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Polymer Informatics: Current Status and Critical Next Steps

Nov 01, 2020
Lihua Chen, Ghanshyam Pilania, Rohit Batra, Tran Doan Huan, Chiho Kim, Christopher Kuenneth, Rampi Ramprasad

Artificial intelligence (AI) based approaches are beginning to impact several domains of human life, science and technology. Polymer informatics is one such domain where AI and machine learning (ML) tools are being used in the efficient development, design and discovery of polymers. Surrogate models are trained on available polymer data for instant property prediction, allowing screening of promising polymer candidates with specific target property requirements. Questions regarding synthesizability, and potential (retro)synthesis steps to create a target polymer, are being explored using statistical means. Data-driven strategies to tackle unique challenges resulting from the extraordinary chemical and physical diversity of polymers at small and large scales are being explored. Other major hurdles for polymer informatics are the lack of widespread availability of curated and organized data, and approaches to create machine-readable representations that capture not just the structure of complex polymeric situations but also synthesis and processing conditions. Methods to solve inverse problems, wherein polymer recommendations are made using advanced AI algorithms that meet application targets, are being investigated. As various parts of the burgeoning polymer informatics ecosystem mature and become integrated, efficiency improvements, accelerated discoveries and increased productivity can result. Here, we review emergent components of this polymer informatics ecosystem and discuss imminent challenges and opportunities.


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Learning from DPPs via Sampling: Beyond HKPV and symmetry

Jul 08, 2020
Rémi Bardenet, Subhroshekhar Ghosh

Determinantal point processes (DPPs) have become a significant tool for recommendation systems, feature selection, or summary extraction, harnessing the intrinsic ability of these probabilistic models to facilitate sample diversity. The ability to sample from DPPs is paramount to the empirical investigation of these models. Most exact samplers are variants of a spectral meta-algorithm due to Hough, Krishnapur, Peres and Vir\'ag (henceforth HKPV), which is in general time and resource intensive. For DPPs with symmetric kernels, scalable HKPV samplers have been proposed that either first downsample the ground set of items, or force the kernel to be low-rank, using e.g. Nystr\"om-type decompositions. In the present work, we contribute a radically different approach than HKPV. Exploiting the fact that many statistical and learning objectives can be effectively accomplished by only sampling certain key observables of a DPP (so-called linear statistics), we invoke an expression for the Laplace transform of such an observable as a single determinant, which holds in complete generality. Combining traditional low-rank approximation techniques with Laplace inversion algorithms from numerical analysis, we show how to directly approximate the distribution function of a linear statistic of a DPP. This distribution function can then be used in hypothesis testing or to actually sample the linear statistic, as per requirement. Our approach is scalable and applies to very general DPPs, beyond traditional symmetric kernels.


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MultiImport: Inferring Node Importance in a Knowledge Graph from Multiple Input Signals

Jun 22, 2020
Namyong Park, Andrey Kan, Xin Luna Dong, Tong Zhao, Christos Faloutsos

Given multiple input signals, how can we infer node importance in a knowledge graph (KG)? Node importance estimation is a crucial and challenging task that can benefit a lot of applications including recommendation, search, and query disambiguation. A key challenge towards this goal is how to effectively use input from different sources. On the one hand, a KG is a rich source of information, with multiple types of nodes and edges. On the other hand, there are external input signals, such as the number of votes or pageviews, which can directly tell us about the importance of entities in a KG. While several methods have been developed to tackle this problem, their use of these external signals has been limited as they are not designed to consider multiple signals simultaneously. In this paper, we develop an end-to-end model MultiImport, which infers latent node importance from multiple, potentially overlapping, input signals. MultiImport is a latent variable model that captures the relation between node importance and input signals, and effectively learns from multiple signals with potential conflicts. Also, MultiImport provides an effective estimator based on attentive graph neural networks. We ran experiments on real-world KGs to show that MultiImport handles several challenges involved with inferring node importance from multiple input signals, and consistently outperforms existing methods, achieving up to 23.7% higher [email protected] than the state-of-the-art method.

