Protein interactions typically arise from a physical interaction of one or more small sites on the surface of the two proteins. Identifying these sites is very important for drug and protein design. In this paper, we propose a computational method based on probabilistic relational model that attempts to address this task using high-throughput protein interaction data and a set of short sequence motifs. We learn the model using the EM algorithm, with a branch-and-bound algorithm as an approximate inference for the E-step. Our method searches for motifs whose presence in a pair of interacting proteins can explain their observed interaction. It also tries to determine which motif pairs have high affinity, and can therefore lead to an interaction. We show that our method is more accurate than others at predicting new protein-protein interactions. More importantly, by examining solved structures of protein complexes, we find that 2/3 of the predicted active motifs correspond to actual interaction sites.

Semantic taxonomies such as WordNet provide a rich source of knowledge for natural 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 (isa) 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 whether two 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.

In this paper we propose to combine two powerful ideas, boosting and manifold learning.

We propose a probabilistic, generative account of configural learning phenomena in classical conditioning. Configural learning experiments probe how animals discriminate and generalize between patterns of simultaneously presented stimuli (such as tones and lights) that are differentially predictive of reinforcement. Previous models of these issues have been successful more on a phenomenological than an explanatory level: they reproduce experimental findings but, lacking formal foundations, provide scant basis for understanding why animals behave as they do. We present a theory that clarifies seemingly arbitrary aspects of previous models while also capturing a broader set of data.

Motivated by the particular problems involved in communicating with "locked-in" paralysed patients, we aim to develop a braincomputer interface that uses auditory stimuli. We describe a paradigm that allows a user to make a binary decision by focusing attention on one of two concurrent auditory stimulus sequences. Using Support Vector Machine classification and Recursive Channel Elimination on the independent components of averaged eventrelated potentials, we show that an untrained user's EEG data can be classified with an encouragingly high level of accuracy. This suggests that it is possible for users to modulate EEG signals in a single trial by the conscious direction of attention, well enough to be useful in BCI.

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.

Clustering and prediction of sets of curves is an important problem in many areas of science and engineering. It is often the case that curves tend to be misaligned from each other in a continuous manner, either in space (across the measurements) or in time. We develop a probabilistic framework that allows for joint clustering and continuous alignment of sets of curves in curve space (as opposed to a fixed-dimensional featurevector space). The proposed methodology integrates new probabilistic alignment models with model-based curve clustering algorithms. The probabilistic approach allows for the derivation of consistent EM learning algorithms for the joint clustering-alignment problem. Experimental results are shown for alignment of human growth data, and joint clustering and alignment of gene expression time-course data.

We study the synthesis of neural coding, selective attention and perceptual decision making. A hierarchical neural architecture is proposed, which implements Bayesian integration of noisy sensory input and top-down attentional priors, leading to sound perceptual discrimination. The model offers an explicit explanation for the experimentally observed modulation that prior information in one stimulus feature (location) can have on an independent feature (orientation). The network's intermediate levels of representation instantiate known physiological properties of visual cortical neurons. The model also illustrates a possible reconciliation of cortical and neuromodulatory representations of uncertainty.

X-ray crystallography is currently the most common way protein structures are elucidated. One of the most time-consuming steps in the crystallographic process is interpretation of the electron density map, a task that involves finding patterns in a three-dimensional picture of a protein. This paper describes DEFT (DEFormable Template), an algorithm using pictorial structures to build a flexible protein model from the protein's amino-acid sequence. Matching this pictorial structure into the density map is a way of automating density-map interpretation. Also described are several extensions to the pictorial structure matching algorithm necessary for this automated interpretation. DEFT is tested on a set of density maps ranging from 2 to 4Å resolution, producing rootmean-squared errors ranging from 1.38 to 1.84Å.

Device mismatch in VLSI degrades the accuracy of analog arithmetic circuits and lowers the learning performance of large-scale neural networks implemented in this technology. We show compact, low-power on-chip calibration techniques that compensate for device mismatch. Our techniques enable large-scale analog VLSI neural networks with learning performance on the order of 10 bits. We demonstrate our techniques on a 64-synapse linear perceptron learning with the Least-Mean-Squares (LMS) algorithm, and fabricated in a 0.35µm CMOS process.