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1.
Commun Med (Lond) ; 4(1): 46, 2024 Mar 14.
Article En | MEDLINE | ID: mdl-38486100

BACKGROUND: Artificial intelligence (AI) models are increasingly used in the medical domain. However, as medical data is highly sensitive, special precautions to ensure its protection are required. The gold standard for privacy preservation is the introduction of differential privacy (DP) to model training. Prior work indicates that DP has negative implications on model accuracy and fairness, which are unacceptable in medicine and represent a main barrier to the widespread use of privacy-preserving techniques. In this work, we evaluated the effect of privacy-preserving training of AI models regarding accuracy and fairness compared to non-private training. METHODS: We used two datasets: (1) A large dataset (N = 193,311) of high quality clinical chest radiographs, and (2) a dataset (N = 1625) of 3D abdominal computed tomography (CT) images, with the task of classifying the presence of pancreatic ductal adenocarcinoma (PDAC). Both were retrospectively collected and manually labeled by experienced radiologists. We then compared non-private deep convolutional neural networks (CNNs) and privacy-preserving (DP) models with respect to privacy-utility trade-offs measured as area under the receiver operating characteristic curve (AUROC), and privacy-fairness trade-offs, measured as Pearson's r or Statistical Parity Difference. RESULTS: We find that, while the privacy-preserving training yields lower accuracy, it largely does not amplify discrimination against age, sex or co-morbidity. However, we find an indication that difficult diagnoses and subgroups suffer stronger performance hits in private training. CONCLUSIONS: Our study shows that - under the challenging realistic circumstances of a real-life clinical dataset - the privacy-preserving training of diagnostic deep learning models is possible with excellent diagnostic accuracy and fairness.


Artificial intelligence (AI), in which computers can learn to do tasks that normally require human intelligence, is particularly useful in medical imaging. However, AI should be used in a way that preserves patient privacy. We explored the balance between maintaining patient data privacy and AI performance in medical imaging. We use an approach called differential privacy to protect the privacy of patients' images. We show that, although training AI with differential privacy leads to a slight decrease in accuracy, it does not substantially increase bias against different age groups, genders, or patients with multiple health conditions. However, we notice that AI faces more challenges in accurately diagnosing complex cases and specific subgroups when trained under these privacy constraints. These findings highlight the importance of designing AI systems that are both privacy-conscious and capable of reliable diagnoses across patient groups.

2.
EBioMedicine ; 101: 105002, 2024 Mar.
Article En | MEDLINE | ID: mdl-38335791

BACKGROUND: With the ever-increasing amount of medical imaging data, the demand for algorithms to assist clinicians has amplified. Unsupervised anomaly detection (UAD) models promise to aid in the crucial first step of disease detection. While previous studies have thoroughly explored fairness in supervised models in healthcare, for UAD, this has so far been unexplored. METHODS: In this study, we evaluated how dataset composition regarding subgroups manifests in disparate performance of UAD models along multiple protected variables on three large-scale publicly available chest X-ray datasets. Our experiments were validated using two state-of-the-art UAD models for medical images. Finally, we introduced subgroup-AUROC (sAUROC), which aids in quantifying fairness in machine learning. FINDINGS: Our experiments revealed empirical "fairness laws" (similar to "scaling laws" for Transformers) for training-dataset composition: Linear relationships between anomaly detection performance within a subpopulation and its representation in the training data. Our study further revealed performance disparities, even in the case of balanced training data, and compound effects that exacerbate the drop in performance for subjects associated with multiple adversely affected groups. INTERPRETATION: Our study quantified the disparate performance of UAD models against certain demographic subgroups. Importantly, we showed that this unfairness cannot be mitigated by balanced representation alone. Instead, the representation of some subgroups seems harder to learn by UAD models than that of others. The empirical "fairness laws" discovered in our study make disparate performance in UAD models easier to estimate and aid in determining the most desirable dataset composition. FUNDING: European Research Council Deep4MI.


