pwc-archive/papers-with-abstracts huggingface dataset:
Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction
Authors: Jiahua Rao, Shuangjia Zheng, Sijie Mai, Yuedong Yang
Date: 2022-05-12 00:00:00
Tasks: Gene Interaction Prediction, Representation Learning

Illuminating the interconnections between drugs and genes is an important topic in drug development and precision medicine. Currently, computational predictions of drug-gene interactions mainly focus on the binding interactions without considering other relation types like agonist, antagonist, etc. In addition, existing methods either heavily rely on high-quality domain features or are intrinsically transductive, which limits the capacity of models to generalize to drugs/genes that lack external information or are unseen during the training process. To address these problems, we propose a novel Communicative Subgraph representation learning for Multi-relational Inductive drug-Gene interactions prediction (CoSMIG), where the predictions of drug-gene relations are made through subgraph patterns, and thus are naturally inductive for unseen drugs/genes without retraining or utilizing external domain features. Moreover, the model strengthened the relations on the drug-gene graph through a communicative message passing mechanism. To evaluate our method, we compiled two new benchmark datasets from DrugBank and DGIdb. The comprehensive experiments on the two datasets showed that our method outperformed state-of-the-art baselines in the transductive scenarios and achieved superior performance in the inductive ones. Further experimental analysis including LINCS experimental validation and literature verification also demonstrated the value of our model.
Exploiting Inductive Bias in Transformers for Unsupervised Disentanglement of Syntax and Semantics with VAEs
Authors: Ghazi Felhi, Joseph Le Roux, Djamé Seddah
Date: 2022-05-12 00:00:00
Proceeding: NAACL 2022 7
Tasks: Decoder, Disentanglement, Inductive Bias, Text Generation

We propose a generative model for text generation, which exhibits disentangled latent representations of syntax and semantics. Contrary to previous work, this model does not need syntactic information such as constituency parses, or semantic information such as paraphrase pairs. Our model relies solely on the inductive bias found in attention-based architectures such as Transformers. In the attention of Transformers, keys handle information selection while values specify what information is conveyed. Our model, dubbed QKVAE, uses Attention in its decoder to read latent variables where one latent variable infers keys while another infers values. We run experiments on latent representations and experiments on syntax/semantics transfer which show that QKVAE displays clear signs of disentangled syntax and semantics. We also show that our model displays competitive syntax transfer capabilities when compared to supervised models and that comparable supervised models need a fairly large amount of data (more than 50K samples) to outperform it on both syntactic and semantic transfer. The code for our experiments is publicly available.
Ensemble Clustering via Co-association Matrix Self-enhancement
Authors: Yuheng Jia, Sirui Tao, Ran Wang, Yongheng Wang
Date: 2022-05-12 00:00:00
Tasks: Clustering

Ensemble clustering integrates a set of base clustering results to generate a stronger one. Existing methods usually rely on a co-association (CA) matrix that measures how many times two samples are grouped into the same cluster according to the base clusterings to achieve ensemble clustering. However, when the constructed CA matrix is of low quality, the performance will degrade. In this paper, we propose a simple yet effective CA matrix self-enhancement framework that can improve the CA matrix to achieve better clustering performance. Specifically, we first extract the high-confidence (HC) information from the base clusterings to form a sparse HC matrix. By propagating the highly-reliable information of the HC matrix to the CA matrix and complementing the HC matrix according to the CA matrix simultaneously, the proposed method generates an enhanced CA matrix for better clustering. Technically, the proposed model is formulated as a symmetric constrained convex optimization problem, which is efficiently solved by an alternating iterative algorithm with convergence and global optimum theoretically guaranteed. Extensive experimental comparisons with twelve state-of-the-art methods on eight benchmark datasets substantiate the effectiveness, flexibility and efficiency of the proposed model in ensemble clustering. The codes and datasets can be downloaded at https://github.com/Siritao/EC-CMS.
Virtual twins of nonlinear vibrating multiphysics microstructures: physics-based versus deep learning-based approaches
Authors: Giorgio Gobat, Stefania Fresca, Andrea Manzoni, Attilio Frangi
Date: 2022-05-12 00:00:00
Tasks: Deep Learning

