pwc-archive/papers-with-abstracts huggingface dataset:
Transformers are uninterpretable with myopic methods: a case study with bounded Dyck grammars
Authors: Kaiyue Wen, Yuchen Li, Bingbin Liu, Andrej Risteski
Date: 2023-12-03 00:00:00
Proceeding: NeurIPS 2023 11
Tasks: LEMMA

Interpretability methods aim to understand the algorithm implemented by a trained model (e.g., a Transofmer) by examining various aspects of the model, such as the weight matrices or the attention patterns. In this work, through a combination of theoretical results and carefully controlled experiments on synthetic data, we take a critical view of methods that exclusively focus on individual parts of the model, rather than consider the network as a whole. We consider a simple synthetic setup of learning a (bounded) Dyck language. Theoretically, we show that the set of models that (exactly or approximately) solve this task satisfy a structural characterization derived from ideas in formal languages (the pumping lemma). We use this characterization to show that the set of optima is qualitatively rich; in particular, the attention pattern of a single layer can be ``nearly randomized'', while preserving the functionality of the network. We also show via extensive experiments that these constructions are not merely a theoretical artifact: even after severely constraining the architecture of the model, vastly different solutions can be reached via standard training. Thus, interpretability claims based on inspecting individual heads or weight matrices in the Transformer can be misleading.
Neural Network Characterization and Entropy Regulated Data Balancing through Principal Component Analysis
Authors: David Yevick, Karolina Hutchison
Date: 2023-12-03 00:00:00

This paper examines the relationship between the behavior of a neural network and the distribution formed from the projections of the data records into the space spanned by the low-order principal components of the training data. For example, in a benchmark calculation involving rotated and unrotated MNIST digits, classes (digits) that are mapped far from the origin in a low-dimensional principal component space and that overlap minimally with other digits converge rapidly and exhibit high degrees of accuracy in neural network calculations that employ the associated components of each data record as inputs. Further, if the space spanned by these low-order principal components is divided into bins and the input data records that are mapped into a given bin averaged, the resulting pattern can be distinguished by its geometric features which interpolate between those of adjacent bins in an analogous manner to variational autoencoders. Based on this observation, a simply realized data balancing procedure can be realized by evaluating the entropy associated with each histogram bin and subsequently repeating the original image data associated with the bin by a number of times that is determined from this entropy.
Regret Optimality of GP-UCB
Authors: Wenjia Wang, Xiaowei Zhang, Lu Zou
Date: 2023-12-03 00:00:00
Tasks: Bayesian Optimization

Gaussian Process Upper Confidence Bound (GP-UCB) is one of the most popular methods for optimizing black-box functions with noisy observations, due to its simple structure and superior performance. Its empirical successes lead to a natural, yet unresolved question: Is GP-UCB regret optimal? In this paper, we offer the first generally affirmative answer to this important open question in the Bayesian optimization literature. We establish new upper bounds on both the simple and cumulative regret of GP-UCB when the objective function to optimize admits certain smoothness property. These upper bounds match the known minimax lower bounds (up to logarithmic factors independent of the feasible region's dimensionality) for optimizing functions with the same smoothness. Intriguingly, our findings indicate that, with the same level of exploration, GP-UCB can simultaneously achieve optimality in both simple and cumulative regret. The crux of our analysis hinges on a refined uniform error bound for online estimation of functions in reproducing kernel Hilbert spaces. This error bound, which we derive from empirical process theory, is of independent interest, and its potential applications may reach beyond the scope of this study.
Relation between PLS and OLS regression in terms of the eigenvalue distribution of the regressor covariance matrix
Authors: David del Val, José R. Berrendero, Alberto Suárez
Date: 2023-12-03 00:00:00
Tasks: Dimensionality Reduction, regression

