pwc-archive/papers-with-abstracts huggingface dataset:
PGraphDTA: Improving Drug Target Interaction Prediction using Protein Language Models and Contact Maps
Authors: Rakesh Bal, Yijia Xiao, Wei Wang
Date: 2023-10-06 00:00:00
Proceeding: Neural Information Processing Systems 2023 AI for Science: from Theory to Practice Workshop 2023 12
Tasks: Binary Classification, Drug Discovery, Inductive Bias

Developing and discovering new drugs is a complex and resource-intensive endeavor that often involves substantial costs, time investment, and safety concerns. A key aspect of drug discovery involves identifying novel drug-target (DT) interactions. Existing computational methods for predicting DT interactions have primarily focused on binary classification tasks, aiming to determine whether a DT pair interacts or not. However, protein-ligand interactions exhibit a continuum of binding strengths, known as binding affinity, presenting a persistent challenge for accurate prediction. In this study, we investigate various techniques employed in Drug Target Interaction (DTI) prediction and propose novel enhancements to enhance their performance. Our approaches include the integration of Protein Language Models (PLMs) and the incorporation of Contact Map information as an inductive bias within current models. Through extensive experimentation, we demonstrate that our proposed approaches outperform the baseline models considered in this study, presenting a compelling case for further development in this direction. We anticipate that the insights gained from this work will significantly narrow the search space for potential drugs targeting specific proteins, thereby accelerating drug discovery. Code and data for PGraphDTA are available at https://github.com/Yijia-Xiao/PgraphDTA/.
Anonymous Learning via Look-Alike Clustering: A Precise Analysis of Model Generalization
Date: 2023-10-06 00:00:00
Proceeding: NeurIPS 2023 11
Tasks: Clustering

While personalized recommendations systems have become increasingly popular, ensuring user data protection remains a top concern in the development of these learning systems. A common approach to enhancing privacy involves training models using anonymous data rather than individual data. In this paper, we explore a natural technique called \emph{look-alike clustering}, which involves replacing sensitive features of individuals with the cluster's average values. We provide a precise analysis of how training models using anonymous cluster centers affects their generalization capabilities. We focus on an asymptotic regime where the size of the training set grows in proportion to the features dimension. Our analysis is based on the Convex Gaussian Minimax Theorem (CGMT) and allows us to theoretically understand the role of different model components on the generalization error. In addition, we demonstrate that in certain high-dimensional regimes, training over anonymous cluster centers acts as a regularization and improves generalization error of the trained models. Finally, we corroborate our asymptotic theory with finite-sample numerical experiments where we observe a perfect match when the sample size is only of order of a few hundreds.
Accelerating optimization over the space of probability measures
Authors: Shi Chen, Qin Li, Oliver Tse, Stephen J. Wright
Date: 2023-10-06 00:00:00

The acceleration of gradient-based optimization methods is a subject of significant practical and theoretical importance, particularly within machine learning applications. While much attention has been directed towards optimizing within Euclidean space, the need to optimize over spaces of probability measures in machine learning motivates exploration of accelerated gradient methods in this context too. To this end, we introduce a Hamiltonian-flow approach analogous to momentum-based approaches in Euclidean space. We demonstrate that, in the continuous-time setting, algorithms based on this approach can achieve convergence rates of arbitrarily high order. We complement our findings with numerical examples.
The Role of Federated Learning in a Wireless World with Foundation Models
Authors: Zihan Chen, Howard H. Yang, Y. C. Tay, Kai Fong Ernest Chong, Tony Q. S. Quek
Date: 2023-10-06 00:00:00
Tasks: Federated Learning

