For many machine learning models, a choice of hyperparameters is a crucial step towards achieving high performance. Prevalent meta-learning approaches focus on obtaining good hyperparameter ...configurations with a limited computational budget for a completely new task based on the results obtained from the prior tasks. This paper proposes a new formulation of the tuning problem, called
consolidated learning
, more suited to practical challenges faced by model developers, in which a large number of predictive models are created on similar datasets. In such settings, we are interested in the total optimization time rather than tuning for a single task. We show that a carefully selected static portfolio of hyperparameter configurations yields good results for anytime optimization, while maintaining the ease of use and implementation. Moreover, we point out how to construct such a portfolio for specific domains. The improvement in the optimization is possible due to the more efficient transfer of hyperparameter configurations between similar tasks. We demonstrate the effectiveness of this approach through an empirical study for the XGBoost algorithm and the newly created metaMIMIC benchmarks of predictive tasks extracted from the MIMIC-IV medical database. In the paper, we show that the potential of
consolidated learning
is considerably greater due to its compatibility with many machine learning application scenarios.
Most point-of-care tests (POCT) use swabs for sampling and/or for applying a sample on the test. A variety of swabs differing in tip materials is commercially available. Different tip materials have ...different chemical and physical characteristics which might influence the specimen collection and release. We investigated properties of various types of swabs used in clinical diagnostics with focusing on two kinds of analytes, DNA and proteins, which are most often used targets in POCT. As the model samples we used diphtheria toxoid NIBSC 69/017 for investigating recovery of protein analytes such as antigens and bacterial strains of
Escherichia coli
ATCC 25922, diphtheria toxin-producing
Corynebacterium diphtheriae
NCTC 10648, and the clinical isolate nontoxigenic
C. diphtheriae
5820/15 for investigating the recovery of nucleic acids. We investigated four types of swabs most commonly used in clinical diagnostics in terms of absorption capacity and efficiency of release of nucleic acids and proteins. Volume uptake was measured in milligrams. For DNA release various washing out buffers were used and the amount of released DNA was measured spectrophotometrically. The amount of protein released from the swabs were examined using the Lowry assay. We observed statistically significant differences (
p
< 0.05) in the mean weights of absorbed liquid, in the DNA recovery and protein recovery by the four variety of swab examined. However, the efficiency of DNA and protein release was not correlated to the absorbed volume of a sample, but rather to the properties of swabs. The swab composition and structure can have a significant impact on the collection and release efficiency of a sample. Therefore, validation of POCT in relation to the used swabs for sampling is really important. The use of inappropriate swabs could lead to false negative or misleading analysis results.
The outbreak of COVID-19 started in December 2019 and spread rapidly all over the world. It became clear that the development of an effective vaccine was the only way to stop the pandemic. It was the ...first time in the history of infectious diseases that the process of the development of a new vaccine was conducted on such a large scale and accelerated so rapidly. At the end of 2020, the first COVID-19 vaccines were approved for marketing. At the end of March 2023, over three years after the outbreak of the COVID-19 pandemic, 199 vaccines were in pre-clinical development and 183 in clinical development. The candidate vaccines in the clinical phase are based on the following platforms: protein subunit, DNA, RNA, non-replication viral vector, replicating viral vector, inactivated virus, virus-like particles, live attenuated virus, replicating viral vector combined with an antigen-presenting cell, non-replication viral vector combined with an antigen-presenting cell, and bacterial antigen-spore expression vector. Some of the new vaccine platforms have been approved for the first time for human application. This review presents COVID-19 vaccines currently available in the world, procedures for assurance of the quality and safety of the vaccines, the vaccinated population, as well as future perspectives for the new vaccine platforms in drug and therapy development for infectious and non-infectious diseases.
Benchmarks are an integral part of machine learning development. However, the most common benchmarks share several limitations. For example, the difference in performance between two models has no ...probabilistic interpretation, it makes no sense to compare such differences between data sets and there is no reference point that indicates a significant performance improvement. Here we introduce an Elo-based predictive power meta-score that is built on other performance measures and allows for interpretable comparisons of models. Differences between this score have a probabilistic interpretation and can be compared directly between data sets. Furthermore, this meta-score allows for an assessment of ranking fitness. We prove the properties of the Elo-based predictive power meta-score and support them with empirical results on a large-scale benchmark of 30 classification data sets. Additionally, we propose a unified benchmark ontology that provides a uniform description of benchmarks.The performance of machine learning models is usually compared via the mean value of a selected performance measure such as the area under the receiver operating characteristic curve on a specific benchmark data set. However, this measure, its mean value or even relative differences between models do not provide a good prediction of whether the results can translate to other data sets. Gosiewska and colleagues present here a comparison based on Elo ranking, which offers a probabilistic interpretation of how much better one model is than another.
