1192208
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
MOTIVATION
Determining protein function is one of the most important problems in the post-genomic era. For the typical proteome, there are no functional annotations for one-third or more of its proteins. Recent high-throughput experiments have determined proteome-scale protein physical interaction maps for several organisms. These physical interactions are complemented by an abundance of data about other types of functional relationships between proteins, including genetic interactions, knowledge about co-expression and shared evolutionary history. Taken together, these pairwise linkages can be used to build whole-proteome protein interaction maps.


RESULTS
We develop a network-flow based algorithm, FunctionalFlow, that exploits the underlying structure of protein interaction maps in order to predict protein function. In cross-validation testing on the yeast proteome, we show that FunctionalFlow has improved performance over previous methods in predicting the function of proteins with few (or no) annotated protein neighbors. By comparing several methods that use protein interaction maps to predict protein function, we demonstrate that FunctionalFlow performs well because it takes advantage of both network topology and some measure of locality. Finally, we show that performance can be improved substantially as we consider multiple data sources and use them to create weighted interaction networks.


AVAILABILITY
http://compbio.cs.princeton.edu/function
660603
Algorithms for portfolio management based on the Newton method
We experimentally study on-line investment algorithms first proposed by Agarwal and Hazan and extended by Hazan et al. which achieve almost the same wealth as the best constant-rebalanced portfolio determined in hindsight. These algorithms are the first to combine optimal logarithmic regret bounds with efficient deterministic computability. They are based on the Newton method for offline optimization which, unlike previous approaches, exploits second order information. After analyzing the algorithm using the potential function introduced by Agarwal and Hazan, we present extensive experiments on actual financial data. These experiments confirm the theoretical advantage of our algorithms, which yield higher returns and run considerably faster than previous algorithms with optimal regret. Additionally, we perform financial analysis using mean-variance calculations and the Sharpe ratio.
117080125
Logarithmic Regret Algorithms for Online Convex Optimization
In an online convex optimization problem a decision-maker makes a sequence of decisions, i.e., chooses a sequence of points in Euclidean space, from a fixed feasible set. After each point is chosen, it encounters a sequence of (possibly unrelated) convex cost functions. Zinkevich [Zin03] introduced this framework, which models many natural repeated decision-making problems and generalizes many existing problems such as Prediction from Expert Advice and Cover’s Universal Portfolios. Zinkevich showed that a simple online gradient descent algorithm achieves additive regret$O({\sqrt{T}})$, for an arbitrary sequence of T convex cost functions (of bounded gradients), with respect to the best single decision in hindsight. 
 
In this paper, we give algorithms that achieve regret O(log(T)) for an arbitrary sequence of strictly convex functions (with bounded first and second derivatives). This mirrors what has been done for the special cases of prediction from expert advice by Kivinen and Warmuth [KW99], and Universal Portfolios by Cover [Cov91]. We propose several algorithms achieving logarithmic regret, which besides being more general are also much more efficient to implement. 
 
