Time Series Prediction using Deep Learning Methods in Healthcare

In plain words

Hospitals and insurers record a patient's history as a long sequence of events: visits, lab results, vital signs, diagnoses and medicines. Predicting what happens next, such as a readmission or a death, is a standard task. Older methods reduce that sequence to a few summary numbers chosen by hand. Neural networks that read the sequence step by step can avoid much of that manual work.

This paper is a literature review rather than a new method. The authors searched four research databases, kept the studies that used deep networks on structured patient time series, and sorted them by technical contribution. The result is a map of ten research streams, with the design choices each one tried and the gaps the authors see. The main pattern is that recurrent networks of the LSTM and GRU kind are the default, and that many design questions have not been compared head to head.

TL;DR

A systematic review of 77 studies from 2016 to 2020 on deep learning for structured patient time series. Recurrent networks are the most common model, and most results are author-reported on different datasets, so they cannot be ranked against one another. The paper's value is the list of open gaps (sequence versus matrix representation, the effect of attention on accuracy, cost-sensitive and transfer learning) and the inventory of which design choices have been tried.

Problem

Healthcare records are high-dimensional and irregular. Traditional machine learning usually needs hand-chosen features and coarse summaries such as means and standard deviations, which fail to capture the order and timing of medical events §1. The authors also note that a recent review found risk models built on EHR data use a median of 27 features §1. Deep learning is proposed as a way to learn representations directly from sequences §1. The review asks six questions: how inputs are represented, how irregularity and incompleteness are handled, which models work best and when, how medical knowledge helps, how outcomes can be interpreted, and whether the models scale to larger data §2.1.

Method

This is a systematic review, not an algorithm, so the steps below are the review protocol and the study-level questions used to sort the literature.

1. Search. MEDLINE, IEEE, Scopus and the ACM Digital Library were searched for studies published before 7 February 2021. Studies from 2020 were searched again on 4 November 2021 §2.2. Full query strings for each database are in tab. S1.
2. Eligibility. English, original, peer-reviewed journal or conference papers only. Posters and preprints were excluded. Papers had to use deep learning on structured patient time series for an outcome prediction task. The scope follows the outcome-prediction category of Shickel et al. §2.3 [ref. 27]. Unstructured data (text, images, sensor signals) and studies missing core characteristics were excluded §2.3 §3.
3. Extraction. Each study was coded on ten characteristics: medical task, database, input features (demographics, vital signs, lab tests, procedure, diagnosis, medication codes and others), preprocessing, patient representation, DL architecture, output temporality (static or dynamic), performance, benchmark and interpretation tab. 1 §2.4. Full-text checks required four of these to be stated: input features, patient representation, architecture and output temporality §3 fig. 1.
4. Categorisation. Each included study's technical contribution was assigned to one of ten categories: patient representation, missing value handling, DL models, addressing temporal irregularity, attention mechanisms, incorporation of medical ontologies, static data inclusion, learning strategy, interpretation and scalability §2.5 fig. 3. Domain-only contributions were summarised briefly §2.5.

# Screening funnel  [§2.2] [§2.3] [§3] [fig. 1]
# Input:  records from MEDLINE, IEEE, Scopus, ACM (1,524 stated)
# Output: included studies (77 stated)

def is_candidate(record):
    # Keep English, original, peer-reviewed work only  [§2.3]
    if not is_english_original_peer_reviewed(record):
        return False
    # Structured EHR or claims data with a temporal dimension  [§3] [fig. 1]
    if not uses_structured_temporal_ehr_or_claims(record):
        return False
    # Deep learning for an outcome prediction task  [§2.3] [§3]
    return uses_dl_for_outcome_prediction(record)

def is_included(record):
    # Four characteristics must be stated in the full text  [§3] [tab. 1]
    return all([
        input_features_stated(record),
        patient_representation_stated(record),
        dl_architecture_stated(record),
        output_temporality_stated(record),
    ])

Each included study is then placed in the ten categories of §2.5 and summarised in §3.1–§3.10 and §4.1–§4.10.

Two findings from the review's synthesis that implementers may act on:

• Recurrent networks (LSTM, GRU, bidirectional variants) are the prevalent architecture. Of the reviewed studies, 84% use RNNs and 63% use a single layer §3.3.
• Pre-trained embeddings of medical codes beat trainable embedding layers in the reviewed EHR studies, and matrix representations look better for claims data. The authors consider this a tendency, not a settled result §4.1.

Hyperparameters

Not applicable: the review trains no model. Protocol parameters from the paper:

Results

Author-reported. Setup: systematic search of MEDLINE, IEEE, Scopus and the ACM Digital Library; 77 included studies, 2016 to 2020 §2.2 §3.

Effects reported by the primary studies, as cited by the review (not re-measured here, not comparable across studies):

Paper vs code

No official code. The paper and its abstract name no repository, and the arXiv record has no comments field with a link. No project page is linked. GitHub repository searches for time series prediction deep learning healthcare morid and morid healthcare returned zero results. The paper is a review and has no method to implement, so there is nothing to compare against code.

Pitfalls

• Search date conflict. The arXiv abstract says studies were searched up to 7 February 2021, but Section 2.2 says 2020 studies were searched again on 4 November 2021, and the in-PDF abstract gives 4 November 2021 as the cut-off §2.2. Treat the effective cut-off as November 2021 for 2020 papers.
• Figure 1 total mismatch. The "311 excluded" box at full-text does not match its own sub-counts or the text, which give 316 (64 + 99 + 129 + 24) fig. 1 §3. The arithmetic 393 − 316 = 77 is consistent with the text.
• Off-by-one in screening. 1,524 − 511 duplicates = 1,013, but the text says 1,014 works went to title and abstract screening §3.
• Year share. The text says 77% of studies were published after 2018. Figure 2 gives 48 of 77 (about 62%) for 2019–2020 and 61 of 77 (about 79%) for 2018 onward §3 fig. 2. Neither matches 77%.
• Author-reported and not comparable. Results come from different datasets, cohorts, tasks and metrics (AUC, F1, precision, recall). The review does not rank them, and neither should you §3 tab. S3.
• Inclusion excludes preprints. Posters and preprints were excluded §2.3, so recent arXiv-only work is absent. The authors acknowledge the risk of incomplete retrieval §5.
• Interpretation. Most studies visualise attention weights for individual patients. Only one study is cited for population-level interpretation (ref. 63) §4.9.
• Gaps the authors name. No systematic comparison of architectures across healthcare settings; no study of how much each static-data method helps; no comparison of attention types; very little transfer learning (one citation, ref. 43) §4 §5.
• Scope. Unstructured data (clinical notes, images) is out of scope §1.
• Table S3 coverage. This card cites the per-study extraction table tab. S3 at the level of its categories only; individual rows were not transcribed.

Lineage

• Builds on: nothing; this is a review.
• Compared against: named benchmark models in the reviewed literature include Doctor AI (ref. 7), RETAIN (ref. 22), DeepCare (ref. 65) and Deepr (ref. 63) §5 §3.10.
• Superseded by: not stated.