pwc-archive/papers-with-abstracts huggingface dataset:
Enhancing Missing Data Imputation through Combined Bipartite Graph and Complete Directed Graph
Authors: Zhaoyang Zhang, Hongtu Zhu, Ziqi Chen, Yingjie Zhang, Hai Shu
Date: 2024-11-07 00:00:00
Tasks: Graph Neural Network, Imputation

In this paper, we aim to address a significant challenge in the field of missing data imputation: identifying and leveraging the interdependencies among features to enhance missing data imputation for tabular data. We introduce a novel framework named the Bipartite and Complete Directed Graph Neural Network (BCGNN). Within BCGNN, observations and features are differentiated as two distinct node types, and the values of observed features are converted into attributed edges linking them. The bipartite segment of our framework inductively learns embedding representations for nodes, efficiently utilizing the comprehensive information encapsulated in the attributed edges. In parallel, the complete directed graph segment adeptly outlines and communicates the complex interdependencies among features. When compared to contemporary leading imputation methodologies, BCGNN consistently outperforms them, achieving a noteworthy average reduction of 15% in mean absolute error for feature imputation tasks under different missing mechanisms. Our extensive experimental investigation confirms that an in-depth grasp of the interdependence structure substantially enhances the model's feature embedding ability. We also highlight the model's superior performance in label prediction tasks involving missing data, and its formidable ability to generalize to unseen data points.
Sampling-guided Heterogeneous Graph Neural Network with Temporal Smoothing for Scalable Longitudinal Data Imputation
Authors: Zhaoyang Zhang, Ziqi Chen, Qiao Liu, Jinhan Xie, Hongtu Zhu
Date: 2024-11-07 00:00:00
Tasks: Computational Efficiency, Graph Neural Network, Imputation

In this paper, we propose a novel framework, the Sampling-guided Heterogeneous Graph Neural Network (SHT-GNN), to effectively tackle the challenge of missing data imputation in longitudinal studies. Unlike traditional methods, which often require extensive preprocessing to handle irregular or inconsistent missing data, our approach accommodates arbitrary missing data patterns while maintaining computational efficiency. SHT-GNN models both observations and covariates as distinct node types, connecting observation nodes at successive time points through subject-specific longitudinal subnetworks, while covariate-observation interactions are represented by attributed edges within bipartite graphs. By leveraging subject-wise mini-batch sampling and a multi-layer temporal smoothing mechanism, SHT-GNN efficiently scales to large datasets, while effectively learning node representations and imputing missing data. Extensive experiments on both synthetic and real-world datasets, including the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset, demonstrate that SHT-GNN significantly outperforms existing imputation methods, even with high missing data rates. The empirical results highlight SHT-GNN's robust imputation capabilities and superior performance, particularly in the context of complex, large-scale longitudinal data.
Non-Euclidean Mixture Model for Social Network Embedding
Authors: Roshni G. Iyer, Yewen Wang, Wei Wang, Yizhou Sun
Date: 2024-11-07 00:00:00
Tasks: Decoder, Graph Representation Learning, model, Network Embedding, Representation Learning

It is largely agreed that social network links are formed due to either homophily or social influence. Inspired by this, we aim at understanding the generation of links via providing a novel embedding-based graph formation model. Different from existing graph representation learning, where link generation probabilities are defined as a simple function of the corresponding node embeddings, we model the link generation as a mixture model of the two factors. In addition, we model the homophily factor in spherical space and the influence factor in hyperbolic space to accommodate the fact that (1) homophily results in cycles and (2) influence results in hierarchies in networks. We also design a special projection to align these two spaces. We call this model Non-Euclidean Mixture Model, i.e., NMM. We further integrate NMM with our non-Euclidean graph variational autoencoder (VAE) framework, NMM-GNN. NMM-GNN learns embeddings through a unified framework which uses non-Euclidean GNN encoders, non-Euclidean Gaussian priors, a non-Euclidean decoder, and a novel space unification loss component to unify distinct non-Euclidean geometric spaces. Experiments on public datasets show NMM-GNN significantly outperforms state-of-the-art baselines on social network generation and classification tasks, demonstrating its ability to better explain how the social network is formed.
OneProt: Towards Multi-Modal Protein Foundation Models
Authors: Klemens Flöge, Srisruthi Udayakumar, Johanna Sommer, Marie Piraud, Stefan Kesselheim, Vincent Fortuin, Stephan Günneman, Karel J van der Weg, Holger Gohlke, Erinc Merdivan, Alina Bazarova
Date: 2024-11-07 00:00:00
Tasks: Drug Discovery, Retrieval

