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| id | Vol-3194/paper47 |
| wikidataid | Q117344945→Q117344945 |
| title | Data–Driven, AI–Based Clinical Practice: Experiences, Challenges, and Research Directions |
| pdfUrl | https://ceur-ws.org/Vol-3194/paper47.pdf |
| dblpUrl | https://dblp.org/rec/conf/sebd/FerrariMMM22 |
| volume | Vol-3194→Vol-3194 |
| session | → |
Data–Driven, AI–Based Clinical Practice: Experiences, Challenges, and Research Directions
Data–Driven, AI–Based Clinical Practice: Experiences,
Challenges, and Research Directions
Davide Ferrari1,2 , Federica Mandreoli3 , Federico Motta3 and Paolo Missier4
1
King’s College London, London, UK
2
Guy’s and St. Thomas’ NHS Fundation Trust, London, UK
3
Università di Modena e Reggio Emilia, Modena, Italy
4
Newcastle University, Newcastle upon Tyne, UK
Abstract
Clinical practice is evolving rapidly, away from the traditional but inefficient detect-and-cure approach,
and towards a Preventive, Predictive, Personalised and Participative (P4) vision that focuses on extending
people’s wellness state. This vision is increasingly data–driven, AI–based, and is underpinned by many
forms of “Big Health Data” including periodic clinical assessments and electronic health records, but
also using new forms of self–assessment, such as mobile–based questionnaires and personal wearable
devices. Over the last few years, we have been conducting a fruitful research collaboration with the
Infectious Disease Clinic of the University Hospital of Modena having the main aim of exploring specific
opportunities offered by data–driven AI–based approaches to support diagnosis, hospital organization
and clinical research. Drawing from this experience, in this paper we provide an overview of the
main research challenges that need to be addressed to design and implement data–driven healthcare
applications. We present concrete instantiations of these challenges in three real–world use cases and
summarise the specific solutions we devised to address them and, finally, we propose a research agenda
that outlines the future of research in this field.
Keywords
Artificial intelligence, Machine learning, P4 medicine, High stake domains
1. Introduction
The promise of data–driven healthcare is underpinned by the availability of “Big Health Data”
to feed machine learning (ML) and artificial intelligence (AI) models to achieve prevention
by prediction. These datasets traditionally include the individual medical history (known as
EHR, for Electronic Health Records), including primary and secondary care (hospital) events
as well as medicine prescription history. In the vision of Preventive, Predictive, Personalised
and Participatory (P4) medicine, these are complemented by a rich “cloud” of additional data
types, ranging from *omics data (genotypes, transcriptomes, proteomes, . . . ), but also new forms
of self–assessment, such as mobile–based questionnaires and automated self–monitoring logs
from personal wearable devices.
SEBD 2022: The 30 th Italian Symposium on Advanced Database Systems, June 19–22, 2022, Tirrenia (PI), Italy
$ davide.ferrari@kcl.ac.uk (D. Ferrari); federica.mandreoli@unimore.it (F. Mandreoli); federico.motta@unimore.it
(F. Motta); paolo.missier@newcastle.ac.uk (P. Missier)
� 0000-0003-2365-4157 (D. Ferrari); 0000-0002-8043-8787 (F. Mandreoli); 0000-0002-5946-0154 (F. Motta);
0000-0002-0978-2446 (P. Missier)
© 2022 Use permitted under Creative Commons Attribution–NonCommercial 4.0 International License (CC BY NC 4.0).
CEUR
Workshop
Proceedings
http://ceur-ws.org
ISSN 1613-0073
CEUR Workshop Proceedings (CEUR-WS.org)
� Realising this vision requires a strong alignment between clinical research questions, data
science and AI methods on one side, and data collection, curation, and engineering practices,
on the other. Out of these three elements, in this paper we focus specifically on the data issues,
reflecting on the main data challenges that need to be overcome to enable AI–based healthcare.