Foundation models (FMs) are general-purpose artificial intelligence (AI) models that have recently enabled multiple brand-new generative AI applications. The rapid advances in FMs serve as an important contextual backdrop for the vision of next-generation wireless networks, where federated learning (FL) is a key enabler of distributed network intelligence. Currently, the exploration of the interplay between FMs and FL is still in its nascent stage. Naturally, FMs are capable of boosting the performance of FL, and FL could also leverage decentralized data and computing resources to assist in the training of FMs. However, the exceptionally high requirements that FMs have for computing resources, storage, and communication overhead would pose critical challenges to FL-enabled wireless networks. In this article, we explore the extent to which FMs are suitable for FL over wireless networks, including a broad overview of research challenges and opportunities. In particular, we discuss multiple new paradigms for realizing future intelligent networks that integrate FMs and FL. We also consolidate several broad research directions associated with these paradigms.
Runtime Monitoring DNN-Based Perception
Authors: Chih-Hong Cheng, Michael Luttenberger, Rongjie Yan
Date: 2023-10-06 00:00:00

Deep neural networks (DNNs) are instrumental in realizing complex perception systems. As many of these applications are safety-critical by design, engineering rigor is required to ensure that the functional insufficiency of the DNN-based perception is not the source of harm. In addition to conventional static verification and testing techniques employed during the design phase, there is a need for runtime verification techniques that can detect critical events, diagnose issues, and even enforce requirements. This tutorial aims to provide readers with a glimpse of techniques proposed in the literature. We start with classical methods proposed in the machine learning community, then highlight a few techniques proposed by the formal methods community. While we surely can observe similarities in the design of monitors, how the decision boundaries are created vary between the two communities. We conclude by highlighting the need to rigorously design monitors, where data availability outside the operational domain plays an important role.
Robust Multimodal Learning with Missing Modalities via Parameter-Efficient Adaptation
Authors: Md Kaykobad Reza, Ashley Prater-Bennette, M. Salman Asif
Date: 2023-10-06 00:00:00
Tasks: Material Segmentation, Multimodal Sentiment Analysis, Semantic Segmentation, Sentiment Analysis

Multimodal learning seeks to utilize data from multiple sources to improve the overall performance of downstream tasks. It is desirable for redundancies in the data to make multimodal systems robust to missing or corrupted observations in some correlated modalities. However, we observe that the performance of several existing multimodal networks significantly deteriorates if one or multiple modalities are absent at test time. To enable robustness to missing modalities, we propose a simple and parameter-efficient adaptation procedure for pretrained multimodal networks. In particular, we exploit modulation of intermediate features to compensate for the missing modalities. We demonstrate that such adaptation can partially bridge performance drop due to missing modalities and outperform independent, dedicated networks trained for the available modality combinations in some cases. The proposed adaptation requires extremely small number of parameters (e.g., fewer than 1% of the total parameters) and applicable to a wide range of modality combinations and tasks. We conduct a series of experiments to highlight the missing modality robustness of our proposed method on five different multimodal tasks across seven datasets. Our proposed method demonstrates versatility across various tasks and datasets, and outperforms existing methods for robust multimodal learning with missing modalities.
Dementia Assessment Using Mandarin Speech with an Attention-based Speech Recognition Encoder
Authors: Zih-Jyun Lin, Yi-Ju Chen, Po-Chih Kuo, Likai Huang, Chaur-Jong Hu, Cheng-Yu Chen
Date: 2023-10-06 00:00:00
Tasks: Alzheimer's Disease Detection, speech-recognition, Speech Recognition

Dementia diagnosis requires a series of different testing methods, which is complex and time-consuming. Early detection of dementia is crucial as it can prevent further deterioration of the condition. This paper utilizes a speech recognition model to construct a dementia assessment system tailored for Mandarin speakers during the picture description task. By training an attention-based speech recognition model on voice data closely resembling real-world scenarios, we have significantly enhanced the model's recognition capabilities. Subsequently, we extracted the encoder from the speech recognition model and added a linear layer for dementia assessment. We collected Mandarin speech data from 99 subjects and acquired their clinical assessments from a local hospital. We achieved an accuracy of 92.04% in Alzheimer's disease detection and a mean absolute error of 9% in clinical dementia rating score prediction.
AURO: Reinforcement Learning for Adaptive User Retention Optimization in Recommender Systems
Authors: Zhenghai Xue, Qingpeng Cai, Bin Yang, Lantao Hu, Peng Jiang, Kun Gai, Bo An
Date: 2023-10-06 00:00:00
Tasks: Navigate, Recommendation Systems, Reinforcement Learning (RL), Sequential Recommendation

