BACKGROUND: This study aims to evaluate the feasibility of generating pseudo-normal single photon emission computed tomography (SPECT) data from potentially abnormal images. These pseudo-normal images are primarily intended for use in an on-the-fly data harmonization technique. MATERIAL AND METHODS: The methodology was tested on brain SPECT with [123I]Ioflupane. The proposed model for generating a pseudo-normal image was based on a variational autoencoder (VAE) designed to process 2D sinograms of the brain [123I]-FP-CIT SPECT, potentially exhibiting abnormal uptake. The model aimed to predict SPECT sinograms with corresponding normal uptake. Training, validation, and testing datasets were created by SPECT simulator from 45 brain masks segmented from real patient's magnetic resonance (MR) scans, using various uptake levels. The training and validation datasets each comprised 612 and 360 samples, respectively, drawn from 36 brain masks. The testing dataset contained 153 samples based on 9 brain masks. VAE performance was evaluated through brain dimensions, Dice similarity coefficient (DSC) and specific binding ratio. RESULTS: Mean DSC was 80% for left basal ganglia and 84% for right basal ganglia. The proposed VAE demonstrated excellent consistency in predicting basal ganglia shape, with a coefficient of variation of DSC being less than 1.1%. CONCLUSIONS: The study demonstrates that VAE can effectively estimate an individualized pseudo-normal distribution of the radiotracer [123I]-FP-CIT SPECT from abnormal SPECT images. The main limitations of this preliminary research are the limited availability of real brain MR data, used as input for the SPECT data simulator, and the simplified simulation setup employed to create the synthetic dataset.

• Keywords
• SPECT, [123I]-FP-CIT, harmonization, variational autoencoder,
• MeSH
• Autoencoder * MeSH
• Tomography, Emission-Computed, Single-Photon * MeSH
• Humans MeSH
• Brain diagnostic imaging   MeSH
• Image Processing, Computer-Assisted * methods   MeSH
• Tropanes MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• 2-carbomethoxy-8-(3-fluoropropyl)-3-(4-iodophenyl)tropane MeSH Browser
• Tropanes MeSH

Enzymes play a crucial role in sustainable industrial applications, with their optimization posing a formidable challenge due to the intricate interplay among residues. Computational methodologies predominantly rely on evolutionary insights of homologous sequences. However, deciphering the evolutionary variability and complex dependencies among residues presents substantial hurdles. Here, we present a new machine-learning method based on variational autoencoders and evolutionary sampling strategy to address those limitations. We customized our method to generate novel sequences of model enzymes, haloalkane dehalogenases. Three design-build-test cycles improved the solubility of variants from 11% to 75%. Thorough experimental validation including the microfluidic device MicroPEX resulted in 20 multiple-point variants. Nine of them, sharing as little as 67% sequence similarity with the template, showed a melting temperature increase of up to 9 °C and an average improvement of 3 °C. The most stable variant demonstrated a 3.5-fold increase in activity compared to the template. High-quality experimental data collected with 20 variants represent a valuable data set for the critical validation of novel protein design approaches. Python scripts, jupyter notebooks, and data sets are available on GitHub (https://github.com/loschmidt/vae-dehalogenases), and interactive calculations will be possible via https://loschmidt.chemi.muni.cz/fireprotasr/.

• Publication type
• Journal Article MeSH

The estimation of the speed of human motion from wearable IMU sensors is required in applications such as pedestrian dead reckoning. In this paper, we test deep learning methods for the prediction of the motion speed from raw readings of a low-cost IMU sensor. Each subject was observed using three sensors at the shoe, shin, and thigh. We show that existing general-purpose architectures outperform classical feature-based approaches and propose a novel architecture tailored for this task. The proposed architecture is based on a semi-supervised variational auto-encoder structure with innovated decoder in the form of a dense layer with a sinusoidal activation function. The proposed architecture achieved the lowest average error on the test data. Analysis of sensor placement reveals that the best location for the sensor is the shoe. Significant accuracy gain was observed when all three sensors were available. All data acquired in this experiment and the code of the estimation methods are available for download.

• Keywords
• autoencoder architecture, deep learning, inertial measurement unit, motion speed estimation, walking speed,
• MeSH
• Leg MeSH
• Pedestrians * MeSH
• Deep Learning * MeSH
• Humans MeSH
• Wearable Electronic Devices * MeSH
• Motion MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH

BACKGROUND: Recent advances in data-driven computational approaches have been helpful in devising tools to objectively diagnose psychiatric disorders. However, current machine learning studies limited to small homogeneous samples, different methodologies, and different imaging collection protocols, limit the ability to directly compare and generalize their results. Here we aimed to classify individuals with PTSD versus controls and assess the generalizability using a large heterogeneous brain datasets from the ENIGMA-PGC PTSD Working group. METHODS: We analyzed brain MRI data from 3,477 structural-MRI; 2,495 resting state-fMRI; and 1,952 diffusion-MRI. First, we identified the brain features that best distinguish individuals with PTSD from controls using traditional machine learning methods. Second, we assessed the utility of the denoising variational autoencoder (DVAE) and evaluated its classification performance. Third, we assessed the generalizability and reproducibility of both models using leave-one-site-out cross-validation procedure for each modality. RESULTS: We found lower performance in classifying PTSD vs. controls with data from over 20 sites (60 % test AUC for s-MRI, 59 % for rs-fMRI and 56 % for d-MRI), as compared to other studies run on single-site data. The performance increased when classifying PTSD from HC without trauma history in each modality (75 % AUC). The classification performance remained intact when applying the DVAE framework, which reduced the number of features. Finally, we found that the DVAE framework achieved better generalization to unseen datasets compared with the traditional machine learning frameworks, albeit performance was slightly above chance. CONCLUSION: These results have the potential to provide a baseline classification performance for PTSD when using large scale neuroimaging datasets. Our findings show that the control group used can heavily affect classification performance. The DVAE framework provided better generalizability for the multi-site data. This may be more significant in clinical practice since the neuroimaging-based diagnostic DVAE classification models are much less site-specific, rendering them more generalizable.

• Keywords
• Classification, Deep learning, Machine learning, Multimodal MRI, Posttraumatic stress disorder,
• MeSH
• Big Data MeSH
• Humans MeSH
• Magnetic Resonance Imaging methods   MeSH
• Brain diagnostic imaging   MeSH
• Neuroimaging MeSH
• Stress Disorders, Post-Traumatic * diagnostic imaging   MeSH
• Reproducibility of Results MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH