pwc-archive/papers-with-abstracts huggingface dataset:
Strain-Minimizing Hyperbolic Network Embeddings with Landmarks
Authors: Martin Keller-Ressel, Stephanie Nargang
Date: 2022-07-14 00:00:00

We introduce L-hydra (landmarked hyperbolic distance recovery and approximation), a method for embedding network- or distance-based data into hyperbolic space, which requires only the distance measurements to a few 'landmark nodes'. This landmark heuristic makes L-hydra applicable to large-scale graphs and improves upon previously introduced methods. As a mathematical justification, we show that a point configuration in d-dimensional hyperbolic space can be perfectly recovered (up to isometry) from distance measurements to just d+1 landmarks. We also show that L-hydra solves a two-stage strain-minimization problem, similar to our previous (unlandmarked) method 'hydra'. Testing on real network data, we show that L-hydra is an order of magnitude faster than existing hyperbolic embedding methods and scales linearly in the number of nodes. While the embedding error of L-hydra is higher than the error of existing methods, we introduce an extension, L-hydra+, which outperforms existing methods in both runtime and embedding quality.
problexity -- an open-source Python library for binary classification problem complexity assessment
Authors: Joanna Komorniczak, Pawel Ksieniewicz
Date: 2022-07-14 00:00:00
Tasks: Binary Classification, Meta-Learning

The classification problem's complexity assessment is an essential element of many topics in the supervised learning domain. It plays a significant role in meta-learning -- becoming the basis for determining meta-attributes or multi-criteria optimization -- allowing the evaluation of the training set resampling without needing to rebuild the recognition model. The tools currently available for the academic community, which would enable the calculation of problem complexity measures, are available only as libraries of the C++ and R languages. This paper describes the software module that allows for the estimation of 22 complexity measures for the Python language -- compatible with the scikit-learn programming interface -- allowing for the implementation of research using them in the most popular programming environment of the machine learning community.
Breaking Correlation Shift via Conditional Invariant Regularizer
Authors: Mingyang Yi, Ruoyu Wang, Jiachen Sun, Zhenguo Li, Zhi-Ming Ma
Date: 2022-07-14 00:00:00

Recently, generalization on out-of-distribution (OOD) data with correlation shift has attracted great attentions. The correlation shift is caused by the spurious attributes that correlate to the class label, as the correlation between them may vary in training and test data. For such a problem, we show that given the class label, the models that are conditionally independent of spurious attributes are OOD generalizable. Based on this, a metric Conditional Spurious Variation (CSV) which controls the OOD generalization error, is proposed to measure such conditional independence. To improve the OOD generalization, we regularize the training process with the proposed CSV. Under mild assumptions, our training objective can be formulated as a nonconvex-concave mini-max problem. An algorithm with a provable convergence rate is proposed to solve the problem. Extensive empirical results verify our algorithm's efficacy in improving OOD generalization.
Equivariant Hypergraph Diffusion Neural Operators
Authors: Peihao Wang, Shenghao Yang, Yunyu Liu, Zhangyang Wang, Pan Li
Date: 2022-07-14 00:00:00
Tasks: Computational Efficiency, Node Classification

Hypergraph neural networks (HNNs) using neural networks to encode hypergraphs provide a promising way to model higher-order relations in data and further solve relevant prediction tasks built upon such higher-order relations. However, higher-order relations in practice contain complex patterns and are often highly irregular. So, it is often challenging to design an HNN that suffices to express those relations while keeping computational efficiency. Inspired by hypergraph diffusion algorithms, this work proposes a new HNN architecture named ED-HNN, which provably represents any continuous equivariant hypergraph diffusion operators that can model a wide range of higher-order relations. ED-HNN can be implemented efficiently by combining star expansions of hypergraphs with standard message passing neural networks. ED-HNN further shows great superiority in processing heterophilic hypergraphs and constructing deep models. We evaluate ED-HNN for node classification on nine real-world hypergraph datasets. ED-HNN uniformly outperforms the best baselines over these nine datasets and achieves more than 2\%$\uparrow$ in prediction accuracy over four datasets therein.
Deep Learning Methods for Protein Family Classification on PDB Sequencing Data
Authors: Aaron Wang
Date: 2022-07-14 00:00:00
Tasks: Deep Learning

