         ______
    __---   )  --_      - - - - - - - - - - - - - - - - - - - - - - - - -
  --       /      -_
 /     o  (         )   Mesh: https://github.com/hbrouwer/mesh
(     o   ____  o    )  (c) 2012-2022 Harm Brouwer <me@hbrouwer.eu>
(    o _--     o      )
 (____/       o _____)  Licensed under the Apache License, Version 2.0
      (____  ---  )
           \ \-__/      - - - - - - - - - - - - - - - - - - - - - - - - -

Mesh

Mesh is a lightweight and versatile artificial neural network simulator, primarily designed as a general-purpose backpropagation (through time) simulator with flexibility and extensibility in mind.

Features

Mesh comes with support for:

Different architectures: feed forward networks (ffn), simple recurrent networks (srn) (Elman, 1990), and recurrent neural networks (rnn);
Training algorithms: backpropagation (bp) (Rumelhart et al., 1986a) and backpropagation through time (bptt) (Rumelhart et al., 1986b);
Weight update algorithms: steepest/gradient descent (steepest), bounded steepest descent (bounded) (Rohde, 2002), four flavours of resilient propagation (rprop+, rprop-, irprop+, and irprop-) (Igel & Husken, 2000), quickprop (qprop) (Fahlman, 1988), and delta-bar-delta (dbd) (Jacobs, 1988);
Activation functions: logistic (sigmoid) (logistic), bipolar sigmoid (bipolar_sigmoid), softmax (softmax), hyperbolic tangent (tanh), linear (linear), (bounded) recitified linear (relu), leaky rectified linear (leaky_relu), and exponential linear (elu);
Error functions: sum squared error (sum_of_squares) , cross entropy error (cross_entropy), and Kullback-Leibler divergence (divergence);
Weight randomization algorithms: gaussian (gaussian), uniform range (range), Nguyen-Widrow (nguyen_windrow) (Nguyen & Widrow, 1990), Fan-In (fan_in), and binary (binary).
Multithreading (through OpenMP);
A module for navigating propositional meaning spaces: meaning spaces derived from the Distributed Situation-state Space (DSS) model (Frank et al., 2003) and Distributional Formal Semantics (DFS) (Venhuizen et al., 2021);
A module for modeling electrophysiological correlates: the N400 and P600 components of the Event-Related brain Potentials (ERP) signal (Brouwer, 2014; Brouwer et al., 2017);
Pretty printing of vectors and matrices (through ANSI escape codes);
And finally, it is dependency-free: you only need a C99-compliant (and for multithreading OpenMP-enabled) compiler to build Mesh.

Why Mesh?

"What I cannot create, I do not understand“ -Richard Feynman

Is Mesh the new PyTorch or TensorFlow? No, Mesh is not the next PyTorch or TensorFlow. Mesh is a simulator that focuses on traditional connectionist / Parallel Distributed Processing (PDP) architectures and learning algorithms (in the tradition of simulators like Tlearn and Lens, among others). It was developed along with my PhD dissertation in cognitive neuroscience (Brouwer, 2014), in which I used it to build a neurocomputational model of the electrophysiology of language comprehension (Brouwer et al., 2017). Mesh is a one-man show; I started developing Mesh before the deep learning revolution, and hence before large-scale deep learning frameworks like PyTorch and TensorFlow, backed by Facebook/Meta and Google, respectively, became available.

I learned a lot implementing Mesh: I built Mesh from scratch using classical papers as technical references. I have waded through many slides, books, and websites, in order to put the different pieces together. Again this was prior to the deep learning revolution, and hence prior to the wealth of information that has become available over the last few years. Indeed, as the late Jeff Elman (author of Tlearn) pointed out to me: I learned an enormous amount about neural networks by implementing Mesh, and for that reason alone it has been worthwhile.

Mesh is lightweight yet versatile: We use Mesh on a daily basis to run cognitive models of human language comprehension. In Brouwer et al. (2017), for instance, it is used to model electrophysiological correlates of online comprehension, and in Venhuizen et al. (2021) we use it to navigate a propositional meaning space from Distributional Formal Semantics (DFS). Moreover, as Mesh is fully command driven, it is also ideal for teaching connectionistm/PDP: it has for instance been used in a course on Connectionist Language Processing at Saarland University.

Building and running Mesh

Building Mesh should be as straightforward as:

$ cmake .
$ make

You can then run Mesh as:

$ ./mesh
Mesh, version 1.0.0: https://github.com/hbrouwer/mesh (`?` for help)
+ [ OpenMP ]: 10 processor(s) available (10 thread(s) max)
+ [ OpenMP ]: Dynamic schedule (chunk size: 1)

Note that as Mesh is fully command driven, it is recommended to use rlwrap.

Usage

$ ./mesh --help
Mesh, version 1.0.0: https://github.com/hbrouwer/mesh (`?` for help)
+ [ OpenMP ]: 10 processor(s) available (10 thread(s) max)
+ [ OpenMP ]: Static schedule (chunk size: 0)

Usage: mesh [file | option]

[file]:
Mesh will load and run the specified script file.