Algorithms , Hydrolases , Humans , Machine Learning
3.
Int J Colorectal Dis ; 39(1): 21, 2024 Jan 25.
Article En | MEDLINE | ID: mdl-38273097

PURPOSE: Sigmoid diverticulitis is a disease with a high socioeconomic burden, accounting for a high number of left-sided colonic resections worldwide. Modern surgical scheduling relies on accurate prediction of operation times to enhance patient care and optimize healthcare resources. This study aims to develop a predictive model for surgery duration in laparoscopic sigmoid resections, based on preoperative CT biometric and demographic patient data. METHODS: This retrospective single-center cohort study included 85 patients who underwent laparoscopic sigmoid resection for diverticular disease. Potentially relevant procedure-specific anatomical parameters recommended by a surgical expert were measured in preoperative CT imaging. After random split into training and test set (75% / 25%) multiclass logistic regression was performed and a Random Forest classifier was trained on CT imaging parameters, patient age, and sex in the training cohort to predict categorized surgery duration. The models were evaluated in the test cohort using established performance metrics including receiver operating characteristics area under the curve (AUROC). RESULTS: The Random Forest model achieved a good average AUROC of 0.78. It allowed a very good prediction of long (AUROC = 0.89; specificity 0.71; sensitivity 1.0) and short (AUROC = 0.81; specificity 0.77; sensitivity 0.56) procedures. It clearly outperformed the multiclass logistic regression model (AUROC: average = 0.33; short = 0.31; long = 0.22). CONCLUSION: A Random Forest classifier trained on demographic and CT imaging biometric patient data could predict procedure duration outliers of laparoscopic sigmoid resections. Pending validation in a multicenter study, this approach could potentially improve procedure scheduling in visceral surgery and be scaled to other procedures.


Laparoscopy , Random Forest , Humans , Cohort Studies , Laparoscopy/methods , Retrospective Studies , Treatment Outcome
4.
IEEE Trans Med Imaging ; 43(1): 241-252, 2024 Jan.
Article En | MEDLINE | ID: mdl-37506004

Deep unsupervised approaches are gathering increased attention for applications such as pathology detection and segmentation in medical images since they promise to alleviate the need for large labeled datasets and are more generalizable than their supervised counterparts in detecting any kind of rare pathology. As the Unsupervised Anomaly Detection (UAD) literature continuously grows and new paradigms emerge, it is vital to continuously evaluate and benchmark new methods in a common framework, in order to reassess the state-of-the-art (SOTA) and identify promising research directions. To this end, we evaluate a diverse selection of cutting-edge UAD methods on multiple medical datasets, comparing them against the established SOTA in UAD for brain MRI. Our experiments demonstrate that newly developed feature-modeling methods from the industrial and medical literature achieve increased performance compared to previous work and set the new SOTA in a variety of modalities and datasets. Additionally, we show that such methods are capable of benefiting from recently developed self-supervised pre-training algorithms, further increasing their performance. Finally, we perform a series of experiments in order to gain further insights into some unique characteristics of selected models and datasets. Our code can be found under https://github.com/iolag/UPD_study/.


Algorithms , Neuroimaging
5.
Med Image Anal ; 92: 103059, 2024 Feb.
Article En | MEDLINE | ID: mdl-38104402

Artificial intelligence (AI) has a multitude of applications in cancer research and oncology. However, the training of AI systems is impeded by the limited availability of large datasets due to data protection requirements and other regulatory obstacles. Federated and swarm learning represent possible solutions to this problem by collaboratively training AI models while avoiding data transfer. However, in these decentralized methods, weight updates are still transferred to the aggregation server for merging the models. This leaves the possibility for a breach of data privacy, for example by model inversion or membership inference attacks by untrusted servers. Somewhat-homomorphically-encrypted federated learning (SHEFL) is a solution to this problem because only encrypted weights are transferred, and model updates are performed in the encrypted space. Here, we demonstrate the first successful implementation of SHEFL in a range of clinically relevant tasks in cancer image analysis on multicentric datasets in radiology and histopathology. We show that SHEFL enables the training of AI models which outperform locally trained models and perform on par with models which are centrally trained. In the future, SHEFL can enable multiple institutions to co-train AI models without forsaking data governance and without ever transmitting any decryptable data to untrusted servers.