Composed of amino acid chains that influence how they fold and thus dictating their function and features, proteins are a class of macromolecules that play a central role in major biological processes and are required for the structure, function, and regulation of the body's tissues. Understanding protein functions is vital to the development of therapeutics and precision medicine, and hence the ability to classify proteins and their functions based on measurable features is crucial; indeed, the automatic inference of a protein's properties from its sequence of amino acids, known as its primary structure, remains an important open problem within the field of bioinformatics, especially given the recent advancements in sequencing technologies and the extensive number of known but uncategorized proteins with unknown properties. In this work, we demonstrate and compare the performance of several deep learning frameworks, including novel bi-directional LSTM and convolutional models, on widely available sequencing data from the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics (RCSB), as well as benchmark this performance against classical machine learning approaches, including k-nearest neighbors and multinomial regression classifiers, trained on experimental data. Our results show that our deep learning models deliver superior performance to classical machine learning methods, with the convolutional architecture providing the most impressive inference performance.
A Meta-learning Formulation of the Autoencoder Problem for Non-linear Dimensionality Reduction
Authors: Andrey A. Popov, Arash Sarshar, Austin Chennault, Adrian Sandu
Date: 2022-07-14 00:00:00
Tasks: Dimensionality Reduction, Meta-Learning

A rapidly growing area of research is the use of machine learning approaches such as autoencoders for dimensionality reduction of data and models in scientific applications. We show that the canonical formulation of autoencoders suffers from several deficiencies that can hinder their performance. Using a meta-learning approach, we reformulate the autoencoder problem as a bi-level optimization procedure that explicitly solves the dimensionality reduction task. We prove that the new formulation corrects the identified deficiencies with canonical autoencoders, provide a practical way to solve it, and showcase the strength of this formulation with a simple numerical illustration.
Have we been Naive to Select Machine Learning Models? Noisy Data are here to Stay!
Authors: Felipe Costa Farias, Teresa Bernarda Ludermir, Carmelo José Albanez Bastos-Filho
Date: 2022-07-14 00:00:00
Tasks: Decision Making, Model Selection

The model selection procedure is usually a single-criterion decision making in which we select the model that maximizes a specific metric in a specific set, such as the Validation set performance. We claim this is very naive and can perform poor selections of over-fitted models due to the over-searching phenomenon, which over-estimates the performance on that specific set. Futhermore, real world data contains noise that should not be ignored by the model selection procedure and must be taken into account when performing model selection. Also, we have defined four theoretical optimality conditions that we can pursue to better select the models and analyze them by using a multi-criteria decision-making algorithm (TOPSIS) that considers proxies to the optimality conditions to select reasonable models.
PIAT: Physics Informed Adversarial Training for Solving Partial Differential Equations
Authors: Simin Shekarpaz, Mohammad Azizmalayeri, Mohammad Hossein Rohban
Date: 2022-07-14 00:00:00

In this paper, we propose the physics informed adversarial training (PIAT) of neural networks for solving nonlinear differential equations (NDE). It is well-known that the standard training of neural networks results in non-smooth functions. Adversarial training (AT) is an established defense mechanism against adversarial attacks, which could also help in making the solution smooth. AT include augmenting the training mini-batch with a perturbation that makes the network output mismatch the desired output adversarially. Unlike formal AT, which relies only on the training data, here we encode the governing physical laws in the form of nonlinear differential equations using automatic differentiation in the adversarial network architecture. We compare PIAT with PINN to indicate the effectiveness of our method in solving NDEs for up to 10 dimensions. Moreover, we propose weight decay and Gaussian smoothing to demonstrate the PIAT advantages. The code repository is available at https://github.com/rohban-lab/PIAT.
Identifying Orientation-specific Lipid-protein Fingerprints using Deep Learning
Authors: Fikret Aydin, Konstantia Georgouli, Gautham Dharuman, James N. Glosli, Felice C. Lightstone, Helgi I. Ingólfsson, Peer-Timo Bremer, Harsh Bhatia
Date: 2022-07-14 00:00:00
Tasks: Deep Learning