Partial least squares (PLS) is a dimensionality reduction technique introduced in the field of chemometrics and successfully employed in many other areas. The PLS components are obtained by maximizing the covariance between linear combinations of the regressors and of the target variables. In this work, we focus on its application to scalar regression problems. PLS regression consists in finding the least squares predictor that is a linear combination of a subset of the PLS components. Alternatively, PLS regression can be formulated as a least squares problem restricted to a Krylov subspace. This equivalent formulation is employed to analyze the distance between ${\hat{\boldsymbol\beta}\;}_{\mathrm{PLS}}^{\scriptscriptstyle {(L)}}$, the PLS estimator of the vector of coefficients of the linear regression model based on $L$ PLS components, and $\hat{\boldsymbol \beta}_{\mathrm{OLS}}$, the one obtained by ordinary least squares (OLS), as a function of $L$. Specifically, ${\hat{\boldsymbol\beta}\;}_{\mathrm{PLS}}^{\scriptscriptstyle {(L)}}$ is the vector of coefficients in the aforementioned Krylov subspace that is closest to $\hat{\boldsymbol \beta}_{\mathrm{OLS}}$ in terms of the Mahalanobis distance with respect to the covariance matrix of the OLS estimate. We provide a bound on this distance that depends only on the distribution of the eigenvalues of the regressor covariance matrix. Numerical examples on synthetic and real-world data are used to illustrate how the distance between ${\hat{\boldsymbol\beta}\;}_{\mathrm{PLS}}^{\scriptscriptstyle {(L)}}$ and $\hat{\boldsymbol \beta}_{\mathrm{OLS}}$ depends on the number of clusters in which the eigenvalues of the regressor covariance matrix are grouped.
Graph Coordinates and Conventional Neural Networks -- An Alternative for Graph Neural Networks
Authors: Zheyi Qin, Randy Paffenroth, Anura P. Jayasumana
Date: 2023-12-03 00:00:00
Tasks: Feature Engineering, Graph Embedding

Graph-based data present unique challenges and opportunities for machine learning. Graph Neural Networks (GNNs), and especially those algorithms that capture graph topology through message passing for neighborhood aggregation, have been a leading solution. However, these networks often require substantial computational resources and may not optimally leverage the information contained in the graph's topology, particularly for large-scale or complex graphs. We propose Topology Coordinate Neural Network (TCNN) and Directional Virtual Coordinate Neural Network (DVCNN) as novel and efficient alternatives to message passing GNNs, that directly leverage the graph's topology, sidestepping the computational challenges presented by competing algorithms. Our proposed methods can be viewed as a reprise of classic techniques for graph embedding for neural network feature engineering, but they are novel in that our embedding techniques leverage ideas in Graph Coordinates (GC) that are lacking in current practice. Experimental results, benchmarked against the Open Graph Benchmark Leaderboard, demonstrate that TCNN and DVCNN achieve competitive or superior performance to message passing GNNs. For similar levels of accuracy and ROC-AUC, TCNN and DVCNN need far fewer trainable parameters than contenders of the OGBN Leaderboard. The proposed TCNN architecture requires fewer parameters than any neural network method currently listed in the OGBN Leaderboard for both OGBN-Proteins and OGBN-Products datasets. Conversely, our methods achieve higher performance for a similar number of trainable parameters. By providing an efficient and effective alternative to message passing GNNs, our work expands the toolbox of techniques for graph-based machine learning.
On Significance of Subword tokenization for Low Resource and Efficient Named Entity Recognition: A case study in Marathi
Authors: Harsh Chaudhari, Anuja Patil, Dhanashree Lavekar, Pranav Khairnar, Raviraj Joshi, Sachin Pande
Date: 2023-12-03 00:00:00
Tasks: Computational Efficiency, Machine Translation, named-entity-recognition, Named Entity Recognition, Named Entity Recognition (NER), NER, Question Answering

