pwc-archive/papers-with-abstracts huggingface dataset:
PDBench: Evaluating Computational Methods for Protein Sequence Design
Authors: Leonardo V. Castorina, Rokas Petrenas, Kartic Subr, Christopher W. Wood
Date: 2021-09-16 00:00:00
Tasks: Protein Design

Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has been sampled in nature, it accounts for a tiny fraction of the possible protein universe. If we could tap into this pool of unexplored protein structures, we could search for novel proteins with useful properties that we could apply to tackle the environmental and medical challenges facing humanity. This is the purpose of protein design. Sequence design is an important aspect of protein design, and many successful methods to do this have been developed. Recently, deep-learning methods that frame it as a classification problem have emerged as a powerful approach. Beyond their reported improvement in performance, their primary advantage over physics-based methods is that the computational burden is shifted from the user to the developers, thereby increasing accessibility to the design method. Despite this trend, the tools for assessment and comparison of such models remain quite generic. The goal of this paper is to both address the timely problem of evaluation and to shine a spotlight, within the Machine Learning community, on specific assessment criteria that will accelerate impact. We present a carefully curated benchmark set of proteins and propose a number of standard tests to assess the performance of deep learning based methods. Our robust benchmark provides biological insight into the behaviour of design methods, which is essential for evaluating their performance and utility. We compare five existing models with two novel models for sequence prediction. Finally, we test the designs produced by these models with AlphaFold2, a state-of-the-art structure-prediction algorithm, to determine if they are likely to fold into the intended 3D shapes.
Behavior of Keyword Spotting Networks Under Noisy Conditions
Authors: Anwesh Mohanty, Adrian Frischknecht, Christoph Gerum, Oliver Bringmann
Date: 2021-09-15 00:00:00
Tasks: Keyword Spotting

Keyword spotting (KWS) is becoming a ubiquitous need with the advancement in artificial intelligence and smart devices. Recent work in this field have focused on several different architectures to achieve good results on datasets with low to moderate noise. However, the performance of these models deteriorates under high noise conditions as shown by our experiments. In our paper, we present an extensive comparison between state-of-the-art KWS networks under various noisy conditions. We also suggest adaptive batch normalization as a technique to improve the performance of the networks when the noise files are unknown during the training phase. The results of such high noise characterization enable future work in developing models that perform better in the aforementioned conditions.
SAFRAN: An interpretable, rule-based link prediction method outperforming embedding models
Authors: Simon Ott, Christian Meilicke, Matthias Samwald
Date: 2021-09-16 00:00:00
Proceeding: AKBC 2021 10
Tasks: Knowledge Graphs, Link Prediction

Neural embedding-based machine learning models have shown promise for predicting novel links in knowledge graphs. Unfortunately, their practical utility is diminished by their lack of interpretability. Recently, the fully interpretable, rule-based algorithm AnyBURL yielded highly competitive results on many general-purpose link prediction benchmarks. However, current approaches for aggregating predictions made by multiple rules are affected by redundancies. We improve upon AnyBURL by introducing the SAFRAN rule application framework, which uses a novel aggregation approach called Non-redundant Noisy-OR that detects and clusters redundant rules prior to aggregation. SAFRAN yields new state-of-the-art results for fully interpretable link prediction on the established general-purpose benchmarks FB15K-237, WN18RR and YAGO3-10. Furthermore, it exceeds the results of multiple established embedding-based algorithms on FB15K-237 and WN18RR and narrows the gap between rule-based and embedding-based algorithms on YAGO3-10.
Super-resolution data assimilation
Authors: Sébastien Barthélémy, Julien Brajard, Laurent Bertino, François Counillon
Date: 2021-09-04 00:00:00
Tasks: Super-Resolution

Increasing the resolution of a model can improve the performance of a data assimilation system: first because model field are in better agreement with high resolution observations, then the corrections are better sustained and, with ensemble data assimilation, the forecast error covariances are improved. However, resolution increase is associated with a cubical increase of the computational costs. Here we are testing an approach inspired from images super-resolution techniques and called "Super-resolution data assimilation" (SRDA). Starting from a low-resolution forecast, a neural network (NN) emulates a high-resolution field that is then used to assimilate high-resolution observations. We apply the SRDA to a quasi-geostrophic model representing simplified surface ocean dynamics, with a model resolution up to four times lower than the reference high-resolution and we use the Ensemble Kalman Filter data assimilation method. We show that SRDA outperforms the low-resolution data assimilation approach and a SRDA version with cubic spline interpolation instead of NN. The NN's ability to anticipate the systematic differences between low and high resolution model dynamics explains the enhanced performance, for example by correcting the difference of propagation speed of eddies. Increasing the computational cost by 55\% above the LR data assimilation system (using a 25-members ensemble), the SRDA reduces the errors by 40\% making the performance very close to the HR system (16\% larger, compared to 92\% larger for the LR EnKF). The reliability of the ensemble system is not degraded by SRDA.
Predicting Users' Value Changes by the Friends' Influence from Social Media Usage
Authors: Md. Saddam Hossain Mukta, Ahmed Shahriar Sakib, Md. Adnanul Islam, Mohiuddin Ahmed, Mumshad Ahamed Rifat
Date: 2021-09-12 00:00:00