Improved understanding of the relation between the behavior of RAS and RAF proteins and the local lipid environment in the cell membrane is critical for getting insights into the mechanisms underlying cancer formation. In this work, we employ deep learning (DL) to learn this relationship by predicting protein orientational states of RAS and RAS-RAF protein complexes with respect to the lipid membrane based on the lipid densities around the protein domains from coarse-grained (CG) molecular dynamics (MD) simulations. Our DL model can predict six protein states with an overall accuracy of over 80%. The findings of this work offer new insights into how the proteins modulate the lipid environment, which in turn may assist designing novel therapies to regulate such interactions in the mechanisms associated with cancer development.
Antibody-Antigen Docking and Design via Hierarchical Equivariant Refinement
Authors: Wengong Jin, Regina Barzilay, Tommi Jaakkola
Date: 2022-07-14 00:00:00
Tasks: Atomic Forces, Decoder

Computational antibody design seeks to automatically create an antibody that binds to an antigen. The binding affinity is governed by the 3D binding interface where antibody residues (paratope) closely interact with antigen residues (epitope). Thus, predicting 3D paratope-epitope complex (docking) is the key to finding the best paratope. In this paper, we propose a new model called Hierarchical Equivariant Refinement Network (HERN) for paratope docking and design. During docking, HERN employs a hierarchical message passing network to predict atomic forces and use them to refine a binding complex in an iterative, equivariant manner. During generation, its autoregressive decoder progressively docks generated paratopes and builds a geometric representation of the binding interface to guide the next residue choice. Our results show that HERN significantly outperforms prior state-of-the-art on paratope docking and design benchmarks.
Near-Optimal Bounds for Testing Histogram Distributions
Authors: Clément L. Canonne, Ilias Diakonikolas, Daniel M. Kane, Sihan Liu
Date: 2022-07-14 00:00:00

We investigate the problem of testing whether a discrete probability distribution over an ordered domain is a histogram on a specified number of bins. One of the most common tools for the succinct approximation of data, $k$-histograms over $[n]$, are probability distributions that are piecewise constant over a set of $k$ intervals. The histogram testing problem is the following: Given samples from an unknown distribution $\mathbf{p}$ on $[n]$, we want to distinguish between the cases that $\mathbf{p}$ is a $k$-histogram versus $\varepsilon$-far from any $k$-histogram, in total variation distance. Our main result is a sample near-optimal and computationally efficient algorithm for this testing problem, and a nearly-matching (within logarithmic factors) sample complexity lower bound. Specifically, we show that the histogram testing problem has sample complexity $\widetilde \Theta (\sqrt{nk} / \varepsilon + k / \varepsilon^2 + \sqrt{n} / \varepsilon^2)$.
Soil Erosion in the United States. Present and Future (2020-2050)
Authors: Shahab Aldin Shojaeezadeh, Malik Al-Wardy, Mohammad Reza Nikoo, Mehrdad Ghorbani Mooselu, Mohammad Reza Alizadeh, Jan Franklin Adamowski, Hamid Moradkhani, Nasrin Alamdari, Amir H. Gandomi
Date: 2022-07-14 00:00:00
Tasks: Management

Soil erosion is a significant threat to the environment and long-term land management around the world. Accelerated soil erosion by human activities inflicts extreme changes in terrestrial and aquatic ecosystems, which is not fully surveyed/predicted for the present and probable future at field-scales (30-m). Here, we estimate/predict soil erosion rates by water erosion, (sheet and rill erosion), using three alternative (2.6, 4.5, and 8.5) Shared Socioeconomic Pathway and Representative Concentration Pathway (SSP-RCP) scenarios across the contiguous United States. Field Scale Soil Erosion Model (FSSLM) estimations rely on a high resolution (30-m) G2 erosion model integrated by satellite- and imagery-based estimations of land use and land cover (LULC), gauge observations of long-term precipitation, and scenarios of the Coupled Model Intercomparison Project Phase 6 (CMIP6). The baseline model (2020) estimates soil erosion rates of 2.32 Mg ha 1 yr 1 with current agricultural conservation practices (CPs). Future scenarios with current CPs indicate an increase between 8% to 21% under different combinations of SSP-RCP scenarios of climate and LULC changes. The soil erosion forecast for 2050 suggests that all the climate and LULC scenarios indicate either an increase in extreme events or a change in the spatial location of extremes largely from the southern to the eastern and northeastern regions of the United States.
Volatility Based Kernels and Moving Average Means for Accurate Forecasting with Gaussian Processes
Authors: Gregory Benton, Wesley J. Maddox, Andrew Gordon Wilson
Date: 2022-07-13 00:00:00
Tasks: Gaussian Processes