Neoplasms , Radiology , Humans , Artificial Intelligence , Learning , Neoplasms/diagnostic imaging , Image Processing, Computer-Assisted
6.
Lancet Digit Health ; 5(11): e840-e847, 2023 11.
Article En | MEDLINE | ID: mdl-37741765

The European Commission's draft for the European Health Data Space (EHDS) aims to empower citizens to access their personal health data and share it with physicians and other health-care providers. It further defines procedures for the secondary use of electronic health data for research and development. Although this planned legislation is undoubtedly a step in the right direction, implementation approaches could potentially result in centralised data silos that pose data privacy and security risks for individuals. To address this concern, we propose federated personal health data spaces, a novel architecture for storing, managing, and sharing personal electronic health records that puts citizens at the centre-both conceptually and technologically. The proposed architecture puts citizens in control by storing personal health data on a combination of personal devices rather than in centralised data silos. We describe how this federated architecture fits within the EHDS and can enable the same features as centralised systems while protecting the privacy of citizens. We further argue that increased privacy and control do not contradict the use of electronic health data for research and development. Instead, data sovereignty and transparency encourage active participation in studies and data sharing. This combination of privacy-by-design and transparent, privacy-preserving data sharing can enable health-care leaders to break the privacy-exploitation barrier, which currently limits the secondary use of health data in many cases.


Electronic Health Records , Physicians , Humans , Computer Security , Privacy , Delivery of Health Care
7.
Cancer Cell ; 41(8): 1498-1515.e10, 2023 08 14.
Article En | MEDLINE | ID: mdl-37451271

Type 1 conventional dendritic cells (cDC1) can support T cell responses within tumors but whether this determines protective versus ineffective anti-cancer immunity is poorly understood. Here, we use imaging-based deep learning to identify intratumoral cDC1-CD8+ T cell clustering as a unique feature of protective anti-cancer immunity. These clusters form selectively in stromal tumor regions and constitute niches in which cDC1 activate TCF1+ stem-like CD8+ T cells. We identify a distinct population of immunostimulatory CCR7neg cDC1 that produce CXCL9 to promote cluster formation and cross-present tumor antigens within these niches, which is required for intratumoral CD8+ T cell differentiation and expansion and promotes cancer immune control. Similarly, in human cancers, CCR7neg cDC1 interact with CD8+ T cells in clusters and are associated with patient survival. Our findings reveal an intratumoral phase of the anti-cancer T cell response orchestrated by tumor-residing cDC1 that determines protective versus ineffective immunity and could be exploited for cancer therapy.


CD8-Positive T-Lymphocytes , Neoplasms , Humans , Receptors, CCR7/metabolism , Neoplasms/therapy , Antigens, Neoplasm , Dendritic Cells
8.
Eur Radiol ; 33(10): 6892-6901, 2023 Oct.
Article En | MEDLINE | ID: mdl-37133518

OBJECTIVES: To examine the effect of high-b-value computed diffusion-weighted imaging (cDWI) on solid lesion detection and classification in pancreatic intraductal papillary mucinous neoplasm (IPMN), using endoscopic ultrasound (EUS) and histopathology as a standard of reference. METHODS: Eighty-two patients with known or suspected IPMN were retrospectively enrolled. Computed high-b-value images at b = 1000 s/mm2 were calculated from standard (b = 0, 50, 300, and 600 s/mm2) DWI images for conventional full field-of-view (fFOV, 3 × 3 × 4 mm3 voxel size) DWI. A subset of 39 patients received additional high-resolution reduced-field-of-view (rFOV, 2.5 × 2.5 × 3 mm3 voxel size) DWI. In this cohort, rFOV cDWI was compared against fFOV cDWI additionally. Two experienced radiologists evaluated (Likert scale 1-4) image quality (overall image quality, lesion detection and delineation, fluid suppression within the lesion). In addition, quantitative image parameters (apparent signal-to-noise ratio (aSNR), apparent contrast-to-noise ratio (aCNR), contrast ratio (CR)) were assessed. Diagnostic confidence regarding the presence/absence of diffusion-restricted solid nodules was assessed in an additional reader study. RESULTS: High-b-value cDWI at b = 1000 s/mm2 outperformed acquired DWI at b = 600 s/mm2 regarding lesion detection, fluid suppression, aCNR, CR, and lesion classification (p = < .001-.002). Comparing cDWI from fFOV and rFOV revealed higher image quality in high-resolution rFOV-DWI compared to conventional fFOV-DWI (p ≤ .001-.018). High-b-value cDWI images were rated non-inferior to directly acquired high-b-value DWI images (p = .095-.655). CONCLUSIONS: High-b-value cDWI may improve the detection and classification of solid lesions in IPMN. Combining high-resolution imaging and high-b-value cDWI may further increase diagnostic precision. CLINICAL RELEVANCE STATEMENT: This study shows the potential of computed high-resolution high-sensitivity diffusion-weighted magnetic resonance imaging for solid lesion detection in pancreatic intraductal papillary mucinous neoplasia (IPMN). The technique may enable early cancer detection in patients under surveillance. KEY POINTS: • Computed high-b-value diffusion-weighted imaging (cDWI) may improve the detection and classification of intraductal papillary mucinous neoplasms (IPMN) of the pancreas. • cDWI calculated from high-resolution imaging increases diagnostic precision compared to cDWI calculated from conventional-resolution imaging. • cDWI has the potential to strengthen the role of MRI for screening and surveillance of IPMN, particularly in view of the rising incidence of IPMNs combined with now more conservative therapeutic approaches.