Micro-Electro-Mechanical-Systems are complex structures, often involving nonlinearites of geometric and multiphysics nature, that are used as sensors and actuators in countless applications. Starting from full-order representations, we apply deep learning techniques to generate accurate, efficient and real-time reduced order models to be used as virtual twin for the simulation and optimization of higher-level complex systems. We extensively test the reliability of the proposed procedures on micromirrors, arches and gyroscopes, also displaying intricate dynamical evolutions like internal resonances. In particular, we discuss the accuracy of the deep learning technique and its ability to replicate and converge to the invariant manifolds predicted using the recently developed direct parametrization approach that allows extracting the nonlinear normal modes of large finite element models. Finally, by addressing an electromechanical gyroscope, we show that the non-intrusive deep learning approach generalizes easily to complex multiphysics problems
Comments on: "Hybrid Semiparametric Bayesian Networks"
Authors: Marco Scutari
Date: 2022-05-12 00:00:00

Invited discussion on the paper "Hybrid Semiparametric Bayesian Networks" by David Atienza, Pedro Larranaga and Concha Bielza (TEST, 2022).
NER-MQMRC: Formulating Named Entity Recognition as Multi Question Machine Reading Comprehension
Authors: Anubhav Shrimal, Avi Jain, Kartik Mehta, Promod Yenigalla
Date: 2022-05-12 00:00:00
Proceeding: NAACL (ACL) 2022 7
Tasks: Attribute, Machine Reading Comprehension, named-entity-recognition, Named Entity Recognition, Named Entity Recognition (NER), NER, Reading Comprehension

NER has been traditionally formulated as a sequence labeling task. However, there has been recent trend in posing NER as a machine reading comprehension task (Wang et al., 2020; Mengge et al., 2020), where entity name (or other information) is considered as a question, text as the context and entity value in text as answer snippet. These works consider MRC based on a single question (entity) at a time. We propose posing NER as a multi-question MRC task, where multiple questions (one question per entity) are considered at the same time for a single text. We propose a novel BERT-based multi-question MRC (NER-MQMRC) architecture for this formulation. NER-MQMRC architecture considers all entities as input to BERT for learning token embeddings with self-attention and leverages BERT-based entity representation for further improving these token embeddings for NER task. Evaluation on three NER datasets show that our proposed architecture leads to average 2.5 times faster training and 2.3 times faster inference as compared to NER-SQMRC framework based models by considering all entities together in a single pass. Further, we show that our model performance does not degrade compared to single-question based MRC (NER-SQMRC) (Devlin et al., 2019) leading to F1 gain of +0.41%, +0.32% and +0.27% for AE-Pub, Ecommerce5PT and Twitter datasets respectively. We propose this architecture primarily to solve large scale e-commerce attribute (or entity) extraction from unstructured text of a magnitude of 50k+ attributes to be extracted on a scalable production environment with high performance and optimised training and inference runtimes.
Training Uncertainty-Aware Classifiers with Conformalized Deep Learning
Authors: Bat-Sheva Einbinder, Yaniv Romano, Matteo Sesia, Yanfei Zhou
Date: 2022-05-12 00:00:00
Tasks: Conformal Prediction, Deep Learning, Multi-class Classification

Deep neural networks are powerful tools to detect hidden patterns in data and leverage them to make predictions, but they are not designed to understand uncertainty and estimate reliable probabilities. In particular, they tend to be overconfident. We begin to address this problem in the context of multi-class classification by developing a novel training algorithm producing models with more dependable uncertainty estimates, without sacrificing predictive power. The idea is to mitigate overconfidence by minimizing a loss function, inspired by advances in conformal inference, that quantifies model uncertainty by carefully leveraging hold-out data. Experiments with synthetic and real data demonstrate this method can lead to smaller conformal prediction sets with higher conditional coverage, after exact calibration with hold-out data, compared to state-of-the-art alternatives.
Towards Robust Unsupervised Disentanglement of Sequential Data -- A Case Study Using Music Audio
Authors: Yin-Jyun Luo, Sebastian Ewert, Simon Dixon
Date: 2022-05-12 00:00:00
Tasks: Data Augmentation, Disentanglement, Inductive Bias