Drawing from our own recent experience working with prospective and retrospective patient
cohort studies to learn a variety of predictive models, we suggest that data–driven healthcare
applications are unique in terms of the challenges generated by the constantly–evolving, and
often poorly controlled and even chaotic environment within which they are developed. For
instance, clinical data is typically highly sensitive, costly to acquire and curate, and subject to
complex governance policies.
The paper describes the data challenges we faced in three case studies coming from the
Infectious Disease Clinic of the University Hospital of Modena, articulates how these were
addressed in an ad hoc fashion to make modelling possible, and finally suggests a research
agenda aimed at making the data engineering approach more principled and systematic.
1.1. Case study: Predicting functional ability in long–term HIV patients
The international study My Smart Age with HIV (MySAwH) is a multi–centre prospective
project aimed at studying and monitoring healthy ageing in older people living with HIV. The
cohort included 260 patients with 3 longitudinal follow–ups over 18 months, consisting of
standardised clinical assessments, but also including an innovative element of patient self–
monitoring, achieved using mobile smartphone apps and commercial–grade activity loggers.
These were used to collect Patient Related Outcomes (PROs), combining questionnaires delivered
with daily physical activity reports (limited to hours of sleep and step counts).
The study [1] used these combined datasets that refer to the notion of intrinsic capacity
(IC), i.e. the combination of all the individual’s physical and mental capacities, as proposed
by the World Health Organization (WHO)1 , to predict individual health outcomes. The main
data challenges associated with the study include ensuring the reliability, consistency, and
completeness of the data collected from self–monitoring individuals.
1.2. Case study: predicting respiratory crisis in hospitalised Covid–19 patients
When Covid–19 hit the world in 2020, hospitals and researchers were not ready to tackle the
emergency and adapted themselves day by day based on the unfolding of new necessities. Covid–
19 brought unexpected complications to patient management, including managing limited ICU
(Intensive Care Unit) resources in local hospitals. One of these was the University Hospital of
Modena, where around 200 patients admitted between February and April 2020, at the start of
the first wave of Covid–19 crisis in Italy, contributed to generate 1068 usable observations. Like
in many other professional healthcare settings around the world, here the clinical staff started to
collect new types of data for the inpatients, through standard blood tests but also specifically to
monitor respiratory efficiency and to track their trajectory through stages of oxygen treatment
and eventual outcome (discharge or death). Many hospitals used similar datasets in combination
with ML algorithms to model mortality risk. In [2] we faced a problem related to resource
1
Ageing and health, WHO, 2018. https://www.who.int/news-room/fact-sheets/detail/ageing-and-health
�management; in detail, we developed a model to estimate the probability that a patient would
experience a respiratory crisis within the next 48 hours. A correct estimate would be able for
instance to prevent the early discharge of patients at risk. This was approached as a probabilistic
classification problem (i.e. estimating the probability that a patient will or will not undergo a
respiratory crisis).
1.3. Case study: predicting oxygen therapy progression in hospitalised
Covid–19 patients
This latter case study shared the same domain of application of the previous one and started
temporally after it; for these reasons several characteristics from its ancestor were actually
inherited. In [3] too the faced problem was related to resource management; in detail we aimed
at predicting a patient’s transition from one type of oxygen therapy to another, which in turn
would have helped to manage limited ICU resources in hospitals. This required a process mod-
elling approach, based on Hidden Markov Models (HMMs), aimed at estimating the transition
probability between any two states representing therapy regimes.
As anticipated, both the studies [2, 3] were underpinned by the same hospital dataset, but
they used different subsets of variables at different time points. These were EHRs consisting of a
combination of routine clinical tests as well as more specialised types of tests and observations.
The experimental nature of these data, collected in a time of emergency, resulted in high
instability (physicians constantly added or removed variables, effectively changing the schema
on a daily basis) and imbalance, as the outcome of interest such as respiratory crisis or death
were inevitably (and fortunately) the minority classes. Critically, modelling for both tasks had
to contend with very small data sizes (in the order of thousands) and the problem of selecting
significant predictors amongst a set of about a hundred ones.
2. Recurring research issues
In this section we present a catalogue of the main research issues that emerged in the three
case studies introduced in Section 1, most concerning data quality. In the next Section we will
articulate how these have been addressed in our case studies.