Pancreatic Intraductal Neoplasms , Pancreatic Neoplasms , Humans , Retrospective Studies , Pancreatic Neoplasms/diagnostic imaging , Signal-To-Noise Ratio , Diffusion Magnetic Resonance Imaging/methods , Pancreas
9.
Crit Care ; 27(1): 201, 2023 05 26.
Article En | MEDLINE | ID: mdl-37237287

BACKGROUND: A quantitative assessment of pulmonary edema is important because the clinical severity can range from mild impairment to life threatening. A quantitative surrogate measure, although invasive, for pulmonary edema is the extravascular lung water index (EVLWI) extracted from the transpulmonary thermodilution (TPTD). Severity of edema from chest X-rays, to date is based on the subjective classification of radiologists. In this work, we use machine learning to quantitatively predict the severity of pulmonary edema from chest radiography. METHODS: We retrospectively included 471 X-rays from 431 patients who underwent chest radiography and TPTD measurement within 24 h at our intensive care unit. The EVLWI extracted from the TPTD was used as a quantitative measure for pulmonary edema. We used a deep learning approach and binned the data into two, three, four and five classes increasing the resolution of the EVLWI prediction from the X-rays. RESULTS: The accuracy, area under the receiver operating characteristic curve (AUROC) and Mathews correlation coefficient (MCC) in the binary classification models (EVLWI < 15, ≥ 15) were 0.93 (accuracy), 0.98 (AUROC) and 0.86(MCC). In the three multiclass models, the accuracy ranged between 0.90 and 0.95, the AUROC between 0.97 and 0.99 and the MCC between 0.86 and 0.92. CONCLUSION: Deep learning can quantify pulmonary edema as measured by EVLWI with high accuracy.


Deep Learning , Pulmonary Edema , Humans , Pulmonary Edema/diagnostic imaging , Pulmonary Edema/etiology , X-Rays , Retrospective Studies , Extravascular Lung Water/diagnostic imaging , Radiography , Thermodilution
10.
IEEE Trans Pattern Anal Mach Intell ; 45(6): 7308-7318, 2023 Jun.
Article En | MEDLINE | ID: mdl-37015371

Graph Neural Networks (GNNs) have established themselves as state-of-the-art for many machine learning applications such as the analysis of social and medical networks. Several among these datasets contain privacy-sensitive data. Machine learning with differential privacy is a promising technique to allow deriving insight from sensitive data while offering formal guarantees of privacy protection. However, the differentially private training of GNNs has so far remained under-explored due to the challenges presented by the intrinsic structural connectivity of graphs. In this work, we introduce a framework for differential private graph-level classification. Our method is applicable to graph deep learning on multi-graph datasets and relies on differentially private stochastic gradient descent (DP-SGD). We show results on a variety of datasets and evaluate the impact of different GNN architectures and training hyperparameters on model performance for differentially private graph classification, as well as the scalability of the method on a large medical dataset. Our experiments show that DP-SGD can be applied to graph classification tasks with reasonable utility losses. Furthermore, we apply explainability techniques to assess whether similar representations are learned in the private and non-private settings. Our results can also function as robust baselines for future work in this area.

11.
Med Image Anal ; 84: 102680, 2023 02.
Article En | MEDLINE | ID: mdl-36481607

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in http://medicaldecathlon.com/. In addition, both data and online evaluation are accessible via https://competitions.codalab.org/competitions/17094.


