. Jawitz et al. [16] found donor age (AGE_DON) and total bilirubin
to investigate the most relevant factors among the selected features and (TBILI) as differentiators between short- and long-term survival after
their criticality level for long-term survival. Given the promising result LTx. Yu et al. [14], by a metanalysis of prior research, studied the trans-
of RF from the previous phase (between 75%–80% for all the evaluation plant type (TX_TYPE) and concluded that bilateral LTx is associated
metrics), we applied RF as the base model in the SHAP algorithm. We with longer survival time.
calculated SHAP values in each fold in a 10-fold cross-validation setting This existing literature, among others, demonstrates the effective-
with RF. Then, we took the average of SHAP values for each variable.
ness of our holistic and advanced study of the donor, recipient, and
Fig. 5 presents the ranking of the top twenty features and their
LTx procedure characteristics. Our findings can shed light on other im-
averaged importance. Table 2 shows the top selected variables by SHAP
portant predictors that have not been investigated by medical scholars
and their definitions. We do not see any irrelevant data or judgment by
for long-term LTx survival. For instance, Dhillon et al. [49] studied the
the predictive models from this table. Next, we explain the variables in
impact of Hepatitis B surface antibody (HBV_SURF_TOTAL) on one-year
Table 2.
thoracic transplant survival. Doershuk et al. [50] evaluated the rela-
Some of the variables in Table 2 have already been studied in-
tionship between forced expiratory volume in one second (FEV1_TRR)
dividually or with a few other factors using traditional methods in
prior research and shown to be significant predictors for long-term LTx and LTx timing and short-term survival.
survival. Mabilangan et al. [42] and Kurihara et al. [43] evaluated the Notice here that we omitted the LAS score from our variable’s list
impact of Cytomegalovirus (CMV_IGG) infection status of lung donors so that it does not affect the variable importance measures. According
and recipients on long-term survival after LTx and found it a significant to the LAS calculation method [29], some variables used in LAS calcu-
risk factor. Lehr et al. [44] showed that the extremes of age (AGE) lation are in our top 20 variable list. The presence of variables such as
decrease the long-term survival in adults after LTx. Kanask et al. [45] AGE, WGT_KG_CALC, TBILI, FUNC_STAT_TRR, END_CREAT, BMI_CALC
indicated that organ recipients who were obese (WGT_KG_CALC) had a in our ranking list is an additional demonstration of the effectiveness
shorter survival time after LTx. Banga et al. [46] found serum albumin of our exploratory analysis. Therefore, our findings can be utilized as a
(TOT_SERUM_ALBUM) as a predictor for prolonged hospital length preliminary study for advanced medical research to improve LAS score
of stay after LTx, which is shown to be associated with long-term calculation and organ allocation continuously.
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M. Amini, A. Bagheri and D. Delen Decision Analytics Journal 3 (2022) 100058
Table 2 transplant, and other characteristics. With the advantage of the SHAP
List of top 20 features and their definitions.
algorithm, our proposed approach can picture how these features can
Variable Definition impact the longevity of this patient. Fig. 6 illustrates contributing
CMV_IGG Recipient CMV by IDD test result at transplant features that push the model output from the base value (the average
HBV_SURF_TOTAL Recipient HBV surface antibody total at transplant model output over the training dataset) to the ‘‘high’’ survival time
AGE Recipient age (year) or ‘‘low’’. Features driving the survival time prediction to ‘‘high’’ are
WGT_KG_CALC Calculated recipient weight (kg) shown in red; those pushing the prediction to ‘‘low’’ are blue.
MED_COND_TRR Recipient medical condition pre-transplant at In this example, for a specific patient, in addition to the model
transplant output (short or long survival), the generated SHAP values clarify
BUN_DON Deceased donor terminal blood urea nitrogen which factors are prominent and what their impact is on the model
TOT_SERUM_ALBUM Patient total serum Albumin at registration output, thereby increasing the trust in the model. Also, SHAP values
allow the physicians to reevaluate the situation for each patient. In the
FUNC_STAT_TRR Recipient functional status at transplant
case of short-time survivability (our example), the transplant should be
DAYSWAIT_CHRON Total days on waiting list
reconsidered, or the conditions should be compared to other patients on
VENT_SUPPORT_AFTER_LIST Events occurring between listing and transplant:
the waitlist. Although, in general, we suggest organ allocation to those
episode of ventilatory support
patients with high survivability, SHAP values for each patient can help
FEV1_TRR Pulmonary status: FEV1% predicted at transplant
compare patients even in the same class.