The field of Reinforcement Learning (RL) has garnered increasing attention for its ability of optimizing user retention in recommender systems. A primary obstacle in this optimization process is the environment non-stationarity stemming from the continual and complex evolution of user behavior patterns over time, such as variations in interaction rates and retention propensities. These changes pose significant challenges to existing RL algorithms for recommendations, leading to issues with dynamics and reward distribution shifts. This paper introduces a novel approach called \textbf{A}daptive \textbf{U}ser \textbf{R}etention \textbf{O}ptimization (AURO) to address this challenge. To navigate the recommendation policy in non-stationary environments, AURO introduces an state abstraction module in the policy network. The module is trained with a new value-based loss function, aligning its output with the estimated performance of the current policy. As the policy performance of RL is sensitive to environment drifts, the loss function enables the state abstraction to be reflective of environment changes and notify the recommendation policy to adapt accordingly. Additionally, the non-stationarity of the environment introduces the problem of implicit cold start, where the recommendation policy continuously interacts with users displaying novel behavior patterns. AURO encourages exploration guarded by performance-based rejection sampling to maintain a stable recommendation quality in the cost-sensitive online environment. Extensive empirical analysis are conducted in a user retention simulator, the MovieLens dataset, and a live short-video recommendation platform, demonstrating AURO's superior performance against all evaluated baseline algorithms.
CUPre: Cross-domain Unsupervised Pre-training for Few-Shot Cell Segmentation
Authors: Weibin Liao, Xuhong LI, Qingzhong Wang, Yanwu Xu, Zhaozheng Yin, Haoyi Xiong
Date: 2023-10-06 00:00:00
Tasks: Cell Segmentation, Contrastive Learning, Few-shot Instance Segmentation, Instance Segmentation, object-detection, Object Detection, Segmentation, Semantic Segmentation, Unsupervised Pre-training

While pre-training on object detection tasks, such as Common Objects in Contexts (COCO) [1], could significantly boost the performance of cell segmentation, it still consumes on massive fine-annotated cell images [2] with bounding boxes, masks, and cell types for every cell in every image, to fine-tune the pre-trained model. To lower the cost of annotation, this work considers the problem of pre-training DNN models for few-shot cell segmentation, where massive unlabeled cell images are available but only a small proportion is annotated. Hereby, we propose Cross-domain Unsupervised Pre-training, namely CUPre, transferring the capability of object detection and instance segmentation for common visual objects (learned from COCO) to the visual domain of cells using unlabeled images. Given a standard COCO pre-trained network with backbone, neck, and head modules, CUPre adopts an alternate multi-task pre-training (AMT2) procedure with two sub-tasks -- in every iteration of pre-training, AMT2 first trains the backbone with cell images from multiple cell datasets via unsupervised momentum contrastive learning (MoCo) [3], and then trains the whole model with vanilla COCO datasets via instance segmentation. After pre-training, CUPre fine-tunes the whole model on the cell segmentation task using a few annotated images. We carry out extensive experiments to evaluate CUPre using LIVECell [2] and BBBC038 [4] datasets in few-shot instance segmentation settings. The experiment shows that CUPre can outperform existing pre-training methods, achieving the highest average precision (AP) for few-shot cell segmentation and detection.
Perfect Alignment May be Poisonous to Graph Contrastive Learning
Authors: Jingyu Liu, Huayi Tang, Yong liu
Date: 2023-10-06 00:00:00
Tasks: Contrastive Learning