BackgroundWe aimed to assess the clinical significance and impact on survival of prevascular mediastinal lymph nodes (3A) in patients with right-sided lung cancer. MethodsProspective data of 6,348 ...patients, who underwent lung resection from 2005 to 2015, were retrospectively analysed. There were 221 patients who underwent 3A dissection (3ALN+), while 6,127 did not (3ALN-). We performed propensity score matching (PSM) to decrease selection bias (221 vs. 221). ResultsThe incidence of 3A metastasis was 8%, and it elevated with pT stage. Between pT1c and pT2a, there was a significant increase in the 3A metastasis incidence, which doubled from 4% to 9%. For pT4, the incidence was 15%. The highest incidence was found among patients undergoing pneumonectomy (10%) and in the N2b1 and N2b2 subgroups (33% and 64%). In univariable analysis, we found no differences in 5-year survival between 3ALN+ and 3ALN- (51% vs. 51%, P=0.74). But, non-metastatic 3ALN+, 3ALN-, and metastatic 3ALN+ differed significantly (P<0.0001). pN2 subgroups (pN2a1, pN2a2, pN2b1, pN2b2) within PSM analysis did not differ significantly in terms of survival. 3A metastasis failed to be an independent prognostic factor in the multivariable analysis of matched pN2 subgroups. ConclusionsRegardless of 3A lymph nodes failing to be an independent prognostic factor in our cohort, the incidence of metastases in lymph nodes increases notably in advanced stages. 3A metastasis rate is comparable to other lymph node stations. Therefore, superior mediastinal lymphadenectomy in advanced cancers may improve from resections of the 3A lymph node station.
Acute kidney injury (AKI) is a serious and common complication of SARS‑CoV‑2 infection. Most risk assessment tools for AKI have been developed in the intensive care unit or in elderly populations. As ...the COVID‑19 pandemic is transitioning into an endemic phase, there is an unmet need for prognostic scores tailored to the population of patients hospitalized for this disease.
We aimed to develop a robust predictive model for the occurrence of AKI in hospitalized patients with COVID‑19.
Electronic medical records of all adult inpatients admitted between March 2020 and January 2022 were extracted from the database of a large, tertiary care center with a reference status in Lesser Poland. We screened 5806 patients with SARS‑CoV‑2 infection confirmed with a polymerase chain reaction test. After excluding individuals with lacking data on serum creatinine levels and those with a mild disease course (<7 days of inpatient care), a total of 4630 records were considered. Data were randomly split into training (n = 3462) and test (n = 1168) sets. A random forest model was tuned with feature engineering based on expert advice and metrics evaluated in nested cross‑validation to reduce bias.
Nested cross‑validation yielded an area under the curve ranging between 0.793 and 0.807, and an average performance of 0.798. Model explanation techniques from a global perspective suggested that a need for respiratory support, chronic kidney disease, and procalcitonin concentration were among the most important variables in permutation tests.
The CRACoV‑AKI model enables AKI risk stratification among hospitalized patients with COVID‑19. Machine learning-based tools may thus offer additional decision‑making support for specialist providers.
We aimed to study the clinical significance of the lack of lymph node assessment (pNx status) and its impact on survival in non-small-cell lung cancer patients.
We retrospectively analysed the Polish ...Lung Cancer Study Group database. pNx status was defined as 0 lymph nodes removed. We included 17,192 patients.
A total of 1080 patients (6%) had pNx status. pNx patients were more likely to be younger, be female, have a different pT distribution, have squamous cell carcinoma, undergo open thoracotomy, be operated on in non-academic hospitals, and have a lower rate of some comorbidities. pNx was more likely to be cN0 than pN1 and pN2 but less likely than pN0 (p < 0.001). pNx patients were less likely to undergo preoperative invasive mediastinal diagnostics than pN1 and pN2 patients but more likely than pN0 patients (p < 0.001). Overall, the five-year overall survival rates were 64%, 45%, 32% and 50% for pN0, pN1, pN2 and pNx, respectively. In pairwise comparisons, all pN descriptors differed significantly from each other (all p < 0.0001 but pNx vs. pN1 p = 0.016). The placement of the pNx survival curve and survival rate depended on histopathology, surgical approach and pT status. In multivariable analysis, pNx was an independent prognostic risk factor (HR = 1.37, 95%CI: 1.23–1.51, p < 0.01).
The resection of lymph nodes in lung cancer remains a crucial step in the surgical treatment of this disease. The survival of pNx patients is similar to that of pN1 patients. pNx survival curve placement depends on the other variables which could be useful in clinical decisions.
•Impact of pNx (0 lymph nodes) status on lung cancer patients survival was analysed.•We found pNx status in 6% of cases.•The 5-year OS rates were 64%, 45%, 32%, 50% for pN0, pN1, pN2, pNx, respectively.•The survival of pNx is similar to that of pN1 rather than pN0.•pNx survival depends on the other variables that could be useful in daily practice.