Benchmarking , Liver Neoplasms , Humans , Retrospective Studies , Liver Neoplasms/diagnostic imaging , Liver Neoplasms/pathology , Liver/diagnostic imaging , Liver/pathology , Algorithms , Image Processing, Computer-Assisted/methods
12.
Eur Radiol ; 33(3): 1844-1851, 2023 Mar.
Article En | MEDLINE | ID: mdl-36282311

OBJECTIVE: To evaluate the perception of different types of AI-based assistance and the interaction of radiologists with the algorithm's predictions and certainty measures. METHODS: In this retrospective observer study, four radiologists were asked to classify Breast Imaging-Reporting and Data System 4 (BI-RADS4) lesions (n = 101 benign, n = 99 malignant). The effect of different types of AI-based assistance (occlusion-based interpretability map, classification, and certainty) on the radiologists' performance (sensitivity, specificity, questionnaire) were measured. The influence of the Big Five personality traits was analyzed using the Pearson correlation. RESULTS: Diagnostic accuracy was significantly improved by AI-based assistance (an increase of 2.8% ± 2.3%, 95 %-CI 1.5 to 4.0 %, p = 0.045) and trust in the algorithm was generated primarily by the certainty of the prediction (100% of participants). Different human-AI interactions were observed ranging from nearly no interaction to humanization of the algorithm. High scores in neuroticism were correlated with higher persuasibility (Pearson's r = 0.98, p = 0.02), while higher consciousness and change of accuracy showed an inverse correlation (Pearson's r = -0.96, p = 0.04). CONCLUSION: Trust in the algorithm's performance was mostly dependent on the certainty of the predictions in combination with a plausible heatmap. Human-AI interaction varied widely and was influenced by personality traits. KEY POINTS: • AI-based assistance significantly improved the diagnostic accuracy of radiologists in classifying BI-RADS 4 mammography lesions. • Trust in the algorithm's performance was mostly dependent on the certainty of the prediction in combination with a reasonable heatmap. • Personality traits seem to influence human-AI collaboration. Radiologists with specific personality traits were more likely to change their classification according to the algorithm's prediction than others.


Breast Neoplasms , Vascular Diseases , Humans , Female , Retrospective Studies , Algorithms , Mammography , Radiologists , Breast Neoplasms/diagnostic imaging
13.
Eur J Nucl Med Mol Imaging ; 50(1): 115-129, 2022 Dec.
Article En | MEDLINE | ID: mdl-36074156

PURPOSE: Pancreatic ductal adenocarcinoma (PDAC) is a molecularly heterogeneous tumor entity with no clinically established imaging biomarkers. We hypothesize that tumor morphology and physiology, including vascularity and perfusion, show variations that can be detected by differences in contrast agent (CA) accumulation measured non-invasively. This work seeks to establish imaging biomarkers for tumor stratification and therapy response monitoring in PDAC, based on this hypothesis. METHODS AND MATERIALS: Regional CA accumulation in PDAC was correlated with tumor vascularization, stroma content, and tumor cellularity in murine and human subjects. Changes in CA distribution in response to gemcitabine (GEM) were monitored longitudinally with computed tomography (CT) Hounsfield Units ratio (HUr) of tumor to the aorta or with magnetic resonance imaging (MRI) ΔR1 area under the curve at 60 s tumor-to-muscle ratio (AUC60r). Tissue analyses were performed on co-registered samples, including endothelial cell proliferation and cisplatin tissue deposition as a surrogate of chemotherapy delivery. RESULTS: Tumor cell poor, stroma-rich regions exhibited high CA accumulation both in human (meanHUr 0.64 vs. 0.34, p < 0.001) and mouse PDAC (meanAUC60r 2.0 vs. 1.1, p < 0.001). Compared to the baseline, in vivo CA accumulation decreased specifically in response to GEM treatment in a subset of human (HUr -18%) and mouse (AUC60r -36%) tumors. Ex vivo analyses of mPDAC showed reduced cisplatin delivery (GEM: 0.92 ± 0.5 mg/g, vs. vehicle: 3.1 ± 1.5 mg/g, p = 0.004) and diminished endothelial cell proliferation (GEM: 22.3% vs. vehicle: 30.9%, p = 0.002) upon GEM administration. CONCLUSION: In PDAC, CA accumulation, which is related to tumor vascularization and perfusion, inversely correlates with tumor cellularity. The standard of care GEM treatment results in decreased CA accumulation, which impedes drug delivery. Further investigation is warranted into potentially detrimental effects of GEM in combinatorial therapy regimens.


