pwc-archive/papers-with-abstracts huggingface dataset:
K-Nearest-Neighbors Induced Topological PCA for scRNA Sequence Data Analysis
Authors: Sean Cottrell, Yuta Hozumi, Guo-Wei Wei
Date: 2023-10-23 00:00:00
Tasks: Dimensionality Reduction, feature selection

Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells, which has given us insights into cell-cell communication, cell differentiation, and differential gene expression. However, analyzing scRNA-seq data is a challenge due to sparsity and the large number of genes involved. Therefore, dimensionality reduction and feature selection are important for removing spurious signals and enhancing downstream analysis. Traditional PCA, a main workhorse in dimensionality reduction, lacks the ability to capture geometrical structure information embedded in the data, and previous graph Laplacian regularizations are limited by the analysis of only a single scale. We propose a topological Principal Components Analysis (tPCA) method by the combination of persistent Laplacian (PL) technique and L$_{2,1}$ norm regularization to address multiscale and multiclass heterogeneity issues in data. We further introduce a k-Nearest-Neighbor (kNN) persistent Laplacian technique to improve the robustness of our persistent Laplacian method. The proposed kNN-PL is a new algebraic topology technique which addresses the many limitations of the traditional persistent homology. Rather than inducing filtration via the varying of a distance threshold, we introduced kNN-tPCA, where filtrations are achieved by varying the number of neighbors in a kNN network at each step, and find that this framework has significant implications for hyper-parameter tuning. We validate the efficacy of our proposed tPCA and kNN-tPCA methods on 11 diverse benchmark scRNA-seq datasets, and showcase that our methods outperform other unsupervised PCA enhancements from the literature, as well as popular Uniform Manifold Approximation (UMAP), t-Distributed Stochastic Neighbor Embedding (tSNE), and Projection Non-Negative Matrix Factorization (NMF) by significant margins.
Chain-of-Factors Paper-Reviewer Matching
Authors: Yu Zhang, Yanzhen Shen, SeongKu Kang, Xiusi Chen, Bowen Jin, Jiawei Han
Date: 2023-10-23 00:00:00
Tasks: Information Retrieval, Language Modelling, Retrieval, Semantic Similarity, Semantic Textual Similarity

With the rapid increase in paper submissions to academic conferences, the need for automated and accurate paper-reviewer matching is more critical than ever. Previous efforts in this area have considered various factors to assess the relevance of a reviewer's expertise to a paper, such as the semantic similarity, shared topics, and citation connections between the paper and the reviewer's previous works. However, most of these studies focus on only one factor, resulting in an incomplete evaluation of the paper-reviewer relevance. To address this issue, we propose a unified model for paper-reviewer matching that jointly considers semantic, topic, and citation factors. To be specific, during training, we instruction-tune a contextualized language model shared across all factors to capture their commonalities and characteristics; during inference, we chain the three factors to enable step-by-step, coarse-to-fine search for qualified reviewers given a submission. Experiments on four datasets (one of which is newly contributed by us) spanning various fields such as machine learning, computer vision, information retrieval, and data mining consistently demonstrate the effectiveness of our proposed Chain-of-Factors model in comparison with state-of-the-art paper-reviewer matching methods and scientific pre-trained language models.
Attention-Enhancing Backdoor Attacks Against BERT-based Models
Authors: Weimin Lyu, Songzhu Zheng, Lu Pang, Haibin Ling, Chao Chen
Date: 2023-10-23 00:00:00
Tasks: Sentiment Analysis, Topic Classification

