Related papers: Efficient Sparse Flow Decomposition Methods for RN…
The Flow Decomposition problem, which asks for the smallest set of weighted paths that "covers" a flow on a DAG, has recently been used as an important computational step in transcript assembly. We prove the problem is in FPT when…
The cost of writing, transferring, and storing large data from unsteady simulations limits access to the entire solution, often leaving much of the flow under-sampled or unanalyzed. For example, modeling transient behavior of rare dynamic…
Minimum flow decomposition (MFD) (the problem of finding a minimum set of paths that perfectly decomposes a flow) is a classical problem in Computer Science, and variants of it are powerful models in multiassembly problems in Bioinformatics…
Minimum flow decomposition (MFD) -- the problem of finding a minimum set of weighted source-to-sink paths that perfectly decomposes a flow -- is a classical problem in Computer Science, and variants of it are powerful models in different…
Dynamic mode decomposition (DMD) represents an effective means for capturing the essential features of numerically or experimentally generated flow fields. In order to achieve a desirable tradeoff between the quality of approximation and…
In this paper, we generalize the minimum flow decomposition problem (MFD) to incorporate uncertain edge capacities and tackle it from the perspective of robust optimization. In the classical flow decomposition problem, a network flow is…
Decomposing a network flow into weighted paths has numerous applications. Some applications require any decomposition that is optimal w.r.t. some property such as number of paths, robustness, or length. Many bioinformatic applications…
Minimum flow decomposition (MFD) is the strongly NP-hard problem of finding a smallest set of integer weighted $s$-$t$ paths in an $s$-$t$ DAG $G$ whose weighted sum is equal to a given flow $f$ on $G$. Despite its many practical…
Minimum flow decomposition (MFD) is the NP-hard problem of finding a smallest decomposition of a network flow/circulation $X$ on a directed graph $G$ into weighted source-to-sink paths whose superposition equals $X$. We show that, for…
In Bioinformatics, the applications of flow decomposition in directed acyclic graphs are highlighted in RNA Assembly problem. However, it admits multiple solutions where exactly one solution correctly represents the underlying transcripts.…
Learning a deep neural network requires solving a challenging optimization problem: it is a high-dimensional, non-convex and non-smooth minimization problem with a large number of terms. The current practice in neural network optimization…
The selective frequency damping (SFD) method is an alternative to classical Newton's method to obtain unstable steady-state solutions of dynamical systems. However this method has two main limitations: it does not converge for arbitrary…
Densest Subgraph Problem (DSP) is an important primitive problem with a wide range of applications, including fraud detection, community detection and DNA motif discovery. Edge-based density is one of the most common metrics in DSP.…
Many important problems in Bioinformatics (e.g., assembly or multi-assembly) admit multiple solutions, while the final objective is to report only one. A common approach to deal with this uncertainty is finding safe partial solutions (e.g.,…
Signal decomposition and multiscale signal analysis provide many useful tools for time-frequency analysis. We proposed a random feature method for analyzing time-series data by constructing a sparse approximation to the spectrogram. The…
The Frank-Wolfe (FW) method is a popular approach for solving optimization problems with structured constraints that arise in machine learning applications. In recent years, stochastic versions of FW have gained popularity, motivated by…
RNA-Seq technology offers new high-throughput ways for transcript identification and quantification based on short reads, and has recently attracted great interest. The problem is usually modeled by a weighted splicing graph whose nodes…
In the context of gridless sparse optimization, the Sliding Frank Wolfe algorithm recently introduced has shown interesting analytical and practical properties. Nevertheless, is application to large data, such as in the case of 3D…
Efficiently solving large-scale optimal power flow (OPF) problems is challenging due to the high dimensionality and interconnectivity of modern power systems. Decomposition methods offer a promising solution via partitioning large problems…
To address memory and computation resource limitations for hardware-oriented acceleration of deep convolutional neural networks (CNNs), we present a computation flow, stacked filters stationary flow (SFS), and a corresponding data encoding…