Basic human values represent a set of values such as security, independence, success, kindness, and pleasure, which we deem important to our lives. Each of us holds different values with different degrees of significance. Existing studies show that values of a person can be identified from their social network usage. However, the value priority of a person may change over time due to different factors such as life experiences, influence, social structure and technology. Existing studies do not conduct any analysis regarding the change of users' value from the social influence, i.e., group persuasion, form the social media usage. In our research, first, we predict users' value score by the influence of friends from their social media usage. We propose a Bounded Confidence Model (BCM) based value dynamics model from 275 different ego networks in Facebook that predicts how social influence may persuade a person to change their value over time. Then, to predict better, we use particle swarm optimization based hyperparameter tuning technique. We observe that these optimized hyperparameters produce accurate future value score. We also run our approach with different machine learning based methods and find support vector regression (SVR) outperforms other regressor models. By using SVR with the best hyperparameters of BCM model, we find the lowest Mean Squared Error (MSE) score 0.00347.
Accurately Modeling Biased Random Walks on Weighted Graphs Using $\textit{Node2vec+}$
Authors: Renming Liu, Matthew Hirn, Arjun Krishnan
Date: 2021-09-15 00:00:00

Node embedding is a powerful approach for representing the structural role of each node in a graph. $\textit{Node2vec}$ is a widely used method for node embedding that works by exploring the local neighborhoods via biased random walks on the graph. However, $\textit{node2vec}$ does not consider edge weights when computing walk biases. This intrinsic limitation prevents $\textit{node2vec}$ from leveraging all the information in weighted graphs and, in turn, limits its application to many real-world networks that are weighted and dense. Here, we naturally extend $\textit{node2vec}$ to $\textit{node2vec+}$ in a way that accounts for edge weights when calculating walk biases, but which reduces to $\textit{node2vec}$ in the cases of unweighted graphs or unbiased walks. We empirically show that $\textit{node2vec+}$ is more robust to additive noise than $\textit{node2vec}$ in weighted graphs using two synthetic datasets. We also demonstrate that $\textit{node2vec+}$ significantly outperforms $\textit{node2vec}$ on a commonly benchmarked multi-label dataset (Wikipedia). Furthermore, we test $\textit{node2vec+}$ against GCN and GraphSAGE using various challenging gene classification tasks on two protein-protein interaction networks. Despite some clear advantages of GCN and GraphSAGE, they show comparable performance with $\textit{node2vec+}$. Finally, $\textit{node2vec+}$ can be used as a general approach for generating biased random walks, benefiting all existing methods built on top of $\textit{node2vec}$. $\textit{Node2vec+}$ is implemented as part of $\texttt{PecanPy}$, which is available at https://github.com/krishnanlab/PecanPy .
Membership Inference Attacks Against Recommender Systems
Authors: Minxing Zhang, Zhaochun Ren, Zihan Wang, Pengjie Ren, Zhumin Chen, Pengfei Hu, Yang Zhang
Date: 2021-09-16 00:00:00
Tasks: Recommendation Systems

Recently, recommender systems have achieved promising performances and become one of the most widely used web applications. However, recommender systems are often trained on highly sensitive user data, thus potential data leakage from recommender systems may lead to severe privacy problems. In this paper, we make the first attempt on quantifying the privacy leakage of recommender systems through the lens of membership inference. In contrast with traditional membership inference against machine learning classifiers, our attack faces two main differences. First, our attack is on the user-level but not on the data sample-level. Second, the adversary can only observe the ordered recommended items from a recommender system instead of prediction results in the form of posterior probabilities. To address the above challenges, we propose a novel method by representing users from relevant items. Moreover, a shadow recommender is established to derive the labeled training data for training the attack model. Extensive experimental results show that our attack framework achieves a strong performance. In addition, we design a defense mechanism to effectively mitigate the membership inference threat of recommender systems.
Frame by frame completion probability of an NFL pass
Authors: Gustavo Pompeu da Silva, Rafael de Andrade Moral
Date: 2021-09-16 00:00:00