The main new ideas give rise to an efficient algorithm based on the Newton method for optimization, a new tool in the field. Our analysis shows a surprising connection to follow-the-leader method, and builds on the recent work of Agarwal and Hazan [AH05]. We also analyze other algorithms, which tie together several different previous approaches including follow-the-leader, exponential weighting, Cover’s algorithm and gradient descent.
5921169
Learning to rank networked entities
Several algorithms have been proposed to learn to rank entities modeled as feature vectors, based on relevance feedback. However, these algorithms do not model network connections or relations between entities. Meanwhile, Pagerank and variants find the stationary distribution of a reasonable but arbitrary Markov walk over a network, but do not learn from relevance feedback. We present a framework for ranking networked entities based on Markov walks with parameterized conductance values associated with the network edges. We propose two flavors of conductance learning problems in our framework. In the first setting, relevance feedback comparing node-pairs hints that the user has one or more hidden preferred communities with large edge conductance, and the algorithm must discover these communities. We present a constrained maximum entropy network flow formulation whose dual can be solved efficiently using a cutting-plane approach and a quasi-Newton optimizer. In the second setting, edges have types, and relevance feedback hints that each edge type has a potentially different conductance, but this is fixed across the whole network. Our algorithm learns the conductances using an approximate Newton method.
34027055
Improvement heuristic for the flow-shop scheduling problem: An adaptive-learning approach
Abstract We propose an improvement-heuristic approach for the general flow-shop problem (n/m/Cmax) based on the idea of adaptive learning. The approach employs a one-pass heuristic to give a good starting solution in the search space and uses a weight parameter to perturb the data of the original problem to obtain improved solutions. The weights are then adjusted employing a learning strategy which involves reinforcement and backtracking. The learning is similar to that in neural networks. The random perturbation allows a non-deterministic local search. We apply the improvement-heuristic approach in conjunction with three well-known heuristics in the literature, namely, Palmer’s Slope Index, CDS and NEH. We test our approach on several benchmark problem sets including Taillard’s, Carlier’s, Heller’s and Reeves’. We compare our results to the best-known upper-bound solutions and find that for many problems we match the best-known upper bound. For one problem we discover a new upper bound.
8220547
A tree division approach to support local failure recovery for multicasting in MPLS networks
This paper introduces a novel approach to support local failure recovery in multicast trees. Although, the presented approach can be implemented in any large backbone network that employs multicast communication mode, we concentrate our discussion on MPLS networks. In the proposed approach, a multicast tree is divided into several domains where each domain represents a sub-tree of the original one. Backup paths are built between the root of the domain and each leaf router which is called a border router. Simulation results conducted on two network topologies show the performance of the proposed approach in terms of the total capacity required for reserving the backup paths and in terms of the maximum delay needed to notify about link/node failure. The results have shown that tree division approach compared with global recovery approach reduces the time needed to notify the router that is responsible for switching the traffic to the backup path.
206717449
Tracking Articulated Motion Using a Mixture of Autoregressive Models
We present a novel approach to modelling the non-linear and time-varying dynamics of human motion, using statistical methods to capture the characteristic motion patterns that exist in typical human activities. Our method is based on automatically clustering the body pose space into connected regions exhibiting similar dynamical characteristics, modelling the dynamics in each region as a Gaussian autoregressive process. Activities that would require large numbers of exemplars in example based methods are covered by comparatively few motion models. Different regions correspond roughly to different action-fragments and our class inference scheme allows for smooth transitions between these, thus making it useful for activity recognition tasks. The method is used to track activities including walking, running, etc., using a planar 2D body model. Its effectiveness is demonstrated by its success in tracking complicated motions like turns, without any key frames or 3D information.
2887541
Recovering 3D human pose from monocular images
We describe a learning-based method for recovering 3D human body pose from single images and monocular image sequences. Our approach requires neither an explicit body model nor prior labeling of body parts in the image. Instead, it recovers pose by direct nonlinear regression against shape descriptor vectors extracted automatically from image silhouettes. For robustness against local silhouette segmentation errors, silhouette shape is encoded by histogram-of-shape-contexts descriptors. We evaluate several different regression methods: ridge regression, relevance vector machine (RVM) regression, and support vector machine (SVM) regression over both linear and kernel bases. The RVMs provide much sparser regressors without compromising performance, and kernel bases give a small but worthwhile improvement in performance. The loss of depth and limb labeling information often makes the recovery of 3D pose from single silhouettes ambiguous. To handle this, the method is embedded in a novel regressive tracking framework, using dynamics from the previous state estimate together with a learned regression value to disambiguate the pose. We show that the resulting system tracks long sequences stably. For realism and good generalization over a wide range of viewpoints, we train the regressors on images resynthesized from real human motion capture data. The method is demonstrated for several representations of full body pose, both quantitatively on independent but similar test data and qualitatively on real image sequences. Mean angular errors of 4-6/spl deg/ are obtained for a variety of walking motions.