Named Entity Recognition (NER) systems play a vital role in NLP applications such as machine translation, summarization, and question-answering. These systems identify named entities, which encompass real-world concepts like locations, persons, and organizations. Despite extensive research on NER systems for the English language, they have not received adequate attention in the context of low resource languages. In this work, we focus on NER for low-resource language and present our case study in the context of the Indian language Marathi. The advancement of NLP research revolves around the utilization of pre-trained transformer models such as BERT for the development of NER models. However, we focus on improving the performance of shallow models based on CNN, and LSTM by combining the best of both worlds. In the era of transformers, these traditional deep learning models are still relevant because of their high computational efficiency. We propose a hybrid approach for efficient NER by integrating a BERT-based subword tokenizer into vanilla CNN/LSTM models. We show that this simple approach of replacing a traditional word-based tokenizer with a BERT-tokenizer brings the accuracy of vanilla single-layer models closer to that of deep pre-trained models like BERT. We show the importance of using sub-word tokenization for NER and present our study toward building efficient NLP systems. The evaluation is performed on L3Cube-MahaNER dataset using tokenizers from MahaBERT, MahaGPT, IndicBERT, and mBERT.
Robust Non-parametric Knowledge-based Diffusion Least Mean Squares over Adaptive Networks
Authors: Soheil Ashkezari-Toussi, Hadi Sadoghi-Yazdi
Date: 2023-12-03 00:00:00
Tasks: Density Estimation

The present study proposes incorporating non-parametric knowledge into the diffusion least-mean-squares algorithm in the framework of a maximum a posteriori (MAP) estimation. The proposed algorithm leads to a robust estimation of an unknown parameter vector in a group of cooperative estimators. Utilizing kernel density estimation and buffering some intermediate estimations, the prior distribution and conditional likelihood of the parameters vector in each node are calculated. Pseudo Huber loss function is used for designing the likelihood function. Also, an error thresholding function is defined to reduce the computational overhead as well as more relaxation against noise, which stops the update every time an error is less than a predefined threshold. The performance of the proposed algorithm is examined in the stationary and non-stationary scenarios in the presence of Gaussian and non-Gaussian noise. Results show the robustness of the proposed algorithm in the presence of different noise types.
Anomaly Detection Under Uncertainty Using Distributionally Robust Optimization Approach
Authors: Amir Hossein Noormohammadia, Seyed Ali MirHassania, Farnaz Hooshmand Khaligh
Date: 2023-12-03 00:00:00
Tasks: Anomaly Detection

Anomaly detection is defined as the problem of finding data points that do not follow the patterns of the majority. Among the various proposed methods for solving this problem, classification-based methods, including one-class Support Vector Machines (SVM) are considered effective and state-of-the-art. The one-class SVM method aims to find a decision boundary to distinguish between normal data points and anomalies using only the normal data. On the other hand, most real-world problems involve some degree of uncertainty, where the true probability distribution of each data point is unknown, and estimating it is often difficult and costly. Assuming partial distribution information such as the first and second-order moments is known, a distributionally robust chance-constrained model is proposed in which the probability of misclassification is low. By utilizing a mapping function to a higher dimensional space, the proposed model will be capable of classifying origin-inseparable datasets. Also, by adopting the kernel idea, the need for explicitly knowing the mapping is eliminated, computations can be performed in the input space, and computational complexity is reduced. Computational results validate the robustness of the proposed model under different probability distributions and also the superiority of the proposed model compared to the standard one-class SVM in terms of various evaluation metrics.
Deep Ensembles Meets Quantile Regression: Uncertainty-aware Imputation for Time Series
Authors: Ying Liu, Peng Cui, WenBo Hu, Richang Hong
Date: 2023-12-03 00:00:00
Tasks: Imputation, Missing Values, quantile regression, regression, Time Series