Graph Contrastive Learning (GCL) aims to learn node representations by aligning positive pairs and separating negative ones. However, few of researchers have focused on the inner law behind specific augmentations used in graph-based learning. What kind of augmentation will help downstream performance, how does contrastive learning actually influence downstream tasks, and why the magnitude of augmentation matters so much? This paper seeks to address these questions by establishing a connection between augmentation and downstream performance. Our findings reveal that GCL contributes to downstream tasks mainly by separating different classes rather than gathering nodes of the same class. So perfect alignment and augmentation overlap which draw all intra-class samples the same can not fully explain the success of contrastive learning. Therefore, in order to understand how augmentation aids the contrastive learning process, we conduct further investigations into the generalization, finding that perfect alignment that draw positive pair the same could help contrastive loss but is poisonous to generalization, as a result, perfect alignment may not lead to best downstream performance, so specifically designed augmentation is needed to achieve appropriate alignment performance and improve downstream accuracy. We further analyse the result by information theory and graph spectrum theory and propose two simple but effective methods to verify the theories. The two methods could be easily applied to various GCL algorithms and extensive experiments are conducted to prove its effectiveness. The code is available at https://github.com/somebodyhh1/GRACEIS
Ultimate limit on learning non-Markovian behavior: Fisher information rate and excess information
Authors: Paul M. Riechers
Date: 2023-10-06 00:00:00
Tasks: Time Series

We address the fundamental limits of learning unknown parameters of any stochastic process from time-series data, and discover exact closed-form expressions for how optimal inference scales with observation length. Given a parametrized class of candidate models, the Fisher information of observed sequence probabilities lower-bounds the variance in model estimation from finite data. As sequence-length increases, the minimal variance scales as the square inverse of the length -- with constant coefficient given by the information rate. We discover a simple closed-form expression for this information rate, even in the case of infinite Markov order. We furthermore obtain the exact analytic lower bound on model variance from the observation-induced metadynamic among belief states. We discover ephemeral, exponential, and more general modes of convergence to the asymptotic information rate. Surprisingly, this myopic information rate converges to the asymptotic Fisher information rate with exactly the same relaxation timescales that appear in the myopic entropy rate as it converges to the Shannon entropy rate for the process. We illustrate these results with a sequence of examples that highlight qualitatively distinct features of stochastic processes that shape optimal learning.
A Learnable Counter-condition Analysis Framework for Functional Connectivity-based Neurological Disorder Diagnosis
Authors: Eunsong Kang, Da-Woon Heo, Jiwon Lee, Heung-Il Suk
Date: 2023-10-06 00:00:00
Tasks: Diagnostic, Explainable Models, feature selection, Functional Connectivity

To understand the biological characteristics of neurological disorders with functional connectivity (FC), recent studies have widely utilized deep learning-based models to identify the disease and conducted post-hoc analyses via explainable models to discover disease-related biomarkers. Most existing frameworks consist of three stages, namely, feature selection, feature extraction for classification, and analysis, where each stage is implemented separately. However, if the results at each stage lack reliability, it can cause misdiagnosis and incorrect analysis in afterward stages. In this study, we propose a novel unified framework that systemically integrates diagnoses (i.e., feature selection and feature extraction) and explanations. Notably, we devised an adaptive attention network as a feature selection approach to identify individual-specific disease-related connections. We also propose a functional network relational encoder that summarizes the global topological properties of FC by learning the inter-network relations without pre-defined edges between functional networks. Last but not least, our framework provides a novel explanatory power for neuroscientific interpretation, also termed counter-condition analysis. We simulated the FC that reverses the diagnostic information (i.e., counter-condition FC): converting a normal brain to be abnormal and vice versa. We validated the effectiveness of our framework by using two large resting-state functional magnetic resonance imaging (fMRI) datasets, Autism Brain Imaging Data Exchange (ABIDE) and REST-meta-MDD, and demonstrated that our framework outperforms other competing methods for disease identification. Furthermore, we analyzed the disease-related neurological patterns based on counter-condition analysis.
Understanding prompt engineering may not require rethinking generalization
Authors: Victor Akinwande, Yiding Jiang, Dylan Sam, J. Zico Kolter
Date: 2023-10-06 00:00:00
Tasks: Generalization Bounds, Language Modelling, Model Selection, Prompt Engineering, Zero-Shot Learning