Recent advances in Artificial Intelligence have enabled multi-modal systems to model and translate diverse information spaces. Extending beyond text and vision, we introduce OneProt, a multi-modal AI for proteins that integrates structural, sequence, text, and binding site data. Using the ImageBind framework, OneProt aligns the latent spaces of protein modality encoders in a lightweight fine-tuning scheme that focuses on pairwise alignment with sequence data rather than requiring full matches. This novel approach comprises a mix of Graph Neural Networks and transformer architectures. It demonstrates strong performance in retrieval tasks and showcases the efficacy of multi-modal systems in Protein Machine Learning through a broad spectrum of downstream baselines, including enzyme function prediction and binding site analysis. Furthermore, OneProt enables the transfer of representational information from specialized encoders to the sequence encoder, enhancing capabilities for distinguishing evolutionarily related and unrelated sequences and exhibiting representational properties where evolutionarily related proteins align in similar directions within the latent space. In addition, we extensively investigate modality ablations to identify the encoders that contribute most to predictive performance, highlighting the significance of the binding site encoder, which has not been used in similar models previously. This work expands the horizons of multi-modal protein models, paving the way for transformative applications in drug discovery, biocatalytic reaction planning, and protein engineering.
Clinicians' Voice: Fundamental Considerations for XAI in Healthcare
Authors: T. E. Röber, R. Goedhart, S. İ. Birbil
Date: 2024-11-07 00:00:00

Explainable AI (XAI) holds the promise of advancing the implementation and adoption of AI-based tools in practice, especially in high-stakes environments like healthcare. However, most of the current research is disconnected from its practical applications and lacks input of end users. To address this, we conducted semi-structured interviews with clinicians to discuss their thoughts, hopes, and concerns. We find that clinicians generally think positively about developing AI-based tools for clinical practice, but they have concerns about how these will fit into their workflow and how it will impact clinician-patient relations. We further identify education of clinicians on AI as a crucial factor for the success of AI in healthcare and highlight aspects clinicians are looking for in (X)AI-based tools. In contrast to other studies, we take on a holistic and exploratory perspective to identify general requirements, which is necessary before moving on to testing specific (X)AI products for healthcare.
Conformalized Credal Regions for Classification with Ambiguous Ground Truth
Authors: Michele Caprio, David Stutz, Shuo Li, Arnaud Doucet
Date: 2024-11-07 00:00:00
Tasks: Conformal Prediction, Disentanglement, Prediction

An open question in \emph{Imprecise Probabilistic Machine Learning} is how to empirically derive a credal region (i.e., a closed and convex family of probabilities on the output space) from the available data, without any prior knowledge or assumption. In classification problems, credal regions are a tool that is able to provide provable guarantees under realistic assumptions by characterizing the uncertainty about the distribution of the labels. Building on previous work, we show that credal regions can be directly constructed using conformal methods. This allows us to provide a novel extension of classical conformal prediction to problems with ambiguous ground truth, that is, when the exact labels for given inputs are not exactly known. The resulting construction enjoys desirable practical and theoretical properties: (i) conformal coverage guarantees, (ii) smaller prediction sets (compared to classical conformal prediction regions) and (iii) disentanglement of uncertainty sources (epistemic, aleatoric). We empirically verify our findings on both synthetic and real datasets.
Asymptotic regularity of a generalised stochastic Halpern scheme with applications
Authors: Nicholas Pischke, Thomas Powell
Date: 2024-11-07 00:00:00
Tasks: Q-Learning, Stochastic Optimization