Real-world time series data frequently have significant amounts of missing values, posing challenges for advanced analysis. A common approach to address this issue is imputation, where the primary challenge lies in determining the appropriate values to fill in. While previous deep learning methods have proven effective for time series imputation, they often produce overconfident imputations, which could brings a potentially overlooked risk to the reliability of the intelligent system. Diffusion methods are proficient in estimating probability distributions but face challenges with high missing rates and moreover, computationally expensive due to the nature of the generative model framework. In this paper, we propose Quantile Sub-Ensembles, a novel method to estimate uncertainty with ensemble of quantile-regression-based task networks and then incorporate Quantile Sub-Ensembles into a non-generative time series imputation method. Our method not only produces accurate imputations that is robust to high missing rates, but also is computationally efficient due to the fast training of its non-generative model. We examine the performance of the proposed method on two real-world datasets, the air quality and health-care datasets, and conduct extensive experiments to show that our method outperforms other most of the baseline methods in making deterministic and probabilistic imputations. Compared with the diffusion method, CSDI, our approach can obtain comparable forecasting results which is better when more data is missing, and moreover consumes a much smaller computation overhead, yielding much faster training and test.
Task-Oriented Edge Networks: Decentralized Learning Over Wireless Fronthaul
Authors: Hoon Lee, Seung-Wook Kim
Date: 2023-12-03 00:00:00

This paper studies task-oriented edge networks where multiple edge internet-of-things nodes execute machine learning tasks with the help of powerful deep neural networks (DNNs) at a network cloud. Separate edge nodes (ENs) result in a partially observable system where they can only get partitioned features of the global network states. These local observations need to be forwarded to the cloud via resource-constrained wireless fronthual links. Individual ENs compress their local observations into uplink fronthaul messages using task-oriented encoder DNNs. Then, the cloud carries out a remote inference task by leveraging received signals. Such a distributed topology requests a decentralized training and decentralized execution (DTDE) learning framework for designing edge-cloud cooperative inference rules and their decentralized training strategies. First, we develop fronthaul-cooperative DNN architecture along with proper uplink coordination protocols suitable for wireless fronthaul interconnection. Inspired by the nomographic function, an efficient cloud inference model becomes an integration of a number of shallow DNNs. This modulized architecture brings versatile calculations that are independent of the number of ENs. Next, we present a decentralized training algorithm of separate edge-cloud DNNs over downlink wireless fronthaul channels. An appropriate downlink coordination protocol is proposed, which backpropagates gradient vectors wirelessly from the cloud to the ENs.
Continuous Convolutional Neural Networks for Disruption Prediction in Nuclear Fusion Plasmas
Authors: William F Arnold, Lucas Spangher, Christina Rea
Date: 2023-12-03 00:00:00

Grid decarbonization for climate change requires dispatchable carbon-free energy like nuclear fusion. The tokamak concept offers a promising path for fusion, but one of the foremost challenges in implementation is the occurrence of energetic plasma disruptions. In this study, we delve into Machine Learning approaches to predict plasma state outcomes. Our contributions are twofold: (1) We present a novel application of Continuous Convolutional Neural Networks for disruption prediction and (2) We examine the advantages and disadvantages of continuous models over discrete models for disruption prediction by comparing our model with the previous, discrete state of the art, and show that continuous models offer significantly better performance (Area Under the Receiver Operating Characteristic Curve = 0.974 v.s. 0.799) with fewer parameters
Mendata: A Framework to Purify Manipulated Training Data
Authors: Zonghao Huang, Neil Gong, Michael K. Reiter
Date: 2023-12-03 00:00:00
Tasks: Data Poisoning

Untrusted data used to train a model might have been manipulated to endow the learned model with hidden properties that the data contributor might later exploit. Data purification aims to remove such manipulations prior to training the model. We propose Mendata, a novel framework to purify manipulated training data. Starting from a small reference dataset in which a large majority of the inputs are clean, Mendata perturbs the training inputs so that they retain their utility but are distributed similarly (as measured by Wasserstein distance) to the reference data, thereby eliminating hidden properties from the learned model. A key challenge is how to find such perturbations, which we address by formulating a min-max optimization problem and developing a two-step method to iteratively solve it. We demonstrate the effectiveness of Mendata by applying it to defeat state-of-the-art data poisoning and data tracing techniques.
A Review of Link Prediction Applications in Network Biology
Authors: Ahmad F. Al Musawi, Satyaki Roy, Preetam Ghosh
Date: 2023-12-03 00:00:00
Tasks: Link Prediction, Prediction