Zero-shot learning in prompted vision-language models, the practice of crafting prompts to build classifiers without an explicit training process, has achieved impressive performance in many settings. This success presents a seemingly surprising observation: these methods suffer relatively little from overfitting, i.e., when a prompt is manually engineered to achieve low error on a given training set (thus rendering the method no longer actually zero-shot), the approach still performs well on held-out test data. In this paper, we show that we can explain such performance well via recourse to classical PAC-Bayes bounds. Specifically, we show that the discrete nature of prompts, combined with a PAC-Bayes prior given by a language model, results in generalization bounds that are remarkably tight by the standards of the literature: for instance, the generalization bound of an ImageNet classifier is often within a few percentage points of the true test error. We demonstrate empirically that this holds for existing handcrafted prompts and prompts generated through simple greedy search. Furthermore, the resulting bound is well-suited for model selection: the models with the best bound typically also have the best test performance. This work thus provides a possible justification for the widespread practice of prompt engineering, even if it seems that such methods could potentially overfit the training data.
On Wasserstein distances for affine transformations of random vectors
Authors: Keaton Hamm, Andrzej Korzeniowski
Date: 2023-10-05 00:00:00

We expound on some known lower bounds of the quadratic Wasserstein distance between random vectors in $\mathbb{R}^n$ with an emphasis on affine transformations that have been used in manifold learning of data in Wasserstein space. In particular, we give concrete lower bounds for rotated copies of random vectors in $\mathbb{R}^2$ by computing the Bures metric between the covariance matrices. We also derive upper bounds for compositions of affine maps which yield a fruitful variety of diffeomorphisms applied to an initial data measure. We apply these bounds to various distributions including those lying on a 1-dimensional manifold in $\mathbb{R}^2$ and illustrate the quality of the bounds. Finally, we give a framework for mimicking handwritten digit or alphabet datasets that can be applied in a manifold learning framework.
LaTeX: Language Pattern-aware Triggering Event Detection for Adverse Experience during Pandemics
Authors: Kaiqun Fu, Yangxiao Bai, Weiwei Zhang, Deepthi Kolady
Date: 2023-10-05 00:00:00
Tasks: Event Detection, Survey

The COVID-19 pandemic has accentuated socioeconomic disparities across various racial and ethnic groups in the United States. While previous studies have utilized traditional survey methods like the Household Pulse Survey (HPS) to elucidate these disparities, this paper explores the role of social media platforms in both highlighting and addressing these challenges. Drawing from real-time data sourced from Twitter, we analyzed language patterns related to four major types of adverse experiences: loss of employment income (LI), food scarcity (FS), housing insecurity (HI), and unmet needs for mental health services (UM). We first formulate a sparsity optimization problem that extracts low-level language features from social media data sources. Second, we propose novel constraints on feature similarity exploiting prior knowledge about the similarity of the language patterns among the adverse experiences. The proposed problem is challenging to solve due to the non-convexity objective and non-smoothness penalties. We develop an algorithm based on the alternating direction method of multipliers (ADMM) framework to solve the proposed formulation. Extensive experiments and comparisons to other models on real-world social media and the detection of adverse experiences justify the efficacy of our model.
Improving classifier decision boundaries using nearest neighbors
Authors: Johannes Schneider
Date: 2023-10-05 00:00:00

Neural networks are not learning optimal decision boundaries. We show that decision boundaries are situated in areas of low training data density. They are impacted by few training samples which can easily lead to overfitting. We provide a simple algorithm performing a weighted average of the prediction of a sample and its nearest neighbors' (computed in latent space) leading to a minor favorable outcomes for a variety of important measures for neural networks. In our evaluation, we employ various self-trained and pre-trained convolutional neural networks to show that our approach improves (i) resistance to label noise, (ii) robustness against adversarial attacks, (iii) classification accuracy, and to some degree even (iv) interpretability. While improvements are not necessarily large in all four areas, our approach is conceptually simple, i.e., improvements come without any modification to network architecture, training procedure or dataset. Furthermore, they are in stark contrast to prior works that often require trade-offs among the four objectives or provide valuable, but non-actionable insights.