Recent studies have revealed that \textit{Backdoor Attacks} can threaten the safety of natural language processing (NLP) models. Investigating the strategies of backdoor attacks will help to understand the model's vulnerability. Most existing textual backdoor attacks focus on generating stealthy triggers or modifying model weights. In this paper, we directly target the interior structure of neural networks and the backdoor mechanism. We propose a novel Trojan Attention Loss (TAL), which enhances the Trojan behavior by directly manipulating the attention patterns. Our loss can be applied to different attacking methods to boost their attack efficacy in terms of attack successful rates and poisoning rates. It applies to not only traditional dirty-label attacks, but also the more challenging clean-label attacks. We validate our method on different backbone models (BERT, RoBERTa, and DistilBERT) and various tasks (Sentiment Analysis, Toxic Detection, and Topic Classification).
Inferring Relational Potentials in Interacting Systems
Authors: Armand Comas-Massagué, Yilun Du, Christian Fernandez, Sandesh Ghimire, Mario Sznaier, Joshua B. Tenenbaum, Octavia Camps
Date: 2023-10-23 00:00:00
Tasks: Trajectory Forecasting, Trajectory Modeling

Systems consisting of interacting agents are prevalent in the world, ranging from dynamical systems in physics to complex biological networks. To build systems which can interact robustly in the real world, it is thus important to be able to infer the precise interactions governing such systems. Existing approaches typically discover such interactions by explicitly modeling the feed-forward dynamics of the trajectories. In this work, we propose Neural Interaction Inference with Potentials (NIIP) as an alternative approach to discover such interactions that enables greater flexibility in trajectory modeling: it discovers a set of relational potentials, represented as energy functions, which when minimized reconstruct the original trajectory. NIIP assigns low energy to the subset of trajectories which respect the relational constraints observed. We illustrate that with these representations NIIP displays unique capabilities in test-time. First, it allows trajectory manipulation, such as interchanging interaction types across separately trained models, as well as trajectory forecasting. Additionally, it allows adding external hand-crafted potentials at test-time. Finally, NIIP enables the detection of out-of-distribution samples and anomalies without explicit training. Website: https://energy-based-model.github.io/interaction-potentials.
Diffusion-Model-Assisted Supervised Learning of Generative Models for Density Estimation
Authors: Yanfang Liu, Minglei Yang, Zezhong Zhang, Feng Bao, Yanzhao Cao, Guannan Zhang
Date: 2023-10-22 00:00:00
Tasks: Density Estimation

We present a supervised learning framework of training generative models for density estimation. Generative models, including generative adversarial networks, normalizing flows, variational auto-encoders, are usually considered as unsupervised learning models, because labeled data are usually unavailable for training. Despite the success of the generative models, there are several issues with the unsupervised training, e.g., requirement of reversible architectures, vanishing gradients, and training instability. To enable supervised learning in generative models, we utilize the score-based diffusion model to generate labeled data. Unlike existing diffusion models that train neural networks to learn the score function, we develop a training-free score estimation method. This approach uses mini-batch-based Monte Carlo estimators to directly approximate the score function at any spatial-temporal location in solving an ordinary differential equation (ODE), corresponding to the reverse-time stochastic differential equation (SDE). This approach can offer both high accuracy and substantial time savings in neural network training. Once the labeled data are generated, we can train a simple fully connected neural network to learn the generative model in the supervised manner. Compared with existing normalizing flow models, our method does not require to use reversible neural networks and avoids the computation of the Jacobian matrix. Compared with existing diffusion models, our method does not need to solve the reverse-time SDE to generate new samples. As a result, the sampling efficiency is significantly improved. We demonstrate the performance of our method by applying it to a set of 2D datasets as well as real data from the UCI repository.
TATA: Stance Detection via Topic-Agnostic and Topic-Aware Embeddings
Authors: Hans W. A. Hanley, Zakir Durumeric
Date: 2023-10-22 00:00:00
Tasks: Articles, Contrastive Learning, Stance Detection, TAG