Data sparsity and scarcity. Individual medical histories like EHR data can be viewed as
an irregular collection of time series, one per–patient, where each data point in the series is a
patient event, consisting of a vector of variables. The collection is irregular because the time
series have different event density for different patients and for different variables. Indeed,
most variables are typically collected on a as–needed clinical basis, especially when involving
expensive instruments or invasive examinations. Other variables, instead, are collected regularly
but with varying frequency over time. Moreover, novel scientific evidence may induce changes
in the data collection protocol.
For example, during the Covid–19 pandemic, routine data was collected from all the patients
at University Hospital in Modena from the beginning; whilst some specific pieces of informa-
tion, e.g. interleukin–6, from the blood laboratory analysis, were regularly collected only after
�scientific evidence of their relevance in the diagnosis of patients affected by Covid–19–induced
pneumonia, and thus they were absent for a substantial proportion of the patients. Similar prob-
lems were present in the data collected from self–monitoring individuals for the MySAwH study
because activity loggers’ data were available daily whilst Emotional Momentary Assessment
data was collected through a smartphone app monthly.
When data are represented in a tabular format as needed to feed ML models, data sparsity
can lead to large amount of missing values in the already collected data, which in turn results
in fewer usable records, when missingness in important variables is not tolerated by the chosen
learning algorithms. This problem is exacerbated when patients are few as it happens, for
instance, in prospective studies like MySAwH or in emergency situation, like Covid–19, when
there is the urgency of developing clinical decision making support systems.
For instance, the second Covid–19 study mentioned above used a later version of the same
dataset with data collected for a longer period (March 2020–May 2021); where, as depicted in
Figure 1, only between 23% and 60% of the available records were used, against the 56% of the
original study.
Figure 1: Percentage variable completeness of the Covid–19 dataset used in [3]
While missing data can sometimes be inferred, or imputed, from available value distributions,
this is not an option when dealing with critical patients vital parameters, which by their
own nature are subject to abrupt changes and thus should not be extrapolated from known
distributions. In fact, one may argue that the value of the data in this context is the change in
data values, signalling an impending crisis.
�Data imbalance Data imbalance is a well–known problem when trying to learn a classifier
predicting a rare event. Yet, these are often precisely the classes of interest, for instance
a respiratory crisis, which is rare relative to the balance of other more positive outcomes.
Similarly, when the focus is on patient’s oxygen state transition, the intubation therapy is
(fortunately) a rare state and, as such, it could perhaps be disregarded. However, as the low
frequency matches of these events are matched by correspondingly low ICU capacity, predicting
such events remains a priority.
Data inconsistency and instability Prospective datasets that are collected for research
purposes, such as for [1], tend to be stable as they are the result of an agreed upon protocol.
Interesting research insights, however, are often derived from retrospective datasets, which may
include a broad variety of observations and are often collected in an opportunistic fashion over
unanticipated periods of time. This has been the case for the Covid–19 datasets used in [2, 3],
where not only the content were updated at irregular intervals, but also the set of variables
and their use and indeed the overall schema evolved over time, driven by the discovery of new
variants, changes in diagnostic strategies, and changes in hospital management policies. For
example, the information about tocilizumab administration was initially collected in a column
containing free text notes, while after a while it became an ad hoc boolean column due to the
fact that patients who received it started being a considerable amount of the total ones. Another
example regards the O2 therapy setup: it has always been a free text entry, so the inconsistencies,
mistyping and individual interpretation while inputting made the programmatic analysis of that
data very complicated (therapies regimes were reported as percentage of oxygen in breathing air,
liters per–minute delivered by the mask or the name of the mask itself, all in the same database
field). A subsequent adaptation and correction of previous values was needed to harmonise the
reporting of such information. In [3] too, we faced similar issues, this time directly involving the
outcome; in fact the oxygen therapy states were initially only 4, i.e.: No O2 , O2 , NIV, Intubated,
plus the two final ones Deceased and Discharged, respectively. Then, when the second wave of
patients began, they were so many that the previously known O2 state, in which patients used
to breath air enriched with oxygen through a venturi mask, had to be partitioned into two states:
a first one with the same name/ventilation support and a second one named HFNO, providing a
High Flow of Oxygen through a Nasal cannula. This change forced the first Hidden Markov
Model [4] to be retrained and pushed towards adopting a more robust ensemble solution.