Carcinoma, Pancreatic Ductal , Pancreatic Neoplasms , Humans , Mice , Animals , Cisplatin/therapeutic use , Xenograft Model Antitumor Assays , Carcinoma, Pancreatic Ductal/diagnostic imaging , Carcinoma, Pancreatic Ductal/drug therapy , Carcinoma, Pancreatic Ductal/pathology , Pancreatic Neoplasms/diagnostic imaging , Pancreatic Neoplasms/drug therapy , Pancreatic Neoplasms/pathology , Neovascularization, Pathologic/diagnostic imaging , Neovascularization, Pathologic/drug therapy , Biomarkers , Tomography, X-Ray Computed , Magnetic Resonance Imaging , Tomography , Cell Line, Tumor , Gemcitabine , Pancreatic Neoplasms
14.
Entropy (Basel) ; 24(5)2022 May 16.
Article En | MEDLINE | ID: mdl-35626597

The increasing prevalence of large-scale data collection in modern society represents a potential threat to individual privacy. Addressing this threat, for example through privacy-enhancing technologies (PETs), requires a rigorous definition of what exactly is being protected, that is, of privacy itself. In this work, we formulate an axiomatic definition of privacy based on quantifiable and irreducible information flows. Our definition synthesizes prior work from the domain of social science with a contemporary understanding of PETs such as differential privacy (DP). Our work highlights the fact that the inevitable difficulties of protecting privacy in practice are fundamentally information-theoretic. Moreover, it enables quantitative reasoning about PETs based on what they are protecting, thus fostering objective policy discourse about their societal implementation.

16.
Genome Biol ; 23(1): 32, 2022 01 24.
Article En | MEDLINE | ID: mdl-35073941

Meta-analysis has been established as an effective approach to combining summary statistics of several genome-wide association studies (GWAS). However, the accuracy of meta-analysis can be attenuated in the presence of cross-study heterogeneity. We present sPLINK, a hybrid federated and user-friendly tool, which performs privacy-aware GWAS on distributed datasets while preserving the accuracy of the results. sPLINK is robust against heterogeneous distributions of data across cohorts while meta-analysis considerably loses accuracy in such scenarios. sPLINK achieves practical runtime and acceptable network usage for chi-square and linear/logistic regression tests. sPLINK is available at https://exbio.wzw.tum.de/splink .


Genome-Wide Association Study , Privacy , Genome-Wide Association Study/methods , Linear Models , Logistic Models , Meta-Analysis as Topic
17.
Genome Biol ; 22(1): 338, 2021 12 14.
Article En | MEDLINE | ID: mdl-34906207

Aggregating transcriptomics data across hospitals can increase sensitivity and robustness of differential expression analyses, yielding deeper clinical insights. As data exchange is often restricted by privacy legislation, meta-analyses are frequently employed to pool local results. However, the accuracy might drop if class labels are inhomogeneously distributed among cohorts. Flimma ( https://exbio.wzw.tum.de/flimma/ ) addresses this issue by implementing the state-of-the-art workflow limma voom in a federated manner, i.e., patient data never leaves its source site. Flimma results are identical to those generated by limma voom on aggregated datasets even in imbalanced scenarios where meta-analysis approaches fail.


Gene Expression , Privacy , Biomedical Research , Computer Communication Networks , Computer Security/legislation & jurisprudence , Computer Security/standards , Databases, Factual/legislation & jurisprudence , Databases, Factual/standards , Gene Expression/ethics , Genes , Government Regulation , Humans , Machine Learning
18.
PLoS One ; 16(8): e0255397, 2021.
Article En | MEDLINE | ID: mdl-34411138