We provide abstract, general and highly uniform rates of asymptotic regularity for a generalized stochastic Halpern-style iteration, which incorporates a second mapping in the style of a Krasnoselskii-Mann iteration. This iteration is general in two ways: First, it incorporates stochasticity in a completely abstract way rather than fixing a sampling method; secondly, it includes as special cases stochastic versions of various schemes from the optimization literature, including Halpern's iteration as well as a Krasnoselskii-Mann iteration with Tikhonov regularization terms in the sense of Bo\c{t}, Csetnek and Meier. For these particular cases, we in particular obtain linear rates of asymptotic regularity, matching (or improving) the currently best known rates for these iterations in stochastic optimization, and quadratic rates of asymptotic regularity are obtained in the context of inner product spaces for the general iteration. We utilize these rates to give bounds on the oracle complexity of such iterations under suitable variance assumptions and batching strategies, again presented in an abstract style. Finally, we sketch how the schemes presented here can be instantiated in the context of reinforcement learning to yield novel methods for Q-learning.
Learning in Budgeted Auctions with Spacing Objectives
Authors: Giannis Fikioris, Robert Kleinberg, Yoav Kolumbus, Raunak Kumar, Yishay Mansour, Éva Tardos
Date: 2024-11-07 00:00:00

In many repeated auction settings, participants care not only about how frequently they win but also how their winnings are distributed over time. This problem arises in various practical domains where avoiding congested demand is crucial, such as online retail sales and compute services, as well as in advertising campaigns that require sustained visibility over time. We introduce a simple model of this phenomenon, modeling it as a budgeted auction where the value of a win is a concave function of the time since the last win. This implies that for a given number of wins, even spacing over time is optimal. We also extend our model and results to the case when not all wins result in "conversions" (realization of actual gains), and the probability of conversion depends on a context. The goal is to maximize and evenly space conversions rather than just wins. We study the optimal policies for this setting in second-price auctions and offer learning algorithms for the bidders that achieve low regret against the optimal bidding policy in a Bayesian online setting. Our main result is a computationally efficient online learning algorithm that achieves $\tilde O(\sqrt T)$ regret. We achieve this by showing that an infinite-horizon Markov decision process (MDP) with the budget constraint in expectation is essentially equivalent to our problem, even when limiting that MDP to a very small number of states. The algorithm achieves low regret by learning a bidding policy that chooses bids as a function of the context and the system's state, which will be the time elapsed since the last win (or conversion). We show that state-independent strategies incur linear regret even without uncertainty of conversions. We complement this by showing that there are state-independent strategies that, while still having linear regret, achieve a $(1-\frac 1 e)$ approximation to the optimal reward.
VTechAGP: An Academic-to-General-Audience Text Paraphrase Dataset and Benchmark Models
Authors: Ming Cheng, Jiaying Gong, Chenhan Yuan, William A. Ingram, Edward Fox, Hoda Eldardiry
Date: 2024-11-07 00:00:00
Tasks: Language Modeling, Language Modelling, Sentence, Text Generation, Text Simplification

Existing text simplification or paraphrase datasets mainly focus on sentence-level text generation in a general domain. These datasets are typically developed without using domain knowledge. In this paper, we release a novel dataset, VTechAGP, which is the first academic-to-general-audience text paraphrase dataset consisting of document-level these and dissertation academic and general-audience abstract pairs from 8 colleges authored over 25 years. We also propose a novel dynamic soft prompt generative language model, DSPT5. For training, we leverage a contrastive-generative loss function to learn the keyword vectors in the dynamic prompt. For inference, we adopt a crowd-sampling decoding strategy at both semantic and structural levels to further select the best output candidate. We evaluate DSPT5 and various state-of-the-art large language models (LLMs) from multiple perspectives. Results demonstrate that the SOTA LLMs do not provide satisfactory outcomes, while the lightweight DSPT5 can achieve competitive results. To the best of our knowledge, we are the first to build a benchmark dataset and solutions for academic-to-general-audience text paraphrase dataset. Models will be public after acceptance.
A Simple Packing Algorithm for Optimized Mapping of Artificial Neural Networks onto Non-Volatile Memory Cross-Bar Arrays
Authors: W. Haensch
Date: 2024-11-07 00:00:00

