529,026 research outputs found
Confidence sets for network structure
Latent variable models are frequently used to identify structure in
dichotomous network data, in part because they give rise to a Bernoulli product
likelihood that is both well understood and consistent with the notion of
exchangeable random graphs. In this article we propose conservative confidence
sets that hold with respect to these underlying Bernoulli parameters as a
function of any given partition of network nodes, enabling us to assess
estimates of 'residual' network structure, that is, structure that cannot be
explained by known covariates and thus cannot be easily verified by manual
inspection. We demonstrate the proposed methodology by analyzing student
friendship networks from the National Longitudinal Survey of Adolescent Health
that include race, gender, and school year as covariates. We employ a
stochastic expectation-maximization algorithm to fit a logistic regression
model that includes these explanatory variables as well as a latent stochastic
blockmodel component and additional node-specific effects. Although
maximum-likelihood estimates do not appear consistent in this context, we are
able to evaluate confidence sets as a function of different blockmodel
partitions, which enables us to qualitatively assess the significance of
estimated residual network structure relative to a baseline, which models
covariates but lacks block structure.Comment: 17 pages, 3 figures, 3 table
Distribution Free Prediction Sets for Node Classification
Graph Neural Networks (GNNs) are able to achieve high classification accuracy
on many important real world datasets, but provide no rigorous notion of
predictive uncertainty. Quantifying the confidence of GNN models is difficult
due to the dependence between datapoints induced by the graph structure. We
leverage recent advances in conformal prediction to construct prediction sets
for node classification in inductive learning scenarios. We do this by taking
an existing approach for conformal classification that relies on
\textit{exchangeable} data and modifying it by appropriately weighting the
conformal scores to reflect the network structure. We show through experiments
on standard benchmark datasets using popular GNN models that our approach
provides tighter and better calibrated prediction sets than a naive application
of conformal prediction.Comment: Appeared at ICML 202
Exploring Geometry of Blind Spots in Vision Models
Despite the remarkable success of deep neural networks in a myriad of
settings, several works have demonstrated their overwhelming sensitivity to
near-imperceptible perturbations, known as adversarial attacks. On the other
hand, prior works have also observed that deep networks can be under-sensitive,
wherein large-magnitude perturbations in input space do not induce appreciable
changes to network activations. In this work, we study in detail the phenomenon
of under-sensitivity in vision models such as CNNs and Transformers, and
present techniques to study the geometry and extent of "equi-confidence" level
sets of such networks. We propose a Level Set Traversal algorithm that
iteratively explores regions of high confidence with respect to the input space
using orthogonal components of the local gradients. Given a source image, we
use this algorithm to identify inputs that lie in the same equi-confidence
level set as the source image despite being perceptually similar to arbitrary
images from other classes. We further observe that the source image is linearly
connected by a high-confidence path to these inputs, uncovering a star-like
structure for level sets of deep networks. Furthermore, we attempt to identify
and estimate the extent of these connected higher-dimensional regions over
which the model maintains a high degree of confidence. The code for this
project is publicly available at
https://github.com/SriramB-98/blindspots-neurips-subComment: 25 pages, 20 figures, Accepted at NeurIPS 2023 (spotlight
Rule Extraction and Insertion to Improve the Performance of a Dynamic Cell Structure Neural Network
Artificial Neural Networks are extremely useful machine learning tools. They are used for many purposes, such as prediction, classification, pattern recognition, etc. Although neural networks have been used for decades, they are still often not completely understood or trusted, especially in safety and mission critical situations. Typically, neural networks are trained on data sets that are representative of what needs to be learned. Sometimes training sets are constructed in order to train the neural network in a certain way, in order to embed appropriate knowledge. The purpose of this research is to determine if there is another method that can be used to embed specific knowledge in a neural network before training and if this improves the performance of a neural network.
This research develops and tests a new method of embedding pre-knowledge into the Dynamic Cell Structure (DCS) neural network. The DCS is a type of self-organizing map neural network that has been used for many purposes, including classification. In the research presented here, the method used for embedding pre-knowledge into the neural network is to start by converting the knowledge to a set of IF/THEN rules, that can be easily understood and/or validated by a human expert. Once the rules are constructed and validated, then they are converted to a beginning neural network structure. This allows pre-knowledge to be embedded before training the neural network. This conversion and embedding process is called Rule Insertion.
In order to determine whether this process improves performance, the neural network was trained with and without pre-knowledge embedded. After the training, the neural network structure was again converted to rules, Rule Extraction, and then the neural network accuracy and the rule accuracy were computed. Also, the agreement between the neural network and the extracted rules was computed.
The findings of this research show that using Rule Insertion to embed pre-knowledge into a DCS neural network can increase the accuracy of the neural network. An expert can create the rules to be embedded and can also examine and validate the rules extracted to give more confidence in what the neural network has learned during training. The extracted rules are also a refinement of the inserted rules, meaning the neural network was able to improve upon the expert knowledge based on the data presented
ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis
Here we present ComPPI, a cellular compartment-specific database of proteins and their interactions enabling an extensive, compartmentalized protein-protein interaction network analysis (URL: http://ComPPI.LinkGroup.hu). ComPPI enables the user to filter biologically unlikely interactions, where the two interacting proteins have no common subcellular localizations and to predict novel properties, such as compartment-specific biological functions. ComPPI is an integrated database covering four species (S. cerevisiae, C. elegans, D. melanogaster and H. sapiens). The compilation of nine protein-protein interaction and eight subcellular localization data sets had four curation steps including a manually built, comprehensive hierarchical structure of >1600 subcellular localizations. ComPPI provides confidence scores for protein subcellular localizations and protein-protein interactions. ComPPI has user-friendly search options for individual proteins giving their subcellular localization, their interactions and the likelihood of their interactions considering the subcellular localization of their interacting partners. Download options of search results, whole-proteomes, organelle-specific interactomes and subcellular localization data are available on its website. Due to its novel features, ComPPI is useful for the analysis of experimental results in biochemistry and molecular biology, as well as for proteome-wide studies in bioinformatics and network science helping cellular biology, medicine and drug design
Social Network Intelligence Analysis to Combat Street Gang Violence
In this paper we introduce the Organization, Relationship, and Contact
Analyzer (ORCA) that is designed to aide intelligence analysis for law
enforcement operations against violent street gangs. ORCA is designed to
address several police analytical needs concerning street gangs using new
techniques in social network analysis. Specifically, it can determine "degree
of membership" for individuals who do not admit to membership in a street gang,
quickly identify sets of influential individuals (under the tipping model), and
identify criminal ecosystems by decomposing gangs into sub-groups. We describe
this software and the design decisions considered in building an intelligence
analysis tool created specifically for countering violent street gangs as well
as provide results based on conducting analysis on real-world police data
provided by a major American metropolitan police department who is partnering
with us and currently deploying this system for real-world use
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