A broad class of stochastic volatility models are defined by systems of stochastic differential equations. While these models have seen widespread success in domains such as finance and statistical climatology, they typically lack an ability to condition on historical data to produce a true posterior distribution. To address this fundamental limitation, we show how to re-cast a class of stochastic volatility models as a hierarchical Gaussian process (GP) model with specialized covariance functions. This GP model retains the inductive biases of the stochastic volatility model while providing the posterior predictive distribution given by GP inference. Within this framework, we take inspiration from well studied domains to introduce a new class of models, Volt and Magpie, that significantly outperform baselines in stock and wind speed forecasting, and naturally extend to the multitask setting.
Self-Play PSRO: Toward Optimal Populations in Two-Player Zero-Sum Games
Authors: Stephen Mcaleer, JB Lanier, Kevin Wang, Pierre Baldi, Roy Fox, Tuomas Sandholm
Date: 2022-07-13 00:00:00
Tasks: Deep Reinforcement Learning, Reinforcement Learning (RL)

In competitive two-agent environments, deep reinforcement learning (RL) methods based on the \emph{Double Oracle (DO)} algorithm, such as \emph{Policy Space Response Oracles (PSRO)} and \emph{Anytime PSRO (APSRO)}, iteratively add RL best response policies to a population. Eventually, an optimal mixture of these population policies will approximate a Nash equilibrium. However, these methods might need to add all deterministic policies before converging. In this work, we introduce \emph{Self-Play PSRO (SP-PSRO)}, a method that adds an approximately optimal stochastic policy to the population in each iteration. Instead of adding only deterministic best responses to the opponent's least exploitable population mixture, SP-PSRO also learns an approximately optimal stochastic policy and adds it to the population as well. As a result, SP-PSRO empirically tends to converge much faster than APSRO and in many games converges in just a few iterations.
Reachability Analysis of a General Class of Neural Ordinary Differential Equations
Authors: Diego Manzanas Lopez, Patrick Musau, Nathaniel Hamilton, Taylor T. Johnson
Date: 2022-07-13 00:00:00

Continuous deep learning models, referred to as Neural Ordinary Differential Equations (Neural ODEs), have received considerable attention over the last several years. Despite their burgeoning impact, there is a lack of formal analysis techniques for these systems. In this paper, we consider a general class of neural ODEs with varying architectures and layers, and introduce a novel reachability framework that allows for the formal analysis of their behavior. The methods developed for the reachability analysis of neural ODEs are implemented in a new tool called NNVODE. Specifically, our work extends an existing neural network verification tool to support neural ODEs. We demonstrate the capabilities and efficacy of our methods through the analysis of a set of benchmarks that include neural ODEs used for classification, and in control and dynamical systems, including an evaluation of the efficacy and capabilities of our approach with respect to existing software tools within the continuous-time systems reachability literature, when it is possible to do so.
Estimating Classification Confidence Using Kernel Densities
Authors: Peter Salamon, David Salamon, V. Adrian Cantu, Michelle An, Tyler Perry, Robert A. Edwards, Anca M. Segall
Date: 2022-07-13 00:00:00
Tasks: Classification

This paper investigates the post-hoc calibration of confidence for "exploratory" machine learning classification problems. The difficulty in these problems stems from the continuing desire to push the boundaries of which categories have enough examples to generalize from when curating datasets, and confusion regarding the validity of those categories. We argue that for such problems the "one-versus-all" approach (top-label calibration) must be used rather than the "calibrate-the-full-response-matrix" approach advocated elsewhere in the literature. We introduce and test four new algorithms designed to handle the idiosyncrasies of category-specific confidence estimation. Chief among these methods is the use of kernel density ratios for confidence calibration including a novel, bulletproof algorithm for choosing the bandwidth. We test our claims and explore the limits of calibration on a bioinformatics application (PhANNs) as well as the classic MNIST benchmark. Finally, our analysis argues that post-hoc calibration should always be performed, should be based only on the test dataset, and should be sanity-checked visually.
A Generalized Framework for Microstructural Optimization using Neural Networks
Authors: Saketh Sridhara, Aaditya Chandrasekhar, Krishnan Suresh
Date: 2022-07-13 00:00:00