Disentangled sequential autoencoders (DSAEs) represent a class of probabilistic graphical models that describes an observed sequence with dynamic latent variables and a static latent variable. The former encode information at a frame rate identical to the observation, while the latter globally governs the entire sequence. This introduces an inductive bias and facilitates unsupervised disentanglement of the underlying local and global factors. In this paper, we show that the vanilla DSAE suffers from being sensitive to the choice of model architecture and capacity of the dynamic latent variables, and is prone to collapse the static latent variable. As a countermeasure, we propose TS-DSAE, a two-stage training framework that first learns sequence-level prior distributions, which are subsequently employed to regularise the model and facilitate auxiliary objectives to promote disentanglement. The proposed framework is fully unsupervised and robust against the global factor collapse problem across a wide range of model configurations. It also avoids typical solutions such as adversarial training which usually involves laborious parameter tuning, and domain-specific data augmentation. We conduct quantitative and qualitative evaluations to demonstrate its robustness in terms of disentanglement on both artificial and real-world music audio datasets.
Over-the-Air Federated Learning with Joint Adaptive Computation and Power Control
Authors: Haibo Yang, Peiwen Qiu, Jia Liu, Aylin Yener
Date: 2022-05-12 00:00:00
Tasks: Federated Learning

This paper considers over-the-air federated learning (OTA-FL). OTA-FL exploits the superposition property of the wireless medium, and performs model aggregation over the air for free. Thus, it can greatly reduce the communication cost incurred in communicating model updates from the edge devices. In order to fully utilize this advantage while providing comparable learning performance to conventional federated learning that presumes model aggregation via noiseless channels, we consider the joint design of transmission scaling and the number of local iterations at each round, given the power constraint at each edge device. We first characterize the training error due to such channel noise in OTA-FL by establishing a fundamental lower bound for general functions with Lipschitz-continuous gradients. Then, by introducing an adaptive transceiver power scaling scheme, we propose an over-the-air federated learning algorithm with joint adaptive computation and power control (ACPC-OTA-FL). We provide the convergence analysis for ACPC-OTA-FL in training with non-convex objective functions and heterogeneous data. We show that the convergence rate of ACPC-OTA-FL matches that of FL with noise-free communications.
A Survey of Risk-Aware Multi-Armed Bandits
Authors: Vincent Y. F. Tan, Prashanth L. A., Krishna Jagannathan
Date: 2022-05-12 00:00:00
Tasks: Multi-Armed Bandits, Portfolio Optimization, Survey

In several applications such as clinical trials and financial portfolio optimization, the expected value (or the average reward) does not satisfactorily capture the merits of a drug or a portfolio. In such applications, risk plays a crucial role, and a risk-aware performance measure is preferable, so as to capture losses in the case of adverse events. This survey aims to consolidate and summarise the existing research on risk measures, specifically in the context of multi-armed bandits. We review various risk measures of interest, and comment on their properties. Next, we review existing concentration inequalities for various risk measures. Then, we proceed to defining risk-aware bandit problems, We consider algorithms for the regret minimization setting, where the exploration-exploitation trade-off manifests, as well as the best-arm identification setting, which is a pure exploration problem -- both in the context of risk-sensitive measures. We conclude by commenting on persisting challenges and fertile areas for future research.
Orthogonal Gromov-Wasserstein Discrepancy with Efficient Lower Bound
Authors: Hongwei Jin, Zishun Yu, Xinhua Zhang
Date: 2022-05-12 00:00:00
Tasks: Graph Classification