American football is an increasingly popular sport, with a growing audience in many countries in the world. The most watched American football league in the world is the United States' National Football League (NFL), where every offensive play can be either a run or a pass, and in this work we focus on passes. Many factors can affect the probability of pass completion, such as receiver separation from the nearest defender, distance from receiver to passer, offense formation, among many others. When predicting the completion probability of a pass, it is essential to know who the target of the pass is. By using distance measures between players and the ball, it is possible to calculate empirical probabilities and predict very accurately who the target will be. The big question is: how likely is it for a pass to be completed in an NFL match while the ball is in the air? We developed a machine learning algorithm to answer this based on several predictors. Using data from the 2018 NFL season, we obtained conditional and marginal predictions for pass completion probability based on a random forest model. This is based on a two-stage procedure: first, we calculate the probability of each offensive player being the pass target, then, conditional on the target, we predict completion probability based on the random forest model. Finally, the general completion probability can be calculated using the law of total probability. We present animations for selected plays and show the pass completion probability evolution.
Weighted Graph-Based Signal Temporal Logic Inference Using Neural Networks
Authors: Nasim Baharisangari, Kazuma Hirota, Ruixuan Yan, Agung Julius, Zhe Xu
Date: 2021-09-16 00:00:00
Tasks: Classification

Extracting spatial-temporal knowledge from data is useful in many applications. It is important that the obtained knowledge is human-interpretable and amenable to formal analysis. In this paper, we propose a method that trains neural networks to learn spatial-temporal properties in the form of weighted graph-based signal temporal logic (wGSTL) formulas. For learning wGSTL formulas, we introduce a flexible wGSTL formula structure in which the user's preference can be applied in the inferred wGSTL formulas. In the proposed framework, each neuron of the neural networks corresponds to a subformula in a flexible wGSTL formula structure. We initially train a neural network to learn the wGSTL operators and then train a second neural network to learn the parameters in a flexible wGSTL formula structure. We use a COVID-19 dataset and a rain prediction dataset to evaluate the performance of the proposed framework and algorithms. We compare the performance of the proposed framework with three baseline classification methods including K-nearest neighbors, decision trees, support vector machine, and artificial neural networks. The classification accuracy obtained by the proposed framework is comparable with the baseline classification methods.
MOFSimplify: Machine Learning Models with Extracted Stability Data of Three Thousand Metal-Organic Frameworks
Authors: A. Nandy, G. Terrones, N. Arunachalam, C. Duan, D. W. Kastner, H. J. Kulik
Date: 2021-09-16 00:00:00
Tasks: Active Learning

We report a workflow and the output of a natural language processing (NLP)-based procedure to mine the extant metal-organic framework (MOF) literature describing structurally characterized MOFs and their solvent removal and thermal stabilities. We obtain over 2,000 solvent removal stability measures from text mining and 3,000 thermal decomposition temperatures from thermogravimetric analysis data. We assess the validity of our NLP methods and the accuracy of our extracted data by comparing to a hand-labeled subset. Machine learning (ML, i.e. artificial neural network) models trained on this data using graph- and pore-geometry-based representations enable prediction of stability on new MOFs with quantified uncertainty. Our web interface, MOFSimplify, provides users access to our curated data and enables them to harness that data for predictions on new MOFs. MOFSimplify also encourages community feedback on existing data and on ML model predictions for community-based active learning for improved MOF stability models.
Studying Up Machine Learning Data: Why Talk About Bias When We Mean Power?
Authors: Milagros Miceli, Julian Posada, Tianling Yang
Date: 2021-09-16 00:00:00
Tasks: BIG-bench Machine Learning

Research in machine learning (ML) has primarily argued that models trained on incomplete or biased datasets can lead to discriminatory outputs. In this commentary, we propose moving the research focus beyond bias-oriented framings by adopting a power-aware perspective to "study up" ML datasets. This means accounting for historical inequities, labor conditions, and epistemological standpoints inscribed in data. We draw on HCI and CSCW work to support our argument, critically analyze previous research, and point at two co-existing lines of work within our community -- one bias-oriented, the other power-aware. This way, we highlight the need for dialogue and cooperation in three areas: data quality, data work, and data documentation. In the first area, we argue that reducing societal problems to "bias" misses the context-based nature of data. In the second one, we highlight the corporate forces and market imperatives involved in the labor of data workers that subsequently shape ML datasets. Finally, we propose expanding current transparency-oriented efforts in dataset documentation to reflect the social contexts of data design and production.
Adversarial Attacks against Deep Learning Based Power Control in Wireless Communications
Authors: Brian Kim, Yi Shi, Yalin E. Sagduyu, Tugba Erpek, Sennur Ulukus
Date: 2021-09-16 00:00:00
Tasks: Deep Learning