* KDD 2020 Research Track. 10 pages 

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No-Regret Learning in Unknown Games with Correlated Payoffs

Oct 28, 2019
Pier Giuseppe Sessa, Ilija Bogunovic, Maryam Kamgarpour, Andreas Krause

We consider the problem of learning to play a repeated multi-agent game with an unknown reward function. Single player online learning algorithms attain strong regret bounds when provided with full information feedback, which unfortunately is unavailable in many real-world scenarios. Bandit feedback alone, i.e., observing outcomes only for the selected action, yields substantially worse performance. In this paper, we consider a natural model where, besides a noisy measurement of the obtained reward, the player can also observe the opponents' actions. This feedback model, together with a regularity assumption on the reward function, allows us to exploit the correlations among different game outcomes by means of Gaussian processes (GPs). We propose a novel confidence-bound based bandit algorithm GP-MW, which utilizes the GP model for the reward function and runs a multiplicative weight (MW) method. We obtain novel kernel-dependent regret bounds that are comparable to the known bounds in the full information setting, while substantially improving upon the existing bandit results. We experimentally demonstrate the effectiveness of GP-MW in random matrix games, as well as real-world problems of traffic routing and movie recommendation. In our experiments, GP-MW consistently outperforms several baselines, while its performance is often comparable to methods that have access to full information feedback.


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Transferable Recognition-Aware Image Processing

Oct 21, 2019
Zhuang Liu, Tinghui Zhou, Zhiqiang Shen, Bingyi Kang, Trevor Darrell

Recent progress in image recognition has stimulated the deployment of vision systems (e.g. image search engines) at an unprecedented scale. As a result, visual data are now often consumed not only by humans but also by machines. Meanwhile, existing image processing methods only optimize for better human perception, whereas the resulting images may not be accurately recognized by machines. This can be undesirable, e.g., the images can be improperly handled by search engines or recommendation systems. In this work, we propose simple approaches to improve machine interpretability of processed images: optimizing the recognition loss directly on the image processing network or through an intermediate transforming model, a process which we show can also be done in an unsupervised manner. Interestingly, the processing model's ability to enhance the recognition performance can transfer when evaluated on different recognition models, even if they are of different architectures, trained on different object categories or even different recognition tasks. This makes the solutions applicable even when we do not have the knowledge about future downstream recognition models, e.g., if we are to upload the processed images to the Internet. We conduct comprehensive experiments on three image processing tasks with two downstream recognition tasks, and confirm our method brings substantial accuracy improvement on both the same recognition model and when transferring to a different one, with minimal or no loss in the image processing quality.


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PINE: Universal Deep Embedding for Graph Nodes via Partial Permutation Invariant Set Functions

Sep 25, 2019
Shupeng Gui, Xiangliang Zhang, Pan Zhong, Shuang Qiu, Mingrui Wu, Jieping Ye, Zhengdao Wang, Ji Liu

Graph node embedding aims at learning a vector representation for all nodes given a graph. It is a central problem in many machine learning tasks (e.g., node classification, recommendation, community detection). The key problem in graph node embedding lies in how to define the dependence to neighbors. Existing approaches specify (either explicitly or implicitly) certain dependencies on neighbors, which may lead to loss of subtle but important structural information within the graph and other dependencies among neighbors. This intrigues us to ask the question: can we design a model to give the maximal flexibility of dependencies to each node's neighborhood. In this paper, we propose a novel graph node embedding (named PINE) via a novel notion of partial permutation invariant set function, to capture any possible dependence. Our method 1) can learn an arbitrary form of the representation function from the neighborhood, withour losing any potential dependence structures, and 2) is applicable to both homogeneous and heterogeneous graph embedding, the latter of which is challenged by the diversity of node types. Furthermore, we provide theoretical guarantee for the representation capability of our method for general homogeneous and heterogeneous graphs. Empirical evaluation results on benchmark data sets show that our proposed PINE method outperforms the state-of-the-art approaches on producing node vectors for various learning tasks of both homogeneous and heterogeneous graphs.

* 24 pages, 4 figures, 3 tables. arXiv admin note: text overlap with arXiv:1805.11182 

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Are Clusterings of Multiple Data Views Independent?