Microstructures, i.e., architected materials, are designed today, typically, by maximizing an objective, such as bulk modulus, subject to a volume constraint. However, in many applications, it is often more appropriate to impose constraints on other physical quantities of interest. In this paper, we consider such generalized microstructural optimization problems where any of the microstructural quantities, namely, bulk, shear, Poisson ratio, or volume, can serve as the objective, while the remaining can serve as constraints. In particular, we propose here a neural-network (NN) framework to solve such problems. The framework relies on the classic density formulation of microstructural optimization, but the density field is represented through the NN's weights and biases. The main characteristics of the proposed NN framework are: (1) it supports automatic differentiation, eliminating the need for manual sensitivity derivations, (2) smoothing filters are not required due to implicit filtering, (3) the framework can be easily extended to multiple-materials, and (4) a high-resolution microstructural topology can be recovered through a simple post-processing step. The framework is illustrated through a variety of microstructural optimization problems.
Sub 8-Bit Quantization of Streaming Keyword Spotting Models for Embedded Chipsets
Authors: Lu Zeng, Sree Hari Krishnan Parthasarathi, Yuzong Liu, Alex Escott, Santosh Kumar Cheekatmalla, Nikko Strom, Shiv Vitaladevuni
Date: 2022-07-13 00:00:00
Tasks: CPU, Keyword Spotting, Quantization

We propose a novel 2-stage sub 8-bit quantization aware training algorithm for all components of a 250K parameter feedforward, streaming, state-free keyword spotting model. For the 1st-stage, we adapt a recently proposed quantization technique using a non-linear transformation with tanh(.) on dense layer weights. In the 2nd-stage, we use linear quantization methods on the rest of the network, including other parameters (bias, gain, batchnorm), inputs, and activations. We conduct large scale experiments, training on 26,000 hours of de-identified production, far-field and near-field audio data (evaluating on 4,000 hours of data). We organize our results in two embedded chipset settings: a) with commodity ARM NEON instruction set and 8-bit containers, we present accuracy, CPU, and memory results using sub 8-bit weights (4, 5, 8-bit) and 8-bit quantization of rest of the network; b) with off-the-shelf neural network accelerators, for a range of weight bit widths (1 and 5-bit), while presenting accuracy results, we project reduction in memory utilization. In both configurations, our results show that the proposed algorithm can achieve: a) parity with a full floating point model's operating point on a detection error tradeoff (DET) curve in terms of false detection rate (FDR) at false rejection rate (FRR); b) significant reduction in compute and memory, yielding up to 3 times improvement in CPU consumption and more than 4 times improvement in memory consumption.
Collaborative Machine Learning-Driven Internet of Medical Things -- A Systematic Literature Review
Authors: Rohit Shaw
Date: 2022-07-13 00:00:00
Tasks: BIG-bench Machine Learning, Systematic Literature Review

The growing adoption of IoT devices for healthcare has enabled researchers to build intelligence using all the data produced by these devices. Monitoring and diagnosing health have been the two most common scenarios where such devices have proven beneficial. Achieving high prediction accuracy was a top priority initially, but the focus has slowly shifted to efficiency and higher throughput, and processing the data from these devices in a distributed manner has proven to help achieve both. Since the field of machine learning is vast with numerous state-of-the-art algorithms in play, it has been a challenge to identify the algorithms that perform best in different scenarios. In this literature review, we explored the distributed machine learning algorithms tested by the authors of the selected studies and identified the ones that achieved the best prediction accuracy in each healthcare scenario. While no algorithm performed consistently, Random Forest performed the best in a few studies. This could serve as a good starting point for future studies on collaborative machine learning on IoMT data.