Changes in data format and units are as common as they are insidious, as they tend to break
the data pre–processing pipelines designed to wrangle the raw data into a training–ready format,
requiring lengthy repairs. These changes are not limited to emergency situations such as the
one described. Indeed, data acquisition and curation practices are also affected by changes in
public policy, hospital resources, collection technology, as well as the ability to link out and
integrate with other data sources.
Importantly, in a scenario where data is used to train ML models, this instability, in turn,
translates into instability of the models trained on these datasets. While simple re–training is
sufficient when the data grows with a stable schema, an evolving and unstable schema affects the
choice of learning algorithm and of its hyper–parameters, as well as variable ranking and overall
model performances, requiring constant maintenance of the models and thus propagating the
�instability problem into the deployment stage.
Not all errors are equally wrong In binary classification problems, predictive performance
is routinely measured by counting false positives and false negatives. When the relative cost of
these errors is the same, standard measures such as F–score and AUROC represent an efficient
way to summarise predictive performance.
This is hardly ever the case with high–stakes medical applications, where a bias towards one
type of error is often preferable. For instance, when predicting respiratory failure (and generally
when predicting a class that represents the undesirable outcome), a conservative stance where
false positives are preferred to false negatives ensures that no unnecessary risk (i.e., of early
discharge) are taken, possibly at the cost of extra attention to patients. In the next Section we
will reflect on how such deliberate bias was introduced in both of our Covid–19 case studies.
Human-in-the-loop The closer predictive models come to being adopted as part of clinical
practice, the more pressing the need becomes to ensure that the models are explainable, on
the assumption that explanations engender trust in the models. What this means in practice,
however, is not always clear. For instance, it is becoming increasingly evident in the health data
science community that trust should include not only the clinician but also the patient.
Thus, even the simplest type of explanations, namely a weight–ranked list of features used in
a linear model, is questionable as those variables mean little to the patient. More sophisticated
technical explanations are now available for non–linear models, too, as well as for the interpre-
tation of histology images, for example. However, these still do not address the patient side of
the “dialogue”, and there is little agreement that they would be sufficient for the physician, too.
Even assuming the model can “explain itself”, this only addresses half of the problem. In a
true human-in-the-loop AI scenario, it should be possible to provide feedback to the learning
algorithm, reflecting agreement or disagreement with the prediction, or perhaps to force a bias
(like discussed briefly in the previous point). While this is technically possible, for instance by
changing ground truth annotations or using one of the many available penalty–based models,
this is again not a level at which clinicians are comfortable to operate.
Data science as a translational science Statistics has been at the basis of clinical practice
for decades, however in the last years also the communities built around the development of AI
and ML techniques have came in touch with medicine; these two fields are nevertheless evolving
at different speeds, as well as some physiological diffidence and resistance are slowing down
this cross–domain integration too. To bridge this gap between physicians and data scientists, a
common language and shared efforts are inevitably needed: clinicians need to better understand
the rationale behind mathematical models in order to allow improving them by providing useful
insights from their domain of expertise, to better overcome the issues arisen by the data; on the
other hand computer scientists and mathematicians need to understand the clinical meaning
of the data they deal with, in order to build really useful and trustworthy applications. In our
experience, the closer this relationship is cultivated, such as in a daily interaction, the quicker
this iterative methodology will converge towards results suitable for both the research fields,
�because the former need new and more powerful tools, the latter real–world problems to tackle
and improve well–known methods.
3. Addressing the challenges, one case study at a time
In this section we are presenting concrete examples of real–world research projects in which
those challenges occurred. We will briefly contextualise the problem in the clinical scenario and
explain the strategies that were put in place to adequately produce functioning data–driven
pipelines. Table 1 provides a summary of such challenges associated with the data used in each
of the studies.