We consider adversarial machine learning based attacks on power allocation where the base station (BS) allocates its transmit power to multiple orthogonal subcarriers by using a deep neural network (DNN) to serve multiple user equipments (UEs). The DNN that corresponds to a regression model is trained with channel gains as the input and returns transmit powers as the output. While the BS allocates the transmit powers to the UEs to maximize rates for all UEs, there is an adversary that aims to minimize these rates. The adversary may be an external transmitter that aims to manipulate the inputs to the DNN by interfering with the pilot signals that are transmitted to measure the channel gain. Alternatively, the adversary may be a rogue UE that transmits fabricated channel estimates to the BS. In both cases, the adversary carefully crafts adversarial perturbations to manipulate the inputs to the DNN of the BS subject to an upper bound on the strengths of these perturbations. We consider the attacks targeted on a single UE or all UEs. We compare these attacks with a benchmark, where the adversary scales down the input to the DNN. We show that the adversarial attacks are much more effective than the benchmark attack in terms of reducing the rate of communications. We also show that adversarial attacks are robust to the uncertainty at the adversary including the erroneous knowledge of channel gains and the potential errors in exercising the attacks exactly as specified.
Evaluating Music Recommendations with Binary Feedback for Multiple Stakeholders
Authors: SASHA STOIKOV, Hongyi Wen
Date: 2021-09-16 00:00:00
Tasks: Music Recommendation

High quality user feedback data is essential to training and evaluating a successful music recommendation system, particularly one that has to balance the needs of multiple stakeholders. Most existing music datasets suffer from noisy feedback and self-selection biases inherent in the data collected by music platforms. Using the Piki Music dataset of 500k ratings collected over a two-year time period, we evaluate the performance of classic recommendation algorithms on three important stakeholders: consumers, well-known artists and lesser-known artists. We show that a matrix factorization algorithm trained on both likes and dislikes performs significantly better compared to one trained only on likes for all three stakeholders.
A Qualitative Evaluation of User Preference for Link-based vs. Text-based Recommendations of Wikipedia Articles
Authors: Malte Ostendorff, Corinna Breitinger, Bela Gipp
Date: 2021-09-16 00:00:00
Tasks: Articles, Recommendation Systems

Literature recommendation systems (LRS) assist readers in the discovery of relevant content from the overwhelming amount of literature available. Despite the widespread adoption of LRS, there is a lack of research on the user-perceived recommendation characteristics for fundamentally different approaches to content-based literature recommendation. To complement existing quantitative studies on literature recommendation, we present qualitative study results that report on users' perceptions for two contrasting recommendation classes: (1) link-based recommendation represented by the Co-Citation Proximity (CPA) approach, and (2) text-based recommendation represented by Lucene's MoreLikeThis (MLT) algorithm. The empirical data analyzed in our study with twenty users and a diverse set of 40 Wikipedia articles indicate a noticeable difference between text- and link-based recommendation generation approaches along several key dimensions. The text-based MLT method receives higher satisfaction ratings in terms of user-perceived similarity of recommended articles. In contrast, the CPA approach receives higher satisfaction scores in terms of diversity and serendipity of recommendations. We conclude that users of literature recommendation systems can benefit most from hybrid approaches that combine both link- and text-based approaches, where the user's information needs and preferences should control the weighting for the approaches used. The optimal weighting of multiple approaches used in a hybrid recommendation system is highly dependent on a user's shifting needs.
Popularity Bias Is Not Always Evil: Disentangling Benign and Harmful Bias for Recommendation
Authors: Zihao Zhao, Jiawei Chen, Sheng Zhou, Xiangnan He, Xuezhi Cao, Fuzheng Zhang, Wei Wu
Date: 2021-09-16 00:00:00
Tasks: Recommendation Systems

Recommender system usually suffers from severe popularity bias -- the collected interaction data usually exhibits quite imbalanced or even long-tailed distribution over items. Such skewed distribution may result from the users' conformity to the group, which deviates from reflecting users' true preference. Existing efforts for tackling this issue mainly focus on completely eliminating popularity bias. However, we argue that not all popularity bias is evil. Popularity bias not only results from conformity but also item quality, which is usually ignored by existing methods. Some items exhibit higher popularity as they have intrinsic better property. Blindly removing the popularity bias would lose such important signal, and further deteriorate model performance. To sufficiently exploit such important information for recommendation, it is essential to disentangle the benign popularity bias caused by item quality from the harmful popularity bias caused by conformity. Although important, it is quite challenging as we lack an explicit signal to differentiate the two factors of popularity bias. In this paper, we propose to leverage temporal information as the two factors exhibit quite different patterns along the time: item quality revealing item inherent property is stable and static while conformity that depends on items' recent clicks is highly time-sensitive. Correspondingly, we further propose a novel Time-aware DisEntangled framework (TIDE), where a click is generated from three components namely the static item quality, the dynamic conformity effect, as well as the user-item matching score returned by any recommendation model. Lastly, we conduct interventional inference such that the recommendation can benefit from the benign popularity bias while circumvent the harmful one. Extensive experiments on three real-world datasets demonstrated the effectiveness of TIDE.