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1. Learning to Branch

   https://doi.org/arXiv:1803.10150  

   Balcan, Maria-Florina; Dick, Travis; Sandholm, Tuomas (January 2018, International Conference on Machine Learning)

   Tree search algorithms, such as branch-and-bound, are the most widely used tools for solving combinatorial and nonconvex problems. For example, they are the foremost method for solving (mixed) integer programs and constraint satisfaction problems. Tree search algorithms recursively partition the search space to find an optimal solution. In order to keep the tree size small, it is crucial to carefully decide, when expanding a tree node, which question (typically variable) to branch on at that node in order to partition the remaining space. Numerous partitioning techniques (e.g., variable selection) have been proposed, but there is no theory describing which technique is optimal. We show how to use machine learning to determine an optimal weighting of any set of partitioning procedures for the instance distribution at hand using samples from the distribution. We provide the first sample complexity guarantees for tree search algorithm configuration. These guarantees bound the number of samples sufficient to ensure that the empirical performance of an algorithm over the samples nearly matches its expected performance on the unknown instance distribution. This thorough theoretical investigation naturally gives rise to our learning algorithm. Via experiments, we show that learning an optimal weighting of partitioning procedures can dramatically reduce tree size, and we prove that this reduction can even be exponential. Through theory and experiments, we show that learning to branch is both practical and hugely beneficial. 

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2. Branch-Pipe: Improving Graph Skeletonization around Branch Points in 3D Point Clouds

   https://doi.org/10.3390/rs13193802  

   Ziamtsov, Illia; Faizi, Kian; Navlakha, Saket (September 2021, Remote sensing)

   Modern plant phenotyping requires tools that are robust to noise and missing data, while being able to efficiently process large numbers of plants. Here, we studied the skeletonization of plant architectures from 3D point clouds, which is critical for many downstream tasks, including analyses of plant shape, morphology, and branching angles. Specifically, we developed an algorithm to improve skeletonization at branch points (forks) by leveraging the geometric properties of cylinders around branch points. We tested this algorithm on a diverse set of high-resolution 3D point clouds of tomato and tobacco plants, grown in five environments and across multiple developmental timepoints. Compared to existing methods for 3D skeletonization, our method efficiently and more accurately estimated branching angles even in areas with noisy, missing, or non-uniformly sampled data. Our method is also applicable to inorganic datasets, such as scans of industrial pipes or urban scenes containing networks of complex cylindrical shapes. 

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3. Slipstream Processors Revisited: Exploiting Branch Sets

   https://doi.org/10.1109/ISCA45697.2020.00020  

   Srinivasan, Vinesh; Chowdhury, Rangeen Basu; Rotenberg, Eric (May 2020, 2020 ACM/IEEE 47th Annual International Symposium on Computer Architecture (ISCA))

   Delinquent branches and loads remain key performance limiters in some applications. One approach to mitigate them is pre-execution. Broadly, there are two classes of pre-execution: one class repeatedly forks small helper threads, each targeting an individual dynamic instance of a delinquent branch or load; the other class begins with two redundant threads in a leader-follower arrangement, and speculatively reduces the leading thread. The objective of this paper is to design a new pre-execution microarchitecture that meets four criteria: (i) retains the simpler coordination of a leader-follower microarchitecture, (ii) is fully automated with just hardware, (iii) targets both branches and loads, (iv) and is effective. We review prior preexecution proposals and show that none of them meet all four criteria. We develop Slipstream 2.0 to meet all four criteria. The key innovation in the space of leader-follower architectures is to remove the forward control-flow slices of delinquent branches and loads, from the leading thread. This innovation overcomes key limitations in the only other hardware-only leader-follower prior works: Slipstream and Dual Core Execution (DCE). Slipstream removes backward slices of confident branches to pre-execute unconfident branches, which is ineffective in phases dominated by unconfident branches when branch pre-execution is most needed. DCE is very effective at tolerating cache-missed loads, unless their dependent branches are mispredicted. Removing forward control-flow slices of delinquent branches and delinquent loads enables two firsts, respectively: (1) leader-follower-style branch pre-execution without relying on confident instruction removal, and (2) tolerance of cache-missed loads that feed mispredicted branches. For SPEC 2006/2017 SimPoints wherein Slipstream 2.0 is auto-enabled, it achieves geomean speedups of 67%, 60%, and 12%, over baseline (one core), Slipstream, and DCE. 

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4. Land Plant Model Systems Branch Out

   https://doi.org/10.1016/j.cell.2017.09.036  

   Delwiche, Charles F.; Goodman, Charles A.; Chang, Caren (October 2017, Cell)
5. Phylogenomic branch length estimation using quartets

   https://doi.org/10.1093/bioinformatics/btad221  

   Tabatabaee, Yasamin; Zhang, Chao; Warnow, Tandy; Mirarab, Siavash (June 2023, Bioinformatics)

   Abstract MotivationBranch lengths and topology of a species tree are essential in most downstream analyses, including estimation of diversification dates, characterization of selection, understanding adaptation, and comparative genomics. Modern phylogenomic analyses often use methods that account for the heterogeneity of evolutionary histories across the genome due to processes such as incomplete lineage sorting. However, these methods typically do not generate branch lengths in units that are usable by downstream applications, forcing phylogenomic analyses to resort to alternative shortcuts such as estimating branch lengths by concatenating gene alignments into a supermatrix. Yet, concatenation and other available approaches for estimating branch lengths fail to address heterogeneity across the genome. ResultsIn this article, we derive expected values of gene tree branch lengths in substitution units under an extension of the multispecies coalescent (MSC) model that allows substitutions with varying rates across the species tree. We present CASTLES, a new technique for estimating branch lengths on the species tree from estimated gene trees that uses these expected values, and our study shows that CASTLES improves on the most accurate prior methods with respect to both speed and accuracy. Availability and implementationCASTLES is available at https://github.com/ytabatabaee/CASTLES. 

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