Comparing structured data from possibly different metric-measure spaces is a fundamental task in machine learning, with applications in, e.g., graph classification. The Gromov-Wasserstein (GW) discrepancy formulates a coupling between the structured data based on optimal transportation, tackling the incomparability between different structures by aligning the intra-relational geometries. Although efficient \emph{local} solvers such as conditional gradient and Sinkhorn are available, the inherent non-convexity still prevents a tractable evaluation, and the existing lower bounds are not tight enough for practical use. To address this issue, we take inspiration from the connection with the quadratic assignment problem, and propose the orthogonal Gromov-Wasserstein (OGW) discrepancy as a surrogate of GW. It admits an efficient and \emph{closed-form} lower bound with $\mathcal{O}(n^3)$ complexity, and directly extends to the fused Gromov-Wasserstein (FGW) distance, incorporating node features into the coupling. Extensive experiments on both the synthetic and real-world datasets show the tightness of our lower bounds, and both OGW and its lower bounds efficiently deliver accurate predictions and satisfactory barycenters for graph sets.
Privacy-Preserving Distributed Machine Learning Made Faster
Authors: Zoe L. Jiang, Jiajing Gu, Hongxiao Wang, Yulin Wu, Junbin Fang, Siu-Ming Yiu, Wenjian Luo, Xuan Wang
Date: 2022-05-12 00:00:00
Tasks: BIG-bench Machine Learning, Privacy Preserving

With the development of machine learning, it is difficult for a single server to process all the data. So machine learning tasks need to be spread across multiple servers, turning the centralized machine learning into a distributed one. However, privacy remains an unsolved problem in distributed machine learning. Multi-key homomorphic encryption is one of the suitable candidates to solve the problem. However, the most recent result of the Multi-key homomorphic encryption scheme (MKTFHE) only supports the NAND gate. Although it is Turing complete, it requires efficient encapsulation of the NAND gate to further support mathematical calculation. This paper designs and implements a series of operations on positive and negative integers accurately. First, we design basic bootstrapped gates with the same efficiency as that of the NAND gate. Second, we construct practical $k$-bit complement mathematical operators based on our basic binary bootstrapped gates. The constructed created can perform addition, subtraction, multiplication, and division on both positive and negative integers. Finally, we demonstrated the generality of the designed operators by achieving a distributed privacy-preserving machine learning algorithm, i.e. linear regression with two different solutions. Experiments show that the operators we designed are practical and efficient.
Representation Learning for Context-Dependent Decision-Making
Authors: Yuzhen Qin, Tommaso Menara, Samet Oymak, ShiNung Ching, Fabio Pasqualetti
Date: 2022-05-12 00:00:00
Tasks: Decision Making, Q-Learning, Representation Learning, Sequential Decision Making

Humans are capable of adjusting to changing environments flexibly and quickly. Empirical evidence has revealed that representation learning plays a crucial role in endowing humans with such a capability. Inspired by this observation, we study representation learning in the sequential decision-making scenario with contextual changes. We propose an online algorithm that is able to learn and transfer context-dependent representations and show that it significantly outperforms the existing ones that do not learn representations adaptively. As a case study, we apply our algorithm to the Wisconsin Card Sorting Task, a well-established test for the mental flexibility of humans in sequential decision-making. By comparing our algorithm with the standard Q-learning and Deep-Q learning algorithms, we demonstrate the benefits of adaptive representation learning.
Open Vocabulary Extreme Classification Using Generative Models
Authors: Daniel Simig, Fabio Petroni, Pouya Yanki, Kashyap Popat, Christina Du, Sebastian Riedel, Majid Yazdani
Date: 2022-05-12 00:00:00
Proceeding: Findings (ACL) 2022 5
Tasks: Classification, Extreme Multi-Label Classification, Multi-Label Classification, MUlTI-LABEL-ClASSIFICATION, TAG, zero-shot-classification, Zero-Shot Learning

