Artificial intelligence publications
-
A Systematic Study of Genome Context Methods: Calibration, Normalization and Combination
We present a thorough study of the four main families of genome context methods found in the literature: phylogenetic profile, gene fusion, gene cluster, and gene neighbor.
-
The BioPAX Community Standard for Pathway Data Sharing
BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share.
-
Efficient Variable Elimination for Semi-Structured Simple Temporal Networks with Continuous Domains
We show that for an Simple Temporal Network, messages can be represented compactly as sub-STNs. We then present an efficient message-passing scheme for computing the minimal constraints of an STN.
-
Creation of a Genome-Wide Metabolic Pathway Database for Populus Trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants
We developed a general approach for reconstructing metabolic pathway complements of plant genomes.
-
GIGA: a Simple, Efficient Algorithm for Gene Tree Inference in the Genomic Age
We describe a simple, fast algorithm for inferring gene phylogenies, which makes use of information that was not available prior to the genomic age: namely, a reliable species tree spanning…
-
Convergence of a Least-Squares Monte Carlo Algorithm for Bounded Approximating Sets
We analyse the convergence properties of the Longstaff–Schwartz algorithm for approximately solving optimal stopping problems that arise in the pricing of American (Bermudan) financial options.
-
Discounted Deterministic Markov Decision Processes and Discounted All-Pairs Shortest Paths
We present algorithms for finding optimal strategies for discounted, infinite-horizon, Determinsitc Markov Decision Processes (DMDPs).
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality...
-
Language Analytics for Assessing Brain Health: Cognitive Impairment, Depression and Pre-Symptomatic Alzheimers Disease
We present data demonstrating how brain health may be assessed by applying data-mining and text analytics to patient language.
-
Recommendations for End-User Development
We provide an overview of the state of the art in end-user development, focusing on the different kinds of recommendations made to users. We identify four classes of suggestion that…
-
Machine Learning Methods for Metabolic Pathway Prediction
ML methods for pathway prediction perform as well as existing methods, and have qualitative advantages in terms of extensibility, tunability, and explainability.
-
Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants
We developed a general approach for reconstructing metabolic pathway complements of plant genomes. Two new reference databases were created and added to the core of the infrastructure: PlantCyc, and RESD.