Output-input ratio in thermally fluctuating biomolecular machines

Output-input coupling in thermally fluctuating biomolecular machines

Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free energy-donating reaction and the free energy-accepting one. Most if not all biologically active proteins display a slow stochastic dynamics of transitions bet...

Learning Moore Machines from Input-Output Traces

The problem of learning automata from example traces (but no equivalence or membership queries) is fundamental in automata learning theory and practice. In this paper we study this problem for finite state machines with inputs and outputs, and in particular for Moore machines. We introduce three algorithms for solving this problem: (1) the PTAP algorithm, which transforms a set of inputoutput t...

Mechanics of thermally fluctuating membranes

Facial Expression Transfer with Input-Output Temporal Restricted Boltzmann Machines

We present a type of Temporal Restricted Boltzmann Machine that defines a probability distribution over an output sequence conditional on an input sequence. It shares the desirable properties of RBMs: efficient exact inference, an exponentially more expressive latent state than HMMs, and the ability to model nonlinear structure and dynamics. We apply our model to a challenging real-world graphi...

Fuzzy-Input Fuzzy-Output One-Against-All Support Vector Machines

We present a novel approach for Fuzzy-Input Fuzzy-Output classification. One-Against-All Support Vector Machines are adapted to deal with the fuzzy memberships encoded in fuzzy labels, and to also give fuzzy classification answers. The mathematical background for the modifications is given. In a benchmark application, the recognition of emotions in human speech, the accuracy of our F-SVM approa...