In the domain of network biology, the interactions among heterogeneous genomic and molecular entities are represented through networks. Link prediction (LP) methodologies are instrumental in inferring missing or prospective associations within these biological networks. In this review, we systematically dissect the attributes of local, centrality, and embedding-based LP approaches, applied to static and dynamic biological networks. We undertake an examination of the current applications of LP metrics for predicting links between diseases, genes, proteins, RNA, microbiomes, drugs, and neurons. We carry out comprehensive performance evaluations on established biological network datasets to show the practical applications of standard LP models. Moreover, we compare the similarity in prediction trends among the models and the specific network attributes that contribute to effective link prediction, before underscoring the role of LP in addressing the formidable challenges prevalent in biological systems, ranging from noise, bias, and data sparseness to interpretability. We conclude the review with an exploration of the essential characteristics expected from future LP models, poised to advance our comprehension of the intricate interactions governing biological systems.
Multiscale Topology in Interactomic Network: From Transcriptome to Antiaddiction Drug Repurposing
Authors: Hongyan Du, Guo-Wei Wei, Tingjun Hou
Date: 2023-12-03 00:00:00
Tasks: Drug Discovery, Topological Data Analysis

The escalating drug addiction crisis in the United States underscores the urgent need for innovative therapeutic strategies. This study embarked on an innovative and rigorous strategy to unearth potential drug repurposing candidates for opioid and cocaine addiction treatment, bridging the gap between transcriptomic data analysis and drug discovery. We initiated our approach by conducting differential gene expression analysis on addiction-related transcriptomic data to identify key genes. We propose a novel topological differentiation to identify key genes from a protein-protein interaction (PPI) network derived from DEGs. This method utilizes persistent Laplacians to accurately single out pivotal nodes within the network, conducting this analysis in a multiscale manner to ensure high reliability. Through rigorous literature validation, pathway analysis, and data-availability scrutiny, we identified three pivotal molecular targets, mTOR, mGluR5, and NMDAR, for drug repurposing from DrugBank. We crafted machine learning models employing two natural language processing (NLP)-based embeddings and a traditional 2D fingerprint, which demonstrated robust predictive ability in gauging binding affinities of DrugBank compounds to selected targets. Furthermore, we elucidated the interactions of promising drugs with the targets and evaluated their drug-likeness. This study delineates a multi-faceted and comprehensive analytical framework, amalgamating bioinformatics, topological data analysis and machine learning, for drug repurposing in addiction treatment, setting the stage for subsequent experimental validation. The versatility of the methods we developed allows for applications across a range of diseases and transcriptomic datasets.
Distributed Reinforcement Learning for Molecular Design: Antioxidant case
Authors: Huanyi Qin, Denis Akhiyarov, Sophie Loehle, Kenneth Chiu, Mauricio Araya-Polo
Date: 2023-12-03 00:00:00
Tasks: Deep Reinforcement Learning, reinforcement-learning, Reinforcement Learning

Deep reinforcement learning has successfully been applied for molecular discovery as shown by the Molecule Deep Q-network (MolDQN) algorithm. This algorithm has challenges when applied to optimizing new molecules: training such a model is limited in terms of scalability to larger datasets and the trained model cannot be generalized to different molecules in the same dataset. In this paper, a distributed reinforcement learning algorithm for antioxidants, called DA-MolDQN is proposed to address these problems. State-of-the-art bond dissociation energy (BDE) and ionization potential (IP) predictors are integrated into DA-MolDQN, which are critical chemical properties while optimizing antioxidants. Training time is reduced by algorithmic improvements for molecular modifications. The algorithm is distributed, scalable for up to 512 molecules, and generalizes the model to a diverse set of molecules. The proposed models are trained with a proprietary antioxidant dataset. The results have been reproduced with both proprietary and public datasets. The proposed molecules have been validated with DFT simulations and a subset of them confirmed in public "unseen" datasets. In summary, DA-MolDQN is up to 100x faster than previous algorithms and can discover new optimized molecules from proprietary and public antioxidants.