Table 1
Challenges faced by each study
Challenge MySAwH Covid–19 𝑃 𝑎𝑂2 /𝐹 𝑖𝑂2 Covid–19 𝑂2
Data imbalance ✓
Data inconsistency and instability ✓
Data sparsity and scarcity ✓ ✓ ✓
Human-in-the-loop ✓ ✓
Not all errors are equally wrong ✓ ✓
3.1. Use case 1: My Smart Age with HIV
The goal of this project was to create ML models using the patient–generated data to predict
three relevant clinical outcomes at the following 9–months visit in hospital; namely, Quality of
Life (QoL), physical activity capability, and the risk of having a fall. Available variables included
(i) physical activity (steps count, sleep hours and calories); (ii) 56 Patient-reported-outcomes
(PROs) on QoL, collected using a smartphone; and (iii) clinical variables, including HIV–specific
variables. Clinical variables built a comprehensive geriatric assessment and were collected by
healthcare workers during hospital visits at time 0, 9 and 18 months generating 2 inner time
windows; 37 of these variables were also used to measure the Frailty Index (FI) as defined in
[5]).
Data heterogeneity and sparsity emerged since the protocol was designed to collect different
type of data at different frequency. Gaps of up to 17 consecutive missing observations were
found in PRO variables, with 108 gaps per–patient on average. Our approach was to impute
by interpolating missing data points in the time series modulating the maximum number of
consecutive missing values imputed to not compromise the model performance. Still, the
remaining missing data resulted in a loss of usable observations. Given the different granularity
of the collected data and the missing data left after the interpolation, we also needed to re–
sample and aggregate the three data sources to a monthly frequency. The two time windows
were used as reference for the prediction task as for each monthly data point, the prediction
target was the clinical outcome at the end of the respective 9–months period.
Despite data scarcity, we were able to compare expert–provided, or “knowledge–driven” (KD)
clinical risk scores to data–driven (DD) scores obtained using the training set. The results,
�indicating superiority of DD, are shown in Figure 2, where we also tested the relevance of a
Frailty Index FI [5] as an additional predictor.
100% 100%
80%
95% 60%
90% 40%
20%
85% 0%
KD DD KD DD KD DD KD DD KD DD KD DD KD DD KD DD KD DD
QoL SPPB Acc Prec - True Prec - False Rec - True Rec - False F1 - True F1 - False
w/o FI 91% 92% 93% 92% w/o FI 84% 93% 22% 97% 85% 93% 2% 52% 99% 100% 4% 68% 91% 96%
w/ FI 92% 94% 93% 95% w/ FI 89% 95% 72% 98% 92% 95% 54% 68% 96% 100% 62% 80% 94% 97%
Figure 2: Performance measures of the three clinical outcomes predictors: QoL and SPPB (left) and
Falls (right)
Shapley values [6, 7] were then used to provide an interpretation of model prediction at
individual level. These provided both a quantitative as well as qualitative view of the relative
importance of the variables in prediction. Figure 3 shows different interpretations for the same
predicted value but for two different patients.
Figure 3: Shapley Values interpretation for two different patients with the same prediction of Short
Physical Performance Battery (SPPB)
3.2. Use case 2: Covid–19, predicting respiratory failure
In [2], respiratory failure was tested by using blood gas analysis, namely when the 𝑃 𝑎𝑂2 /𝐹 𝑖𝑂2
ratio falls below the 150 mmHg threshold, within two days from admission to hospital. Thus,
its prediction translated into a binary classification problem.
Data instability resulted from the irregular and experimental collection of 91 variables,
including 39 from blood and urine tests, 7 from the blood gas analysis, 29 different disease
specific symptoms, 14 co–morbidities and demographics.
