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 formulate the problem of graph inference where part of the graph is known as a supervised learning problem, and propose an algorithm to solve it. The method involves the learning of a mapping of the vertices to a Euclidean space where the graph is easy to infer, and can be formulated asan optimization problem in a reproducing kernel Hilbert space. We report encouraging results on the problem of metabolic network reconstruction fromgenomic data.

We address the problem of learning a symmetric positive definite matrix. The central issue is to design parameter updates that preserve positive definiteness. Our updates are motivated with the von Neumann divergence. Ratherthan treating the most general case, we focus on two key applications that exemplify our methods: Online learning with a simple square loss and finding a symmetric positive definite matrix subject to symmetric linear constraints. The updates generalize the Exponentiated Gradient (EG) update and AdaBoost, respectively: the parameter is now a symmetric positive definite matrix of trace one instead of a probability vector (which in this context is a diagonal positive definite matrix with trace one). The generalized updates use matrix logarithms and exponentials topreserve positive definiteness. Most importantly, we show how the analysis of each algorithm generalizes to the non-diagonal case. We apply both new algorithms, called the Matrix Exponentiated Gradient (MEG) update and DefiniteBoost, to learn a kernel matrix from distance measurements.

This paper explores the computational consequences of simultaneous intrinsic andsynaptic plasticity in individual model neurons. It proposes a new intrinsic plasticity mechanism for a continuous activation model neuron based on low order moments of the neuron's firing rate distribution. Thegoal of the intrinsic plasticity mechanism is to enforce a sparse distribution of the neuron's activity level. In conjunction with Hebbian learning at the neuron's synapses, the neuron is shown to discover sparse directions in the input.

The game of G0 originated in China over 4000 years ago.

Semantic taxonomies such as WordNet provide a rich source of knowledge fornatural language processing applications, but are expensive to build, maintain, and extend. Motivated by the problem of automatically constructing and extending such taxonomies, in this paper we present a new algorithm for automatically learning hypernym (is-a) relations from text. Our method generalizes earlier work that had relied on using small numbers of handcrafted regular expression patterns to identify hypernym pairs.Using "dependency path" features extracted from parse trees, we introduce a general-purpose formalization and generalization of these patterns. Given a training set of text containing known hypernym pairs, our algorithm automatically extracts useful dependency paths and applies them to new corpora to identify novel pairs. On our evaluation task (determining whethertwo nouns in a news article participate in a hypernym relationship), our automatically extracted database of hypernyms attains both higher precision and higher recall than WordNet.

The representation of acoustic signals at the cochlear nerve must serve a wide range of auditory tasks that require exquisite sensitivity in both time and frequency. Lewicki (2002) demonstrated that many of the filtering properties of the cochlea could be explained in terms of efficient coding of natural sounds. This model, however, did not account for properties such as phase-locking or how sound could be encoded in terms of action potentials. Here, we extend this theoretical approach with algorithm for learning efficient auditory codes using a spiking population code. Here, we propose an algorithm for learning efficient auditory codes using a theoretical model for coding sound in terms of spikes.

We devise and experiment with a dynamical kernel-based system for tracking hand movements from neural activity. The state of the system corresponds to the hand location, velocity, and acceleration, while the system's input are the instantaneous spike rates. The system's state dynamics isdefined as a combination of a linear mapping from the previous estimated state and a kernel-based mapping tailored for modeling neural activities. In contrast to generative models, the activity-to-state mapping is learned using discriminative methods by minimizing a noise-robust loss function. We use this approach to predict hand trajectories on the basis of neural activity in motor cortex of behaving monkeys and find that the proposed approach is more accurate than both a static approach based on support vector regression and the Kalman filter.

Alternative splicing (AS) is an important and frequent step in mammalian gene expression that allows a single gene to specify multiple products, and is crucial for the regulation of fundamental biological processes. The extent of AS regulation, and the mechanisms involved, are not well understood. We have developed a custom DNA microarray platform for surveying AS levels on a large scale. We present here a generative model for the AS Array Platform (GenASAP) and demonstrate its utility for quantifying AS levels in different mouse tissues. Learning is performed using a variational expectation maximization algorithm, and the parameters are shown to correctly capture expected AS trends. A comparison of the results obtained with a well-established but low throughput experimental method demonstrate that AS levels obtained from GenASAP are highly predictive of AS levels in mammalian tissues.

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