[option]:
`--help`                         Show this help message
`--version`                      Show version information

When no arguments are specified, Mesh will start in CLI mode.

Documentation and Examples

Documentation is available within Mesh, by typing ? or help, as well as here in Markdown format.

Tutorials are available in the mesh-examples repository, and cover networks implementing simple boolean functions, as well as various psycholinguistic connectionist models.

Multithreading

When Mesh is compiled with -DOPENMP=ON (default), multithreading is implemented through OpenMP, and controlled with its environment variables. For example, the following limits the number of threads to 2, and enables auto scheduling:

$ OMP_NUM_THREADS=2 OMP_SCHEDULE=auto ./mesh
Mesh, version 1.0.0: https://github.com/hbrouwer/mesh (`?` for help)
+ [ OpenMP ]: 10 processor(s) available (2 thread(s) max)
+ [ OpenMP ]: Auto schedule
  [:>

Note that in order to use multithreading, you need to activate it in Mesh as well for a given network using toggleMultithreading (default: off):

$ OMP_NUM_THREADS=2 mesh plaut.mesh
Mesh, version 1.0.0: https://github.com/hbrouwer/mesh (`?` for help)
+ [ OpenMP ]: 10 processor(s) available (2 thread(s) max)
+ [ OpenMP ]: Dynamic schedule (chunk size: 1)
...
> Loaded file                    [ plaut.mesh ]
  [plaut:train> toggleMultithreading
> Toggled multithreading         [ on ]

You can inspect the multithreading status of an active network using inspect:

  [plaut:train> inspect
| Name:                          plaut
| Type:                          ffn
...
| Multithreading enabled:        true
| Processor(s) available:        10
| Maximum #threads:              2
| Schedule:                      dynamic
| Chunk size                     1

To compile Mesh without multithreading, pass the flag -DOPENMP=OFF to CMake.

Warning: If multithreading is enabled, Mesh will always distribute computations among the available threads. Depending on network size, however, this may not always lead to improved performance over single-threaded execution. In fact, the overhead of multithreading may even damage performance.

Fast exponentiation

Mesh implements Nicol N. Schraudolph's fast, compact approximation of the exponential function (Schraudolph, 1999). This feature is disabled by default, but can be enabled by passing the flag -DFAST_EXP=ON to CMake. If enabled, Mesh will report this on startup:

$ ./mesh
Mesh, version 1.0.0: https://github.com/hbrouwer/mesh (`?` for help)
+ [ FastExp ]: Using Schraudolph's exp() approximation (c: 60801)
...
  [:>

References

Brouwer, H. (2014). The Electrophysiology of Language Comprehension: A Neurocomputational Model. PhD thesis, University of Groningen.

Brouwer, H., Crocker, M. W., Venhuizen, N. J., and Hoeks, J. C. J. (2017). A Neurocomputational Model of the N400 and the P600 in Language Processing. Cognitive Science, 41(S6), 1318-1352.

Elman, J. L. (1990). Finding structure in time. Cognitive Science, 14(2), 179-211.

Fahlman, S. E. (1988). An empirical study of learning speed in back-propagation networks. Technical report CMU-CS-88-162. School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213.

Frank, S. L., Koppen, M., Noordman, L. G., & Vonk, W. (2003). Modeling knowledge-based inferences in story comprehension. Cognitive Science, 27(6), 875–910. doi:10.1207/s15516709cog2706_3

Igel, C., & Husken, M. (2000). Improving the Rprop Algorithm. Proceedings of the Second International Symposium on Neural Computation, NC'2000, pp. 115-121, ICSC, Academic Press, 2000.

Jacobs, R. A. (1988). Increased Rates of Convergence Through Learning Rate Adapation. Neural Networks, 1, 295-307.

Nguyen, D. & Widrow, B. (1990). Improving the learning speed of 2-layer neural networks by choosing initial values of adaptive weights. Proceedings of the International Joint Conference on Neural Networks (IJCNN), 3:21-26, June 1990.

Rohde, D. L. T. (2002). A connectionist model of sentence comprehension and production. PhD thesis, Carnegie Mellon University.

Rumelhart, D. E., Hinton, G. E., & Williams, R. J. (1986a). Learning representations by back-propagating errors. Nature, 323, 553-536.

Rumelhart, D. E., Hinton, G. E., & Williams, R. J. (1986b). Learning internal representations by error propagation. In: D. E. Rumelhart & J. L. McClelland (Eds.), Parallel distributed processing: Explorations in the microstructure of cognition, Volume 1: Foundations, pp. 318-362, Cambridge, MA: MIT Press.

Schraudolph, N. N. (1999). A fast, compact approximation of the exponential function. Neural Computation, 11, 854-862.

Venhuizen, N. J., Hendriks, P., Crocker, M. W., and Brouwer, H. (in press). Distributional Formal Semantics. Information and Computation. arXiv preprint arXiv:2103.01713

hbrouwer / mesh