� Our milestone data extractions of 2,454 and 2,888 data points each provided an average
completeness of 62% ± 22 and 57% ± 22 respectively. Some of the variables were collected
on–demand based on clinical needs and few were introduced in the data collection only after
their need was proven by scientific literature. For example, lymphocytes were present only
in 7.5% of the samples in a first data extraction and 7.8% in a subsequent one; interleukin–6
instead was collected in about 20% of the daily samples and given its rapid variability in time,
imputation was not a reliable strategy. To handle this inevitable lack of data we created a model
trained using the robust Python implementation of LightGBM [8] which supports missing
values without the need of imputing them.
Data inconsistency was also introduced, as the information systems used by the hospital
evolved almost daily. For example, oxygen therapy measures were progressively refined, but
the units of measure changed in the process from liters per–minute to percentage of oxygen in
breathable air, making it difficult to discern automatically with which the clinician recorded the
value.
In this high–stake domain we want to prevent as much as possible false negative (FN)
predictions because they are extremely more dangerous than false positives (FP) and they can
imply the discharge of a patient at high risk; to address this issue, a bias was introduced into
the binary cross entropy in order to penalise FP, possibly at the expense of additional FN. The
employed equation was the following:
𝐿(𝑦, 𝑝 (𝑥)) = −𝛽 · 𝑦 ln 𝑝(𝑥) − (1 − 𝑦) ln (1 − 𝑝 (𝑥)) (1)
where 𝛽 parameter was used to modulate the increasing penalty given to FN and we experi-
mentally found the best balance with 𝛽 = 2 (i.e., the penalty for a FN prediction is double of
the penalty for a FP).
As in the previous case study, we relied on Shaply values [7] to provide per–individual explana-
tions of the predictions in terms of the variables. Moreover, the global Shapley value ranking
was used to identify the top features out of the initial 91, resulting in a more parsimonious
model with no appreciable performance loss (AUROC 84% for the leaner model, compared with
85% of the one using the full feature set). More precisely, we removed the less relevant features
until the performance started to detriment significantly; this produced a list of 20 final variables
which accounted for the vast majority of information delivered by the dataset for this learning
task.
3.3. Use case 3: Covid–19, predicting oxygen therapy states
In [3] the aim was to predict the patients’ state transitions, where each state represented an
oxygen therapy state, which could change for each patient on a daily basis.
The initial approach involved training an HMM over a set of 17 observable variables, 2
cross–sectional (age and Charlson Comorbidity Index) and 15 longitudinal, including oxygen
therapy. This was complicated by data sparsity, as shown in Figure 1, which was addressed
using a library robust to missing data [9]; and more importantly, by a strong imbalance on the
state transitions, whereby the most common state [4] was also the clinically least interesting.
�Table 2
Per–state performance in terms of E–measure(𝛽 = 0.5)
e d
ed
d
rg
se
at
Performance Global
ha
O
ea
2
b
O
FN
isc
tu
IV
ec
o
2
In
O
H
N
N
D
D
measure (𝜀 < 0.01%) accuracy
a) Single HMM 38.7 – – – – – – –
b) Majority voting ensemble – 𝜀 94.7 𝜀 𝜀 𝜀 𝜀 𝜀
c) HMM–ensemble – 𝜀 97.3 95.1 98.5 98.1 37.5 25.9
As standard re–sampling does not work well on such small datasets (14, 249 EHRs for about
1, 040 patients), we implemented an ensemble–based approach based on two main strategies.
Firstly, we made the model overfitting aware, which made it possible to prune out some
models/outcomes a priori. And secondly, we gave it the ability to compare and eventually
combine outcomes coming from each one of the models, by “cherry–picking” simple pieces of
solution from a partition of the explored space, in order to mitigate and better face the imbalance
problem in a divide et impera manner; in fact each sub–problem had more balanced outcomes,
which allowed the respective HMMs to overfit less.
The elements of novelty were the choice of two hyper–parameters, able to tune the aggres-
siveness of the aforementioned overfitting–aware pruning mechanism; as well as the choice
of the functions used to measure the degree of support of each model for each outcome. The
latter ones are in facts, the key point around which the pieces of solution are compared, i.e.
ranked, and combined; in our experience they produced better performance when including
among the terms: a model performance metric (e.g. F1 –score, Recall) and either the number
of classifiers which did not vote for the outcome, rather than the outcome inverse probability
or its logarithm. As visible in Table 2, our algorithm (c) had remarkable performance (> 95%)
in terms of E–measure𝛽=0.5 in all the severe/critical states, as well as it better performed than
state of the art approaches (a, b) with regard to the final ones (i.e. deceased and discharged).