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Accidental freezing of aluminum-based vaccines occurs during their storage and transportation, in both developed and developing countries. Freezing damages the freeze-sensitive ...aluminum adjuvanted vaccines, through separation of lattice between aluminum adjuvant and antigen, leading to formation of aluminum aggregates, and loss of potency. In this study, we examined Alhydrogel™ (AlO(OH)xnH2O, aluminum hydroxide, hydrated for adsorption) stored under recommended conditions, and exposed to freezing temperature until solid-frozen. The main purpose of our research was to determine the destruction areas of the solid-frozen Alhydrogel™ using selected methods of scanning electron microscopy, energy dispersive X-ray spectroscopy, Raman spectroscopy, Fourier-transform infrared spectroscopy and transmission electron microscopy working in diffraction mode. The Zeta potential evaluation, measurements of albumin adsorption power, thermogravimetric analysis and estimation of the mass loss after drying indicated significant structural (physical) and chemical differences between the freeze-damaged and non-frozen vaccine adjuvant. The presented results are important to better understand the type and nature of damages occurring in freeze-damaged aluminum-based vaccines. These results can be used in future studies to improve the temperature stability of aluminum adjuvanted vaccines.
The involvement of the larynx in plasma cell myeloma (PCM) may manifest as solitary extramedullary plasmacytoma of the larynx (sEMP-L) or as infiltration of the larynx during newly diagnosed or ...relapsed systemic disease with bone marrow involvement (plasma cell myeloma with laryngeal involvement, PCM-L). To increase knowledge about these rare conditions, we performed a retrospective analysis along with a comprehensive literature review of cases of sEMP-L or PCM-L. Six patients (two sEMP-L and four PCM-L) were identified in our tertiary laryngological centre from 2009 to 2021, constituting 0.88% of all malignant laryngeal tumours. The literature search yielded 187 cases, including 152 sEMP-L and 35 sPCM-L. A comparison of baseline characteristics between sEMP-L and PCM-L performed in the combined cohort of cases from literature review and retrospective analysis revealed that patients with sEMP-L were younger (56 vs. 64 years, p ≤ 0.001) and presented less commonly with thyroid or cricoid cartilage involvement (2.2% vs. 30.8%, p ≤ 0.001). The prognosis of sEMP-L was better than PCM-L (overall survival 86% vs. 55% at 5 years, p = 0.002). Analysis of potential factors that could influence progression-free survival (PFS) in the group of sEMP-L revealed that male sex and cartilage involvement negatively affected PFS in univariate analyses, while only cartilage involvement retained statistical significance in multivariate analysis (HR = 19.94, p = 0.024). In conclusion, PCM with laryngeal involvement is sporadic. Secondary involvement of the larynx during PCM might be more common than sEMP-L and is associated with worse survival. The involvement of cartilage adversely influences the outcome of sEMP-L.
Background. Cardiovascular disease (CVD) with significant involvement of coronary artery disease (CAD) remains a major cause of death and disability among the diabetic population. Although ...percutaneous coronary intervention (PCI) continues to evolve, type 2 diabetes mellitus (T2DM) is a well-established marker of poor clinical prognosis after PCI, which is mainly attributed to the rapid progression of atherosclerosis requiring recurrent revascularizations. Hence, the use of bioresorbable materials could provide some solution to this problem. Material and Methods. The study was divided into two arms. For the first one, we qualified 169 patients with NSTE-ACS treated with PCI who received the drug-eluting stent (DES) coated with a biodegradable polymer Ultimaster (Terumo, Tokyo, Japan). The second arm was composed of 193 patients with ACS who underwent PCI with a magnesium bioresorbable scaffold Magmaris (Biotronik, Berlin, Germany). Both arms were divided into two subsequent groups: the T2DM (59 and 72) and the non-DM (110 and 121, respectively). The primary outcomes were cardiovascular death, myocardial infarction, and in-stent thrombosis. The main secondary outcomes included target lesion failure (TLF) and were recorded at a 1-year-follow-up. Results. There were no significant differences between the diabetic and nondiabetic populations in the primary endpoints or main secondary endpoints (TLF, scaffold restenosis, death from any reason, and other cardiovascular events) either in the Ultimaster or Magmaris group. At a 1-year follow-up, the primary endpoint in the DM t.2 population was recorded in 2.7% Ultimaster vs. 5.1% Magmaris, respectively. Conclusion. Both, Ultimaster and Magmaris revealed relative safety and efficiency at a one-year follow-up in the diabetic population in ACS settings. The observed rates of TLF were low, which combined with a lack of in-stent thrombosis suggests that both investigated devices might be an interesting therapeutic option for diabetics with ACS. Nevertheless, further large randomized clinical trials are needed to confirm fully our results.
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