END_CREAT Serum Creatinine at
Another benefit of SHAP values for each individual is the ability
transplant/offer/removal/current time (HL, LU
only) to provide patients with recommendations. For example, if a patient’s
AGE_DON Donor age (year)
weight is striking his survivability, the doctor can give practical advice
or postpone the transplant. Finally, in the case of any discrepancies
BMI_CALC Calculated candidate BMI
or underlying conditions, the doctors can reject or adjust the model’s
BRONCHO_RT_DON DDR right lung bronchoscopy
output by looking at the individual SHAP values.
PROTEIN_URINE Deceased donor protein in urine
TX_TYPE Type of transplant 5. Summary and conclusion
WGT_KG_DON_CALC Calculated donor weight (kg)
TBILI Most recent serum total Bilirubin at transplant In this paper, we studied factors indicative of patients’ long- versus
TX_PROCEDUR_TY Recipient procedure type short-term survival after LTx by proposing an explanatory analytics
framework. We collected a comprehensive dataset of LTx operations
from the United Network for Organ Sharing (UNOS) registry database,
including recipient, donor, and LTx procedure characteristics. Based
on the survival time of lung recipients, we defined two categories of
patients representing short- and long-term survival after LTx. After
going through a comprehensive data cleaning and preprocessing in the
proposed framework, we trained and tested various ML algorithms to
find the best predictive one for our binary classification problem and
preprocessed data in hand. We found RF as the one with the best
predictive performance and chose it for further analysis. In the next
step, to interpret and explain the predictions, we employed a novel
explainable AI method accompanied by RF to understand the most
critical factors affecting the long-term survival after LTx. As a result,
our proposed framework provided a list of the top 20 important factors
and their corresponding importance measures. Policymakers can use
our findings in improving the lung allocation system. In addition, our
framework can predict and explain the individual long-term survival
of LTx candidates and can be utilized as a recommendation system for
organ matching and allocation.
One limitation of this study is that the data is limited to only US
Fig. 6. SHAP values for an individual patient. LTx patients. Although we believe that our data set is large enough to
obtain robust results, our framework and results could be validated by
scholars who have access to larger organ transplant registries’ data like
ISHLT.
We also did not have access to the patients’ medical history and
4.3. Individual explanation
underlying condition before the transplant. This variable and others
such as gender and race could be controlled for in future studies.
In healthcare analytics, it is crucial to investigate the process of
any decision support system for an individual patient. This way, the Moreover, each of the top variables in Table 2 calls for a more focused
performance of advanced algorithms can help physicians by providing investigation through statistical and causal models.
the main contributing factors for each patient. In addition, physicians Finally, from a broader perspective, LTx has brought patients hope
can enforce necessary adjustments based on the patient’s underlying for prolonged survival and enhanced health-related quality of life
conditions. SHAP algorithm is an appropriate tool in this regard. On (HRQoL). Although these hopes come true for many patients, some
the one hand, it provides a holistic picture of the major risk factors die earlier than they would have without LTx and a considerable
and their relative importance (Fig. 5). On the other hand, it delivers an proportion of lung recipients face comorbidities and adverse health
individual-level analysis of the features and their contribution to each events. Hence, survival analysis alone cannot provide an adequate
patient’s probability of an outcome. measure of the level of success or failure of LTx, and studying the
Consider a patient in his fifties with positive HBV and CMV, who HRQoL of lung recipients is an essential task. Previous studies on
is above the average weight, has poor functionality at the time of HRQoL after LTx often relied on survey data from living and well
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M. Amini, A. Bagheri and D. Delen Decision Analytics Journal 3 (2022) 100058
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