4. Concluding remarks and future research agenda
In this paper we illustrated three examples where data quality challenges that are common to
many problems in Health Data Science have been addressed in an ad hoc fashion, by customizing
out-of-the-box ML algorithms to meet specific requirements.
Here we advocate a more systematic and principled approach, possibly leading to an interest-
ing research agenda. Such approach should be centred on data–centric AI, i.e. the systematic
engineering of the data used to build an AI system [10]. This consists of a number of techniques
that are perhaps less known in ML. Firstly data augmentation, a data–centric AI technique
that can be employed to overcome real–world data challenges including data sparsity, scarcity,
and unbalance.Data augmentation involves combining limited labeled data with synthetic data.
While this line of research is still in its infancy, interesting advances are found in the devel-
opment of generative models [11, 12], a promising direction specifically when dealing with
�clinical data.
Secondly, self–supervision and semi–supervision provide a way to overcome the scarcity of
labelled data, by combining it with existing and more abundant unlabeled data. However,
current solutions like the VIME system [13] have limited applicability in clinical practice as they
do not tolerate the large portion of null feature values that characterises this type of data, whilst
at the same time state-of-the art data imputation approaches, applied to our clinical datasets,
reduce ML model performance to unacceptable levels.
In the data–centric AI vision of system production, most of the complexity of ML systems is
tied to data processing, handling and monitoring. Preparing data pipelines in clinical practice
currently requires considerable human effort and is very time consuming. Extensive domain
knowledge is necessary to address the problem of inconsistency in such kind of data. A more
comprehensive approach to improve the quality of the data itself, along with the various
dimensions discussed in this paper, are therefore also required.
However, when trying to automate data cleaning and preparation using scripts or workflows,
we see that data instability, caused by successive data extractions from a source, runs counter
to these efforts, as changes in data format and schema may easily break the data pipelines. One
possible direction to alleviate this problem involves adding more robust debugging facilities to
the pipeline. Capturing and querying the provenance of the transformations produced by the
pipeline may just be the tip of the solution.
Another research field which could contribute in making the P4 medicine vision concrete in
clinical practice is the human-in-the-loop ML. Indeed, a real iterative process where the model
provides comprehensible explanations and in turn is incrementally improved based on user
feedback is not yet part of routine health data science practice. Nevertheless, according to the
physicians we work with, this is one of the most expected revolutions in the near future.
As far as explainability is concerned, although Shapley values represent a valuable concrete
option in medicine [14], it will become important in the next future to study more intuitive
forms of explanation that better meet physicians’ and patients’ needs like example–based, image,
and textual explanations [15]. Last but not least, future research investment should be devoted
to the development of ML models that are able to alter their decision [16] and act on modifiable
variables [17] according to external inputs like expert domain knowledge and user feedback.
According to the clinicians we reached out and us, both our communities should push towards
the implementation of these human-in-the-loop aspects; which may contribute in closing the
gap in the cross talk between the patients, the physicians and the data scientists, finally building
mutual trust between them and providing qualitatively better healthcare solutions.
Acknowledgments
The authors would like to thank Prof. Giovanni Guaraldi for providing the datasets which made
these studies possible, but also all the healthcare workers of the Infections Diseases Clinic of the
University Hospital of Modena which contributed to their collection and constantly provided
constructive feedback during the designing, developing and testing phases of the models built
for the three use cases presented in this paper.
�References
[1] D. Ferrari, G. Guaraldi, F. Mandreoli, R. Martoglia, J. Milić, P. Missier, Data–driven vs
knowledge–driven inference of health outcomes in the ageing population: A case study,
in: CEUR Workshop Proc., 2020. URL: http://ceur-ws.org/Vol-2578/DARLIAP8.pdf.