Stance detection is important for understanding different attitudes and beliefs on the Internet. However, given that a passage's stance toward a given topic is often highly dependent on that topic, building a stance detection model that generalizes to unseen topics is difficult. In this work, we propose using contrastive learning as well as an unlabeled dataset of news articles that cover a variety of different topics to train topic-agnostic/TAG and topic-aware/TAW embeddings for use in downstream stance detection. Combining these embeddings in our full TATA model, we achieve state-of-the-art performance across several public stance detection datasets (0.771 $F_1$-score on the Zero-shot VAST dataset). We release our code and data at https://github.com/hanshanley/tata.
URegM: a unified prediction model of resource consumption for refactoring software smells in open source cloud
Authors: Asif Imran, Tevfik Kosar
Date: 2023-10-22 00:00:00
Tasks: Cloud Computing

The low cost and rapid provisioning capabilities have made the cloud a desirable platform to launch complex scientific applications. However, resource utilization optimization is a significant challenge for cloud service providers, since the earlier focus is provided on optimizing resources for the applications that run on the cloud, with a low emphasis being provided on optimizing resource utilization of the cloud computing internal processes. Code refactoring has been associated with improving the maintenance and understanding of software code. However, analyzing the impact of the refactoring source code of the cloud and studying its impact on cloud resource usage require further analysis. In this paper, we propose a framework called Unified Regression Modelling (URegM) which predicts the impact of code smell refactoring on cloud resource usage. We test our experiments in a real-life cloud environment using a complex scientific application as a workload. Results show that URegM is capable of accurately predicting resource consumption due to code smell refactoring. This will permit cloud service providers with advanced knowledge about the impact of refactoring code smells on resource consumption, thus allowing them to plan their resource provisioning and code refactoring more effectively.
EDGE++: Improved Training and Sampling of EDGE
Authors: Mingyang Wu, Xiaohui Chen, Li-Ping Liu
Date: 2023-10-22 00:00:00
Tasks: Computational Efficiency, Denoising, Graph Generation

Recently developed deep neural models like NetGAN, CELL, and Variational Graph Autoencoders have made progress but face limitations in replicating key graph statistics on generating large graphs. Diffusion-based methods have emerged as promising alternatives, however, most of them present challenges in computational efficiency and generative performance. EDGE is effective at modeling large networks, but its current denoising approach can be inefficient, often leading to wasted computational resources and potential mismatches in its generation process. In this paper, we propose enhancements to the EDGE model to address these issues. Specifically, we introduce a degree-specific noise schedule that optimizes the number of active nodes at each timestep, significantly reducing memory consumption. Additionally, we present an improved sampling scheme that fine-tunes the generative process, allowing for better control over the similarity between the synthesized and the true network. Our experimental results demonstrate that the proposed modifications not only improve the efficiency but also enhance the accuracy of the generated graphs, offering a robust and scalable solution for graph generation tasks.
Fairness-aware Optimal Graph Filter Design
Authors: O. Deniz Kose, Yanning Shen, Gonzalo Mateos
Date: 2023-10-22 00:00:00
Tasks: Decision Making, Fairness, Node Classification

Graphs are mathematical tools that can be used to represent complex real-world interconnected systems, such as financial markets and social networks. Hence, machine learning (ML) over graphs has attracted significant attention recently. However, it has been demonstrated that ML over graphs amplifies the already existing bias towards certain under-represented groups in various decision-making problems due to the information aggregation over biased graph structures. Faced with this challenge, here we take a fresh look at the problem of bias mitigation in graph-based learning by borrowing insights from graph signal processing. Our idea is to introduce predesigned graph filters within an ML pipeline to reduce a novel unsupervised bias measure, namely the correlation between sensitive attributes and the underlying graph connectivity. We show that the optimal design of said filters can be cast as a convex problem in the graph spectral domain. We also formulate a linear programming (LP) problem informed by a theoretical bias analysis, which attains a closed-form solution and leads to a more efficient fairness-aware graph filter. Finally, for a design whose degrees of freedom are independent of the input graph size, we minimize the bias metric over the family of polynomial graph convolutional filters. Our optimal filter designs offer complementary strengths to explore favorable fairness-utility-complexity tradeoffs. For performance evaluation, we conduct extensive and reproducible node classification experiments over real-world networks. Our results show that the proposed framework leads to better fairness measures together with similar utility compared to state-of-the-art fairness-aware baselines.
Clustering Students Based on Gamification User Types and Learning Styles
Authors: Emre Arslan, Atilla Özkaymak, Nesrin Özdener Dönmez
Date: 2023-10-22 00:00:00
Tasks: Clustering

