We describe how we used a data set of chorale harmonisations composed by Johann Sebastian Bach to train Hidden Markov Models. Using a probabilistic framework allows us to create a harmonisation system which learns from examples, and which can compose new harmonisations. We make a quantitative comparison of our system's harmonisation performance against simpler models, and provide example harmonisations.

Directed graphical models with one layer of observed random variables and one or more layers of hidden random variables have been the dominant modelling paradigm in many research fields. Although this approach has met with considerable success, the causal semantics of these models can make it difficult to infer the posterior distribution over the hidden variables. In this paper we propose an alternative two-layer model based on exponential family distributions and the semantics of undirected models. Inference in these "exponential family harmoniums" is fast while learning is performed by minimizing contrastive divergence. A member of this family is then studied as an alternative probabilistic model for latent semantic indexing. In experiments it is shown that they perform well on document retrieval tasks and provide an elegant solution to searching with keywords.

An analog system-on-Chip for kernel-based pattern Classification and sequence estimation is presented.

We describe an approach to building brain-computer interfaces (BCI) based on graphical models for probabilistic inference and learning. We show how a dynamic Bayesian network (DBN) can be used to infer probability distributions over brain-and body-states during planning and execution of actions. The DBN is learned directly from observed data and allows measured signals such as EEG and EMG to be interpreted in terms of internal states such as intent to move, preparatory activity, and movement execution. Unlike traditional classification-based approaches to BCI, the proposed approach (1) allows continuous tracking and prediction ofinternal states over time, and (2) generates control signals based on an entire probability distribution over states rather than binary yes/no decisions. We present preliminary results of brain-and body-state estimation usingsimultaneous EEG and EMG signals recorded during a self-paced left/right hand movement task.

Many cellular functions are carried out through physical interactions between proteins. Discovering the protein interaction map can therefore help to better understand the workings of the cell.

We propose a new method for estimating intrinsic dimension of a dataset derived by applying the principle of maximum likelihood to the distances between close neighbors. We derive the estimator by a Poisson process approximation, assess its bias and variance theoretically andby simulations, and apply it to a number of simulated and real datasets. We also show it has the best overall performance compared with two other intrinsic dimension estimators.

We propose a new interpretation of spiking neurons as Bayesian integrators accumulatingevidence over time about events in the external world or the body, and communicating to other neurons their certainties about these events. In this model, spikes signal the occurrence of new information, i.e.what cannot be predicted from the past activity. As a result, firing statistics are close to Poisson, albeit providing a deterministic representation ofprobabilities. We proceed to develop a theory of Bayesian inference in spiking neural networks, recurrent interactions implementing avariant of belief propagation. Many perceptual and motor tasks performed by the central nervous system are probabilistic, andcan be described in a Bayesian framework [4, 3].

Agents learning to act in a partially observable domain may need to overcome the problem of perceptual aliasing - i.e., different states that appear similar but require different responses. This problem is exacerbated whenthe agent's sensors are noisy, i.e., sensors may produce different observationsin the same state. We show that many well-known reinforcement learning methods designed to deal with perceptual aliasing, suchas Utile Suffix Memory, finite size history windows, eligibility traces, and memory bits, do not handle noisy sensors well. We suggest a new algorithm, Noisy Utile Suffix Memory (NUSM), based on USM, that uses a weighted classification of observed trajectories. We compare NUSM to the above methods and show it to be more robust to noise.

These models have been able to account for human responses in tasks ranging from 3D shape perception t0 Visuomotor control.

Choice-based conjoint analysis builds models of consumer preferences over products with answers gathered in questionnaires. Our main goal is to bring tools from the machine learning community to solve this problem moreefficiently. Thus, we propose two algorithms to quickly and accurately estimate consumer preferences.