Neuromorphic computing with crossbar arrays has emerged as a promising alternative to improve computing efficiency for machine learning. Previous work has focused on implementing crossbar arrays to perform basic mathematical operations. However, in this paper, we explore the impact of mapping the layers of an artificial neural network onto physical cross-bar arrays arranged in tiles across a chip. We have developed a simplified mapping algorithm to determine the number of physical tiles, with fixed optimal array dimensions, and to estimate the minimum area occupied by these tiles for a given design objective. This simplified algorithm is compared with conventional binary linear optimization, which solves the equivalent bin-packing problem. We have found that the optimum solution is not necessarily related to the minimum number of tiles; rather, it is shown to be an interaction between tile array capacity and the scaling properties of its peripheral circuits. Additionally, we have discovered that square arrays are not always the best choice for optimal mapping, and that performance optimization comes at the cost of total tile area
Soft Hoeffding Tree: A Transparent and Differentiable Model on Data Streams
Authors: Kirsten Köbschall, Lisa Hartung, Stefan Kramer
Date: 2024-11-07 00:00:00

We propose soft Hoeffding trees (SoHoT) as a new differentiable and transparent model for possibly infinite and changing data streams. Stream mining algorithms such as Hoeffding trees grow based on the incoming data stream, but they currently lack the adaptability of end-to-end deep learning systems. End-to-end learning can be desirable if a feature representation is learned by a neural network and used in a tree, or if the outputs of trees are further processed in a deep learning model or workflow. Different from Hoeffding trees, soft trees can be integrated into such systems due to their differentiability, but are neither transparent nor explainable. Our novel model combines the extensibility and transparency of Hoeffding trees with the differentiability of soft trees. We introduce a new gating function to regulate the balance between univariate and multivariate splits in the tree. Experiments are performed on 20 data streams, comparing SoHoT to standard Hoeffding trees, Hoeffding trees with limited complexity, and soft trees applying a sparse activation function for sample routing. The results show that soft Hoeffding trees outperform Hoeffding trees in estimating class probabilities and, at the same time, maintain transparency compared to soft trees, with relatively small losses in terms of AUROC and cross-entropy. We also demonstrate how to trade off transparency against performance using a hyperparameter, obtaining univariate splits at one end of the spectrum and multivariate splits at the other.
Learn to Solve Vehicle Routing Problems ASAP: A Neural Optimization Approach for Time-Constrained Vehicle Routing Problems with Finite Vehicle Fleet
Authors: Elija Deineko, Carina Kehrt
Date: 2024-11-07 00:00:00
Tasks: Benchmarking, Combinatorial Optimization, Decoder

Finding a feasible and prompt solution to the Vehicle Routing Problem (VRP) is a prerequisite for efficient freight transportation, seamless logistics, and sustainable mobility. Traditional optimization methods reach their limits when confronted with the real-world complexity of VRPs, which involve numerous constraints and objectives. Recently, the ability of generative Artificial Intelligence (AI) to solve combinatorial tasks, known as Neural Combinatorial Optimization (NCO), demonstrated promising results, offering new perspectives. In this study, we propose an NCO approach to solve a time-constrained capacitated VRP with a finite vehicle fleet size. The approach is based on an encoder-decoder architecture, formulated in line with the Policy Optimization with Multiple Optima (POMO) protocol and trained via a Proximal Policy Optimization (PPO) algorithm. We successfully trained the policy with multiple objectives (minimizing the total distance while maximizing vehicle utilization) and evaluated it on medium and large instances, benchmarking it against state-of-the-art heuristics. The method is able to find adequate and cost-efficient solutions, showing both flexibility and robust generalization. Finally, we provide a critical analysis of the solution generated by NCO and discuss the challenges and opportunities of this new branch of intelligent learning algorithms emerging in optimization science, focusing on freight transportation.
Learning dynamical systems from data: Gradient-based dictionary optimization
Authors: Mohammad Tabish, Neil K. Chada, Stefan Klus
Date: 2024-11-07 00:00:00
Tasks: Protein Folding