The aim of this study is clustering students according to their gamification user types and learning styles with the purpose of providing instructors with a new perspective of grouping students in case of clustering which cannot be done by hand when there are multiple scales in data. The data used consists of 251 students who were enrolled at a Turkish state university. When grouping students, K-means algorithm has been utilized as clustering algorithm. As for determining the gamification user types and learning styles of students, Gamification User Type Hexad Scale and Grasha-Riechmann Student Learning Style Scale have been used respectively. Silhouette coefficient is utilized as clustering quality measure. After fitting the algorithm in several ways, highest Silhouette coefficient obtained was 0.12 meaning that results are neutral but not satisfactory. All the statistical operations and data visualizations were made using Python programming language.
A Quadratic Synchronization Rule for Distributed Deep Learning
Authors: Xinran Gu, Kaifeng Lyu, Sanjeev Arora, Jingzhao Zhang, Longbo Huang
Date: 2023-10-22 00:00:00
Tasks: Deep Learning

In distributed deep learning with data parallelism, synchronizing gradients at each training step can cause a huge communication overhead, especially when many nodes work together to train large models. Local gradient methods, such as Local SGD, address this issue by allowing workers to compute locally for $H$ steps without synchronizing with others, hence reducing communication frequency. While $H$ has been viewed as a hyperparameter to trade optimization efficiency for communication cost, recent research indicates that setting a proper $H$ value can lead to generalization improvement. Yet, selecting a proper $H$ is elusive. This work proposes a theory-grounded method for determining $H$, named the Quadratic Synchronization Rule (QSR), which recommends dynamically setting $H$ in proportion to $\frac{1}{\eta^2}$ as the learning rate $\eta$ decays over time. Extensive ImageNet experiments on ResNet and ViT show that local gradient methods with QSR consistently improve the test accuracy over other synchronization strategies. Compared with the standard data parallel training, QSR enables Local AdamW on ViT-B to cut the training time on 16 or 64 GPUs down from 26.7 to 20.2 hours or from 8.6 to 5.5 hours and, at the same time, achieves $1.16\%$ or $0.84\%$ higher top-1 validation accuracy.
Data Augmentation: a Combined Inductive-Deductive Approach featuring Answer Set Programming
Authors: Pierangela Bruno, Francesco Calimeri, Cinzia Marte, Simona Perri
Date: 2023-10-22 00:00:00
Tasks: Data Augmentation

Although the availability of a large amount of data is usually given for granted, there are relevant scenarios where this is not the case; for instance, in the biomedical/healthcare domain, some applications require to build huge datasets of proper images, but the acquisition of such images is often hard for different reasons (e.g., accessibility, costs, pathology-related variability), thus causing limited and usually imbalanced datasets. Hence, the need for synthesizing photo-realistic images via advanced Data Augmentation techniques is crucial. In this paper we propose a hybrid inductive-deductive approach to the problem; in particular, starting from a limited set of real labeled images, the proposed framework makes use of logic programs for declaratively specifying the structure of new images, that is guaranteed to comply with both a set of constraints coming from the domain knowledge and some specific desiderata. The resulting labeled images undergo a dedicated process based on Deep Learning in charge of creating photo-realistic images that comply with the generated label.
Universal representation by Boltzmann machines with Regularised Axons
Authors: Przemysław R. Grzybowski, Antoni Jankiewicz, Eloy Piñol, David Cirauqui, Dorota H. Grzybowska, Paweł M. Petrykowski, Miguel Ángel García-March, Maciej Lewenstein, Gorka Muñoz-Gil, Alejandro Pozas-Kerstjens
Date: 2023-10-22 00:00:00
Tasks: Retrieval

