Quantum Hopfield neural network

Quantum computing allows for the potential of significant advancements in both the speed and the capacity of widely used machine learning techniques. Here we employ quantum algorithms for the Hopfield network, which can be used for pattern recognition, reconstruction, and optimization as a realization of a content-addressable memory system. We show that an exponentially large network can be stored in a polynomial number of quantum bits by encoding the network into the amplitudes of quantum states. By introducing a classical technique for operating the Hopfield network, we can leverage quantum algorithms to obtain a quantum computational complexity that is logarithmic in the dimension of the data. We also present an application of our method as a genetic sequence recognizer.Comment: 13 pages, 3 figures, final versio

Stacked Denoising Autoencoders and Transfer Learning for Immunogold Particles Detection and Recognition

In this paper we present a system for the detection of immunogold particles and a Transfer Learning (TL) framework for the recognition of these immunogold particles. Immunogold particles are part of a high-magnification method for the selective localization of biological molecules at the subcellular level only visible through Electron Microscopy. The number of immunogold particles in the cell walls allows the assessment of the differences in their compositions providing a tool to analise the quality of different plants. For its quantization one requires a laborious manual labeling (or annotation) of images containing hundreds of particles. The system that is proposed in this paper can leverage significantly the burden of this manual task. For particle detection we use a LoG filter coupled with a SDA. In order to improve the recognition, we also study the applicability of TL settings for immunogold recognition. TL reuses the learning model of a source problem on other datasets (target problems) containing particles of different sizes. The proposed system was developed to solve a particular problem on maize cells, namely to determine the composition of cell wall ingrowths in endosperm transfer cells. This novel dataset as well as the code for reproducing our experiments is made publicly available. We determined that the LoG detector alone attained more than 84\% of accuracy with the F-measure. Developing immunogold recognition with TL also provided superior performance when compared with the baseline models augmenting the accuracy rates by 10\%

Peak Alignment of Gas Chromatography-Mass Spectrometry Data with Deep Learning

We present ChromAlignNet, a deep learning model for alignment of peaks in Gas Chromatography-Mass Spectrometry (GC-MS) data. In GC-MS data, a compound's retention time (RT) may not stay fixed across multiple chromatograms. To use GC-MS data for biomarker discovery requires alignment of identical analyte's RT from different samples. Current methods of alignment are all based on a set of formal, mathematical rules. We present a solution to GC-MS alignment using deep learning neural networks, which are more adept at complex, fuzzy data sets. We tested our model on several GC-MS data sets of various complexities and analysed the alignment results quantitatively. We show the model has very good performance (AUC $\sim 1$ for simple data sets and AUC $\sim 0.85$ for very complex data sets). Further, our model easily outperforms existing algorithms on complex data sets. Compared with existing methods, ChromAlignNet is very easy to use as it requires no user input of reference chromatograms and parameters. This method can easily be adapted to other similar data such as those from liquid chromatography. The source code is written in Python and available online

SchNet - a deep learning architecture for molecules and materials

Deep learning has led to a paradigm shift in artificial intelligence, including web, text and image search, speech recognition, as well as bioinformatics, with growing impact in chemical physics. Machine learning in general and deep learning in particular is ideally suited for representing quantum-mechanical interactions, enabling to model nonlinear potential-energy surfaces or enhancing the exploration of chemical compound space. Here we present the deep learning architecture SchNet that is specifically designed to model atomistic systems by making use of continuous-filter convolutional layers. We demonstrate the capabilities of SchNet by accurately predicting a range of properties across chemical space for \emph{molecules and materials} where our model learns chemically plausible embeddings of atom types across the periodic table. Finally, we employ SchNet to predict potential-energy surfaces and energy-conserving force fields for molecular dynamics simulations of small molecules and perform an exemplary study of the quantum-mechanical properties of C$_{20}$-fullerene that would have been infeasible with regular ab initio molecular dynamics