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Register a new userIMG2SMI: Translating Molecular Structure Images to Simplified Molecular-input Line-entry System
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Like many scientific fields, new chemistry literature has grown at a staggering pace, with thousands of papers released every month. A large portion of chemistry literature focuses on new molecules and reactions between molecules. Most vital information is conveyed through 2-D images of molecules, representing the underlying molecules or reactions described. In order to ensure reproducible and machine-readable molecule representations, text-based molecule descriptors like SMILES and SELFIES were created. These text-based molecule representations provide molecule generation but are unfortunately rarely present in published literature. In the absence of molecule descriptors, the generation of molecule descriptors from the 2-D images present in the literature is necessary to understand chemistry literature at scale. Successful methods such as Optical Structure Recognition Application (OSRA), and ChemSchematicResolver are able to extract the locations of molecules structures in chemistry papers and infer molecular descriptions and reactions. While effective, existing systems expect chemists to correct outputs, making them unsuitable for unsupervised large-scale data mining. Leveraging the task formulation of image captioning introduced by DECIMER, we introduce IMG2SMI, a model which leverages Deep Residual Networks for image feature extraction and an encoder-decoder Transformer layers for molecule description generation. Unlike previous Neural Network-based systems, IMG2SMI builds around the task of molecule description generation, which enables IMG2SMI to outperform OSRA-based systems by 163% in molecule similarity prediction as measured by the molecular MACCS Fingerprint Tanimoto Similarity. Additionally, to facilitate further research on this task, we release a new molecule prediction dataset. including 81 million molecules for molecule description generation
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Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structure of proteins and other macromolecular complexes at near-atomic resolution. In single particle cryo-EM, the central problem is to reconstruct the three-dimensional structure of a macromolecule from $10^{4-7}$ noisy and randomly oriented two-dimensional projections. However, the imaged protein complexes may exhibit structural variability, which complicates reconstruction and is typically addressed using discrete clustering approaches that fail to capture the full range of protein dynamics. Here, we introduce a novel method for cryo-EM reconstruction that extends naturally to modeling continuous generative factors of structural heterogeneity. This method encodes structures in Fourier space using coordinate-based deep neural networks, and trains these networks from unlabeled 2D cryo-EM images by combining exact inference over image orientation with variational inference for structural heterogeneity. We demonstrate that the proposed method, termed cryoDRGN, can perform ab initio reconstruction of 3D protein complexes from simulated and real 2D cryo-EM image data. To our knowledge, cryoDRGN is the first neural network-based approach for cryo-EM reconstruction and the first end-to-end method for directly reconstructing continuous ensembles of protein structures from cryo-EM images.
Quantification of myocardial perfusion has the potential to improve detection of regional and global flow reduction. Significant effort has been made to automate the workflow, where one essential step is the arterial input function (AIF) extraction. Since failure here invalidates quantification, high accuracy is required. For this purpose, this study presents a robust AIF detection method using the convolutional neural net (CNN) model. CNN models were trained by assembling 25,027 scans (N=12,984 patients) from three hospitals, seven scanners. A test set of 5,721 scans (N=2,805 patients) evaluated model performance. The 2D+T AIF time series was inputted into CNN. Two variations were investigated: a) Two Classes (2CS) for background and foreground (LV mask); b) Three Classes (3CS) for background, foreground LV and RV. Final model was deployed on MR scanners via the Gadgetron InlineAI. Model loading time on MR scanner was ~340ms and applying it took ~180ms. The 3CS model successfully detect LV for 99.98% of all test cases (1 failed out of 5,721 cases). The mean Dice ratio for 3CS was 0.87+/-0.08 with 92.0% of all test cases having Dice ratio >0.75, while the 2CS model gave lower Dice of 0.82+/-0.22 (P<1e-5). Extracted AIF signals using CNN were further compared to manual ground-truth for foot-time, peak-time, first-pass duration, peak value and area-under-curve. No significant differences were found for all features (P>0.2). This study proposed, validated, and deployed a robust CNN solution to detect the LV for the extraction of the AIF signal used in fully automated perfusion flow mapping. A very large data cohort was assembled and resulting models were deployed to MR scanners for fully inline AI in clinical hospitals.
Reconstructing a map of neuronal connectivity is a critical challenge in contemporary neuroscience. Recent advances in high-throughput serial section electron microscopy (EM) have produced massive 3D image volumes of nanoscale brain tissue for the first time. The resolution of EM allows for individual neurons and their synaptic connections to be directly observed. Recovering neuronal networks by manually tracing each neuronal process at this scale is unmanageable, and therefore researchers are developing automated image processing modules. Thus far, state-of-the-art algorithms focus only on the solution to a particular task (e.g., neuron segmentation or synapse identification). In this manuscript we present the first fully automated images-to-graphs pipeline (i.e., a pipeline that begins with an imaged volume of neural tissue and produces a brain graph without any human interaction). To evaluate overall performance and select the best parameters and methods, we also develop a metric to assess the quality of the output graphs. We evaluate a set of algorithms and parameters, searching possible operating points to identify the best available brain graph for our assessment metric. Finally, we deploy a reference end-to-end version of the pipeline on a large, publicly available data set. This provides a baseline result and framework for community analysis and future algorithm development and testing. All code and data derivatives have been made publicly available toward eventually unlocking new biofidelic computational primitives and understanding of neuropathologies.
COVID-19 clinical presentation and prognosis are highly variable, ranging from asymptomatic and paucisymptomatic cases to acute respiratory distress syndrome and multi-organ involvement. We developed a hybrid machine learning/deep learning model to classify patients in two outcome categories, non-ICU and ICU (intensive care admission or death), using 558 patients admitted in a northern Italy hospital in February/May of 2020. A fully 3D patient-level CNN classifier on baseline CT images is used as feature extractor. Features extracted, alongside with laboratory and clinical data, are fed for selection in a Boruta algorithm with SHAP game theoretical values. A classifier is built on the reduced feature space using CatBoost gradient boosting algorithm and reaching a probabilistic AUC of 0.949 on holdout test set. The model aims to provide clinical decision support to medical doctors, with the probability score of belonging to an outcome class and with case-based SHAP interpretation of features importance.
Infection by many viruses begins with fusion of viral and cellular lipid membranes, followed by entry of viral contents into the target cell and ultimately, after many biochemical steps, integration of viral DNA into that of the host cell. The early steps of membrane fusion and viral capsid entry are mediated by adsorption to the cell surface, and receptor and coreceptor binding. HIV-1 specifically targets CD4+ helper T-cells of the human immune system and binds to the receptor CD4 and coreceptor CCR5 before fusion is initiated. Previous experiments have been performed using a cell line (293-Affinofile) in which the expression of CD4 and CCR5 concentration were independently controlled. After exposure to HIV-1 of various strains, the resulting infectivity was measured through the fraction of infected cells. To design and evaluate the effectiveness of drug therapies that target the inhibition of the entry processes, an accurate functional relationship between the CD4/CCR5 concentrations and infectivity is desired in order to more quantitatively analyze experimental data. We propose three kinetic models describing the possible mechanistic processes involved in HIV entry and fit their predictions to infectivity measurements, contrasting and comparing different outcomes. Our approach allows interpretation of the clustering of infectivity of different strains of HIV-1 in the space of mechanistic kinetic parameters. Our model fitting also allows inference of nontrivial stoichiometries of receptor and coreceptor binding and provides a framework through which to quantitatively investigate the effectiveness of fusion inhibitors and neutralizing antibodies.
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