It is widely known that Boltzmann machines are capable of representing arbitrary probability distributions over the values of their visible neurons, given enough hidden ones. However, sampling -- and thus training -- these models can be numerically hard. Recently we proposed a regularisation of the connections of Boltzmann machines, in order to control the energy landscape of the model, paving a way for efficient sampling and training. Here we formally prove that such regularised Boltzmann machines preserve the ability to represent arbitrary distributions. This is in conjunction with controlling the number of energy local minima, thus enabling easy \emph{guided} sampling and training. Furthermore, we explicitly show that regularised Boltzmann machines can store exponentially many arbitrarily correlated visible patterns with perfect retrieval, and we connect them to the Dense Associative Memory networks.
Bi-Encoders based Species Normalization -- Pairwise Sentence Learning to Rank
Authors: Zainab Awan, Tim Kahlke, Peter Ralph, Paul Kennedy
Date: 2023-10-22 00:00:00
Tasks: Data Integration, Feature Engineering, Information Retrieval, Learning-To-Rank, Sentence

Motivation: Biomedical named-entity normalization involves connecting biomedical entities with distinct database identifiers in order to facilitate data integration across various fields of biology. Existing systems for biomedical named entity normalization heavily rely on dictionaries, manually created rules, and high-quality representative features such as lexical or morphological characteristics. However, recent research has investigated the use of neural network-based models to reduce dependence on dictionaries, manually crafted rules, and features. Despite these advancements, the performance of these models is still limited due to the lack of sufficiently large training datasets. These models have a tendency to overfit small training corpora and exhibit poor generalization when faced with previously unseen entities, necessitating the redesign of rules and features. Contribution: We present a novel deep learning approach for named entity normalization, treating it as a pair-wise learning to rank problem. Our method utilizes the widely-used information retrieval algorithm Best Matching 25 to generate candidate concepts, followed by the application of bi-directional encoder representation from the encoder (BERT) to re-rank the candidate list. Notably, our approach eliminates the need for feature-engineering or rule creation. We conduct experiments on species entity types and evaluate our method against state-of-the-art techniques using LINNAEUS and S800 biomedical corpora. Our proposed approach surpasses existing methods in linking entities to the NCBI taxonomy. To the best of our knowledge, there is no existing neural network-based approach for species normalization in the literature.
Is ChatGPT a game changer for geocoding -- a benchmark for geocoding address parsing techniques
Authors: Zhengcong Yin, Diya Li, Daniel W. Goldberg
Date: 2023-10-22 00:00:00

The remarkable success of GPT models across various tasks, including toponymy recognition motivates us to assess the performance of the GPT-3 model in the geocoding address parsing task. To ensure that the evaluation more accurately mirrors performance in real-world scenarios with diverse user input qualities and resolve the pressing need for a 'gold standard' evaluation dataset for geocoding systems, we introduce a benchmark dataset of low-quality address descriptions synthesized based on human input patterns mining from actual input logs of a geocoding system in production. This dataset has 21 different input errors and variations; contains over 239,000 address records that are uniquely selected from streets across all U.S. 50 states and D.C.; and consists of three subsets to be used as training, validation, and testing sets. Building on this, we train and gauge the performance of the GPT-3 model in extracting address components, contrasting its performance with transformer-based and LSTM-based models. The evaluation results indicate that Bidirectional LSTM-CRF model has achieved the best performance over these transformer-based models and GPT-3 model. Transformer-based models demonstrate very comparable results compared to the Bidirectional LSTM-CRF model. The GPT-3 model, though trailing in performance, showcases potential in the address parsing task with few-shot examples, exhibiting room for improvement with additional fine-tuning. We open source the code and data of this presented benchmark so that researchers can utilize it for future model development or extend it to evaluate similar tasks, such as document geocoding.