The success of deep learning in recent years has arguably been driven by the availability of large datasets for training powerful predictive algorithms. In medical applications however, the sensitive nature of the data limits the collection and exchange of large-scale datasets. Privacy-preserving and collaborative learning systems can enable the successful application of machine learning in medicine. However, collaborative protocols such as federated learning require the frequent transfer of parameter updates over a network. To enable the deployment of such protocols to a wide range of systems with varying computational performance, efficient deep learning architectures for resource-constrained environments are required. Here we present MoNet, a small, highly optimized neural-network-based segmentation algorithm leveraging efficient multi-scale image features. MoNet is a shallow, U-Net-like architecture based on repeated, dilated convolutions with decreasing dilation rates. We apply and test our architecture on the challenging clinical tasks of pancreatic segmentation in computed tomography (CT) images as well as brain tumor segmentation in magnetic resonance imaging (MRI) data. We assess our model's segmentation performance and demonstrate that it provides performance on par with compared architectures while providing superior out-of-sample generalization performance, outperforming larger architectures on an independent validation set, while utilizing significantly fewer parameters. We furthermore confirm the suitability of our architecture for federated learning applications by demonstrating a substantial reduction in serialized model storage requirement as a surrogate for network data transfer. Finally, we evaluate MoNet's inference latency on the central processing unit (CPU) to determine its utility in environments without access to graphics processing units. Our implementation is publicly available as free and open-source software.


Image Processing, Computer-Assisted , Deep Learning , Neural Networks, Computer , Semantics , Tomography, X-Ray Computed
19.
EJNMMI Res ; 11(1): 70, 2021 Jul 28.
Article En | MEDLINE | ID: mdl-34322781

PURPOSE: In this prospective exploratory study, we evaluated the feasibility of [18F]fluorodeoxyglucose ([18F]FDG) PET/MRI-based chemotherapy response prediction in pancreatic ductal adenocarcinoma at two weeks upon therapy onset. MATERIAL AND METHODS: In a mixed cohort, seventeen patients treated with chemotherapy in neoadjuvant or palliative intent were enrolled. All patients were imaged by [18F]FDG PET/MRI before and two weeks after onset of chemotherapy. Response per RECIST1.1 was then assessed at 3 months [18F]FDG PET/MRI-derived parameters (MTV50%, TLG50%, MTV2.5, TLG2.5, SUVmax, SUVpeak, ADCmax, ADCmean and ADCmin) were assessed, using multiple t-test, Man-Whitney-U test and Fisher's exact test for binary features. RESULTS: At 72 ± 43 days, twelve patients were classified as responders and five patients as non-responders. An increase in ∆MTV50% and ∆ADC (≥ 20% and 15%, respectively) and a decrease in ∆TLG50% (≤ 20%) at 2 weeks after chemotherapy onset enabled prediction of responders and non-responders, respectively. Parameter combinations (∆TLG50% and ∆ADCmax or ∆MTV50% and ∆ADCmax) further improved discrimination. CONCLUSION: Multiparametric [18F]FDG PET/MRI-derived parameters, in particular indicators of a change in tumor glycolysis and cellularity, may enable very early chemotherapy response prediction. Further prospective studies in larger patient cohorts are recommended to their clinical impact.

20.
Sci Rep ; 11(1): 13524, 2021 06 29.
Article En | MEDLINE | ID: mdl-34188157

The successful training of deep learning models for diagnostic deployment in medical imaging applications requires large volumes of data. Such data cannot be procured without consideration for patient privacy, mandated both by legal regulations and ethical requirements of the medical profession. Differential privacy (DP) enables the provision of information-theoretic privacy guarantees to patients and can be implemented in the setting of deep neural network training through the differentially private stochastic gradient descent (DP-SGD) algorithm. We here present deepee, a free-and-open-source framework for differentially private deep learning for use with the PyTorch deep learning framework. Our framework is based on parallelised execution of neural network operations to obtain and modify the per-sample gradients. The process is efficiently abstracted via a data structure maintaining shared memory references to neural network weights to maintain memory efficiency. We furthermore offer specialised data loading procedures and privacy budget accounting based on the Gaussian Differential Privacy framework, as well as automated modification of the user-supplied neural network architectures to ensure DP-conformity of its layers. We benchmark our framework's computational performance against other open-source DP frameworks and evaluate its application on the paediatric pneumonia dataset, an image classification task and on the Medical Segmentation Decathlon Liver dataset in the task of medical image segmentation. We find that neural network training with rigorous privacy guarantees is possible while maintaining acceptable classification performance and excellent segmentation performance. Our framework compares favourably to related work with respect to memory consumption and computational performance. Our work presents an open-source software framework for differentially private deep learning, which we demonstrate in medical imaging analysis tasks. It serves to further the utilisation of privacy-enhancing techniques in medicine and beyond in order to assist researchers and practitioners in addressing the numerous outstanding challenges towards their widespread implementation.

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