The extreme multi-label classification (XMC) task aims at tagging content with a subset of labels from an extremely large label set. The label vocabulary is typically defined in advance by domain experts and assumed to capture all necessary tags. However in real world scenarios this label set, although large, is often incomplete and experts frequently need to refine it. To develop systems that simplify this process, we introduce the task of open vocabulary XMC (OXMC): given a piece of content, predict a set of labels, some of which may be outside of the known tag set. Hence, in addition to not having training data for some labels - as is the case in zero-shot classification - models need to invent some labels on-the-fly. We propose GROOV, a fine-tuned seq2seq model for OXMC that generates the set of labels as a flat sequence and is trained using a novel loss independent of predicted label order. We show the efficacy of the approach, experimenting with popular XMC datasets for which GROOV is able to predict meaningful labels outside the given vocabulary while performing on par with state-of-the-art solutions for known labels.
Performing Video Frame Prediction of Microbial Growth with a Recurrent Neural Network
Authors: Connor Robertson, Jared L. Wilmoth, Scott Retterer, Miguel Fuentes-Cabrera
Date: 2022-05-12 00:00:00

A Recurrent Neural Network (RNN) was used to perform video frame prediction of microbial growth for a population of two mutants of Pseudomonas aeruginosa. The RNN was trained on videos of 20 frames that were acquired using fluorescence microscopy and microfluidics. The network predicted the last 10 frames of each video, and the accuracy's of the predictions was assessed by comparing raw images, population curves, and the number and size of individual colonies. Overall, we found the predictions to be accurate using this approach. The implications this result has on designing autonomous experiments in microbiology, and the steps that can be taken to make the predictions even more accurate, are discussed.
Stochastic first-order methods for average-reward Markov decision processes
Authors: Tianjiao Li, Feiyang Wu, Guanghui Lan
Date: 2022-05-11 00:00:00
Tasks: Policy Gradient Methods

We study average-reward Markov decision processes (AMDPs) and develop novel first-order methods with strong theoretical guarantees for both policy optimization and policy evaluation. Compared with intensive research efforts in finite sample analysis of policy gradient methods for discounted MDPs, existing studies on policy gradient methods for AMDPs mostly focus on regret bounds under restrictive assumptions, and they often lack guarantees on the overall sample complexities. Towards this end, we develop an average-reward stochastic policy mirror descent (SPMD) method for solving AMDPs with and without regularizers and provide convergence guarantees in terms of the long-term average reward. For policy evaluation, existing on-policy methods suffer from sub-optimal convergence rates as well as failure in handling insufficiently random policies due to the lack of exploration in the action space. To remedy these issues, we develop a variance-reduced temporal difference (VRTD) method with linear function approximation for randomized policies along with optimal convergence guarantees, and design an exploratory VRTD method that resolves the exploration issue and provides comparable convergence guarantees. By combining the policy evaluation and policy optimization parts, we establish sample complexity results for solving AMDPs under both generative and Markovian noise models. It is worth noting that when linear function approximation is utilized, our algorithm only needs to update in the low-dimensional parameter space and thus can handle MDPs with large state and action spaces.
Algebraic Machine Learning with an Application to Chemistry
Authors: Ezzeddine El Sai, Parker Gara, Markus J. Pflaum
Date: 2022-05-11 00:00:00
Tasks: BIG-bench Machine Learning

As datasets used in scientific applications become more complex, studying the geometry and topology of data has become an increasingly prevalent part of the data analysis process. This can be seen for example with the growing interest in topological tools such as persistent homology. However, on the one hand, topological tools are inherently limited to providing only coarse information about the underlying space of the data. On the other hand, more geometric approaches rely predominately on the manifold hypothesis, which asserts that the underlying space is a smooth manifold. This assumption fails for many physical models where the underlying space contains singularities. In this paper we develop a machine learning pipeline that captures fine-grain geometric information without having to rely on any smoothness assumptions. Our approach involves working within the scope of algebraic geometry and algebraic varieties instead of differential geometry and smooth manifolds. In the setting of the variety hypothesis, the learning problem becomes to find the underlying variety using sample data. We cast this learning problem into a Maximum A Posteriori optimization problem which we solve in terms of an eigenvalue computation. Having found the underlying variety, we explore the use of Gr\"obner bases and numerical methods to reveal information about its geometry. In particular, we propose a heuristic for numerically detecting points lying near the singular locus of the underlying variety.