The Koopman operator plays a crucial role in analyzing the global behavior of dynamical systems. Existing data-driven methods for approximating the Koopman operator or discovering the governing equations of the underlying system typically require a fixed set of basis functions, also called dictionary. The optimal choice of basis functions is highly problem-dependent and often requires domain knowledge. We present a novel gradient descent-based optimization framework for learning suitable and interpretable basis functions from data and show how it can be used in combination with EDMD, SINDy, and PDE-FIND. We illustrate the efficacy of the proposed approach with the aid of various benchmark problems such as the Ornstein-Uhlenbeck process, Chua's circuit, a nonlinear heat equation, as well as protein-folding data.
Mining the Minoria: Unknown, Under-represented, and Under-performing Minority Groups
Authors: Mohsen Dehghankar, Abolfazl Asudeh
Date: 2024-11-07 00:00:00
Tasks: Attribute

Due to a variety of reasons, such as privacy, data in the wild often misses the grouping information required for identifying minorities. On the other hand, it is known that machine learning models are only as good as the data they are trained on and, hence, may underperform for the under-represented minority groups. The missing grouping information presents a dilemma for responsible data scientists who find themselves in an unknown-unknown situation, where not only do they not have access to the grouping attributes but do not also know what groups to consider. This paper is an attempt to address this dilemma. Specifically, we propose a minority mining problem, where we find vectors in the attribute space that reveal potential groups that are under-represented and under-performing. Technically speaking, we propose a geometric transformation of data into a dual space and use notions such as the arrangement of hyperplanes to design an efficient algorithm for the problem in lower dimensions. Generalizing our solution to the higher dimensions is cursed by dimensionality. Therefore, we propose a solution based on smart exploration of the search space for such cases. We conduct comprehensive experiments using real-world and synthetic datasets alongside the theoretical analysis. Our experiment results demonstrate the effectiveness of our proposed solutions in mining the unknown, under-represented, and under-performing minorities.
Zero-Shot Temporal Resolution Domain Adaptation for Spiking Neural Networks
Authors: Sanja Karilanova, Maxime Fabre, Emre Neftci, Ayça Özçelikkale
Date: 2024-11-07 00:00:00
Tasks: Domain Adaptation, image-classification, Image Classification, Keyword Spotting, State Space Models

Spiking Neural Networks (SNNs) are biologically-inspired deep neural networks that efficiently extract temporal information while offering promising gains in terms of energy efficiency and latency when deployed on neuromorphic devices. However, SNN model parameters are sensitive to temporal resolution, leading to significant performance drops when the temporal resolution of target data at the edge is not the same with that of the pre-deployment source data used for training, especially when fine-tuning is not possible at the edge. To address this challenge, we propose three novel domain adaptation methods for adapting neuron parameters to account for the change in time resolution without re-training on target time-resolution. The proposed methods are based on a mapping between neuron dynamics in SNNs and State Space Models (SSMs); and are applicable to general neuron models. We evaluate the proposed methods under spatio-temporal data tasks, namely the audio keyword spotting datasets SHD and MSWC as well as the image classification NMINST dataset. Our methods provide an alternative to - and in majority of the cases significantly outperform - the existing reference method that simply scales the time constant. Moreover, our results show that high accuracy on high temporal resolution data can be obtained by time efficient training on lower temporal resolution data and model adaptation.