[2] D. Ferrari, J. Milić, F. Mandreoli, P. Missier, G. Guaraldi, et al., ML in predicting respiratory
failure in patients with COVID–19 pneumonia: challenges, strengths, and opportunities in a
global health emergency, PLOS ONE (2020)1–14. doi:10.1371/journal.pone.0239172.
[3] F. Mandreoli, F. Motta, P. Missier, An HMM–ensemble approach to predict severity
progression of ICU treatment for hospitalized COVID–19 patients, in: 20th IEEE Int. Conf.
on ML and Appl., 2021, pp. 1299–1306. doi:10.1109/ICMLA52953.2021.00211.
[4] F. Motta, Hidden Markov Models to predict the transitions of SARS–CoV–2 patients’ state,
Master’s thesis, Università degli studi di Modena e Reggio Emilia, 2020.
[5] I. Franconi, O. Theou, L. Wallace, A. Malagoli, C. Mussini, K. Rockwood, G. Guaraldi,
Construct validation of a Frailty Index, an HIV Index and a Protective Index from a clinical
HIV database, PLOS ONE (2018). doi:10.1371/journal.pone.0201394.
[6] S. M. Lundberg, et al., Explainable ML predictions for the prevention of hypoxaemia during
surgery, Nature Biomedical Eng. (2018) 749–760. doi:10.1038/s41551-018-0304-0.
[7] S. M. Lundberg, et al., From local explanations to global understanding with explainable
AI for trees, Nature Machine Intell. (2020) 56–67. doi:10.1038/s42256-019-0138-9.
[8] G. Ke, et al., LightGBM: A highly efficient gradient boosting decision tree, in: Adv.
in Neural Inf. Process. Syst., 2017. URL: https://proceedings.neurips.cc/paper/2017/file/
6449f44a102fde848669bdd9eb6b76fa-Paper.pdf.
[9] J. Schreiber, Pomegranate: fast and flexible probabilistic modeling in Python, Journal of
ML Research (2018) 1–6. URL: http://www.jmlr.org/papers/volume18/17-636/17-636.pdf.
[10] N. Polyzotis, M. Zaharia, What can data–centric AI learn from data and ML engineering?,
in: Adv. in Neural Inf. Process. Syst., 2021. doi:10.48550/arXiv.2112.06439.
[11] J. Zhang, G. Cormode, C. M. Procopiuc, D. Srivastava, X. Xiao, Privbayes: Private data
release via bayesian networks, ACM Trans. Database Syst. (2017). doi:10.1145/3134428.
[12] J. Jordon, J. Yoon, M. van der Schaar, PATE–GAN: Generating synthetic data with differen-
tial privacy guarantees, in: 7th Int. Conf. on Learning Representations (ICLR), 2019. URL:
https://openreview.net/forum?id=S1zk9iRqF7.
[13] J. Yoon, M. van der Schaar, et al., VIME: Extending the success of self and semi–supervised
learning to tabular domain, in: Adv. in Neural Inf. Process. Syst., 2020. URL: https:
//proceedings.neurips.cc/paper/2020/file/7d97667a3e056acab9aaf653807b4a03-Paper.pdf.
[14] K. D. Pandl, F. Feiland, S. Thiebes, A. Sunyaev, Trustworthy ML for health care: Scalable
data valuation with the shapley value, in: Proc. of the ACM Conf. on Health, Inference,
and Learning, 2021, pp. 47–57. doi:10.1145/3450439.3451861.
[15] G. Vilone, et al., Classification of explainable AI methods through their output formats, Ma-
chine Learning and Knowledge Extraction (2021) 615–661. doi:10.3390/make3030032.
[16] N. Boer, T. Milo, et al., Personal insights for altering decisions of tree–based ensembles
over time, Proc. VLDB Endow. (2020) 798–811. doi:10.14778/3380750.3380752.
[17] A. Hall, et al., Identifying modifiable predictors of patient outcomes after intracerebral hem-
orrhage with ML, Neurocritical Care (2021) 73–84. doi:10.1007/s12028-020-00982-8.
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