https://www2.econ.iastate.edu/tesfatsi/DeepLearningInNeuralNetworksOverview.JSchmidhuber2015.pdf

Deep learning in neural networks

Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Machine learning

Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Many underlying relationships among data in several areas of science and engineering, e.g., computer vision, molecular chemistry, molecular biology, pattern recognition, and data mining, can be represented in terms of graphs. In this paper, we propose a new neural network model, called graph neural network (GNN) model, that extends existing neural network methods for processing the data represented in graph domains. This GNN model, which can directly process most of the practically useful types of graphs, e.g., acyclic, cyclic, directed, and undirected, implements a function tau(G,n) isin IRm that maps a graph G and one of its nodes n into an m-dimensional Euclidean space. A supervised learning algorithm is derived to estimate the parameters of the proposed GNN model. The computational cost of the proposed algorithm is also considered. Some experimental results are shown to validate the proposed learning algorithm, and to demonstrate its generalization capabilities.

/pdf/the-graph-neural-network-model-1nfbg1hdkj.pdf

The Graph Neural Network Model

Generalized relevance learning vector quantization

We propose a new matrix learning scheme to extend relevance learning vector quantization (RLVQ), an efficient prototype-based classification algorithm, toward a general adaptive metric By introducing a full matrix of relevance factors in the distance measure, correlations between different features and their importance for the classification scheme can be taken into account and automated, and general metric adaptation takes place during training In comparison to the weighted Euclidean metric used in RLVQ and its variations, a full matrix is more powerful to represent the internal structure of the data appropriately Large margin generalization bounds can be transferred to this case, leading to bounds that are independent of the input dimensionality This also holds for local metrics attached to each prototype, which corresponds to piecewise quadratic decision boundaries The algorithm is tested in comparison to alternative learning vector quantization schemes using an artificial data set, a benchmark multiclass problem from the VCI repository, and a problem from bioinformatics, the recognition of splice sites for C elegans

/pdf/adaptive-relevance-matrices-in-learning-vector-quantization-5fy43r9202.pdf

Adaptive relevance matrices in learning vector quantization

Incremental on-line learning: A review and comparison of state of the art algorithms

Incremental learning refers to learning from streaming data, which arrive over time, with limited memory resources and, ideally, without sacrificing model accuracy. This setting fits different application scenarios where lifelong learning is relevant, e.g. due to changing environments , and it offers an elegant scheme for big data processing by means of its sequential treatment. In this contribution, we formalise the concept of incremental learning, we discuss particular challenges which arise in this setting, and we give an overview about popular approaches, its theoretical foundations, and applications which emerged in the last years.

https://hal.archives-ouvertes.fr/hal-01418129/document

Barbara Hammer

Papers

Generalized relevance learning vector quantization

Adaptive relevance matrices in learning vector quantization

Incremental on-line learning: A review and comparison of state of the art algorithms

Incremental learning algorithms and applications

Neural Smithing --- Supervised Learning in Feedforward Artificial Neural Networks