Jan 12, 2019
Lucy L. Gao, Jacob Bien, Daniela Witten

In the Pioneer 100 (P100) Wellness Project (Price and others, 2017), multiple types of data are collected on a single set of healthy participants at multiple timepoints in order to characterize and optimize wellness. One way to do this is to identify clusters, or subgroups, among the participants, and then to tailor personalized health recommendations to each subgroup. It is tempting to cluster the participants using all of the data types and timepoints, in order to fully exploit the available information. However, clustering the participants based on multiple data views implicitly assumes that a single underlying clustering of the participants is shared across all data views. If this assumption does not hold, then clustering the participants using multiple data views may lead to spurious results. In this paper, we seek to evaluate the assumption that there is some underlying relationship among the clusterings from the different data views, by asking the question: are the clusters within each data view dependent or independent? We develop a new test for answering this question, which we then apply to clinical, proteomic, and metabolomic data, across two distinct timepoints, from the P100 study. We find that while the subgroups of the participants defined with respect to any single data type seem to be dependent across time, the clustering among the participants based on one data type (e.g. proteomic data) appears not to be associated with the clustering based on another data type (e.g. clinical data).

* 20 pages, 4 figures, 1 table (main text); 15 pages, 9 figures (supplement) 

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Cheating Automatic Short Answer Grading: On the Adversarial Usage of Adjectives and Adverbs

Jan 20, 2022
Anna Filighera, Sebastian Ochs, Tim Steuer, Thomas Tregel

Automatic grading models are valued for the time and effort saved during the instruction of large student bodies. Especially with the increasing digitization of education and interest in large-scale standardized testing, the popularity of automatic grading has risen to the point where commercial solutions are widely available and used. However, for short answer formats, automatic grading is challenging due to natural language ambiguity and versatility. While automatic short answer grading models are beginning to compare to human performance on some datasets, their robustness, especially to adversarially manipulated data, is questionable. Exploitable vulnerabilities in grading models can have far-reaching consequences ranging from cheating students receiving undeserved credit to undermining automatic grading altogether - even when most predictions are valid. In this paper, we devise a black-box adversarial attack tailored to the educational short answer grading scenario to investigate the grading models' robustness. In our attack, we insert adjectives and adverbs into natural places of incorrect student answers, fooling the model into predicting them as correct. We observed a loss of prediction accuracy between 10 and 22 percentage points using the state-of-the-art models BERT and T5. While our attack made answers appear less natural to humans in our experiments, it did not significantly increase the graders' suspicions of cheating. Based on our experiments, we provide recommendations for utilizing automatic grading systems more safely in practice.


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US-Rule: Discovering Utility-driven Sequential Rules

Nov 29, 2021
Gengsen Huang, Wensheng Gan, Jian Weng, Philip S. Yu

Utility-driven mining is an important task in data science and has many applications in real life. High utility sequential pattern mining (HUSPM) is one kind of utility-driven mining. HUSPM aims to discover all sequential patterns with high utility. However, the existing algorithms of HUSPM can not provide an accurate probability to deal with some scenarios for prediction or recommendation. High-utility sequential rule mining (HUSRM) was proposed to discover all sequential rules with high utility and high confidence. There is only one algorithm proposed for HUSRM, which is not enough efficient. In this paper, we propose a faster algorithm, called US-Rule, to efficiently mine high-utility sequential rules. It utilizes rule estimated utility co-occurrence pruning strategy (REUCP) to avoid meaningless computation. To improve the efficiency on dense and long sequence datasets, four tighter upper bounds (LEEU, REEU, LERSU, RERSU) and their corresponding pruning strategies (LEEUP, REEUP, LERSUP, RERSUP) are proposed. Besides, US-Rule proposes rule estimated utility recomputing pruning strategy (REURP) to deal with sparse datasets. At last, a large number of experiments on different datasets compared to the state-of-the-art algorithm demonstrate that US-Rule can achieve better performance in terms of execution time, memory consumption and scalability.

* Preprint. 3 figures, 9 tables 

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