pwc-archive/papers-with-abstracts huggingface dataset:
Model-agnostic clean-label backdoor mitigation in cybersecurity environments
Authors: Giorgio Severi, Simona Boboila, John Holodnak, Kendra Kratkiewicz, Rauf Izmailov, Michael J. De Lucia, Alina Oprea
Date: 2024-07-11 00:00:00
Tasks: backdoor defense, Classification, Malware Classification

The training phase of machine learning models is a delicate step, especially in cybersecurity contexts. Recent research has surfaced a series of insidious training-time attacks that inject backdoors in models designed for security classification tasks without altering the training labels. With this work, we propose new techniques that leverage insights in cybersecurity threat models to effectively mitigate these clean-label poisoning attacks, while preserving the model utility. By performing density-based clustering on a carefully chosen feature subspace, and progressively isolating the suspicious clusters through a novel iterative scoring procedure, our defensive mechanism can mitigate the attacks without requiring many of the common assumptions in the existing backdoor defense literature. To show the generality of our proposed mitigation, we evaluate it on two clean-label model-agnostic attacks on two different classic cybersecurity data modalities: network flows classification and malware classification, using gradient boosting and neural network models.
Real-Time Summarization of Twitter
Authors: Yixin Jin, Meiqi Wang, Meng Li, Wenjing Zhou, Yi Shen, Hao liu
Date: 2024-07-11 00:00:00

In this paper, we describe our approaches to TREC Real-Time Summarization of Twitter. We focus on real time push notification scenario, which requires a system monitors the stream of sampled tweets and returns the tweets relevant and novel to given interest profiles. Dirichlet score with and with very little smoothing (baseline) are employed to classify whether a tweet is relevant to a given interest profile. Using metrics including Mean Average Precision (MAP, cumulative gain (CG) and discount cumulative gain (DCG), the experiment indicates that our approach has a good performance. It is also desired to remove the redundant tweets from the pushing queue. Due to the precision limit, we only describe the algorithm in this paper.
Advanced Meta-Ensemble Machine Learning Models for Early and Accurate Sepsis Prediction to Improve Patient Outcomes
Authors: MohammadAmin Ansari Khoushabar, Parviz Ghafariasl
Date: 2024-07-11 00:00:00

Sepsis, a critical condition from the body's response to infection, poses a major global health crisis affecting all age groups. Timely detection and intervention are crucial for reducing healthcare expenses and improving patient outcomes. This paper examines the limitations of traditional sepsis screening tools like Systemic Inflammatory Response Syndrome, Modified Early Warning Score, and Quick Sequential Organ Failure Assessment, highlighting the need for advanced approaches. We propose using machine learning techniques - Random Forest, Extreme Gradient Boosting, and Decision Tree models - to predict sepsis onset. Our study evaluates these models individually and in a combined meta-ensemble approach using key metrics such as Accuracy, Precision, Recall, F1 score, and Area Under the Receiver Operating Characteristic Curve. Results show that the meta-ensemble model outperforms individual models, achieving an AUC-ROC score of 0.96, indicating superior predictive accuracy for early sepsis detection. The Random Forest model also performs well with an AUC-ROC score of 0.95, while Extreme Gradient Boosting and Decision Tree models score 0.94 and 0.90, respectively.
Non-convergence of Adam and other adaptive stochastic gradient descent optimization methods for non-vanishing learning rates
Authors: Steffen Dereich, Robin Graeber, Arnulf Jentzen
Date: 2024-07-11 00:00:00

Deep learning algorithms - typically consisting of a class of deep neural networks trained by a stochastic gradient descent (SGD) optimization method - are nowadays the key ingredients in many artificial intelligence (AI) systems and have revolutionized our ways of working and living in modern societies. For example, SGD methods are used to train powerful large language models (LLMs) such as versions of ChatGPT and Gemini, SGD methods are employed to create successful generative AI based text-to-image creation models such as Midjourney, DALL-E, and Stable Diffusion, but SGD methods are also used to train DNNs to approximately solve scientific models such as partial differential equation (PDE) models from physics and biology and optimal control and stopping problems from engineering. It is known that the plain vanilla standard SGD method fails to converge even in the situation of several convex optimization problems if the learning rates are bounded away from zero. However, in many practical relevant training scenarios, often not the plain vanilla standard SGD method but instead adaptive SGD methods such as the RMSprop and the Adam optimizers, in which the learning rates are modified adaptively during the training process, are employed. This naturally rises the question whether such adaptive optimizers, in which the learning rates are modified adaptively during the training process, do converge in the situation of non-vanishing learning rates. In this work we answer this question negatively by proving that adaptive SGD methods such as the popular Adam optimizer fail to converge to any possible random limit point if the learning rates are asymptotically bounded away from zero. In our proof of this non-convergence result we establish suitable pathwise a priori bounds for a class of accelerated and adaptive SGD methods, which are also of independent interest.
Density Estimation via Binless Multidimensional Integration
Authors: Matteo Carli, Alex Rodriguez, Alessandro Laio, Aldo Glielmo
Date: 2024-07-10 00:00:00
Tasks: Density Estimation

We introduce the Binless Multidimensional Thermodynamic Integration (BMTI) method for nonparametric, robust, and data-efficient density estimation. BMTI estimates the logarithm of the density by initially computing log-density differences between neighbouring data points. Subsequently, such differences are integrated, weighted by their associated uncertainties, using a maximum-likelihood formulation. This procedure can be seen as an extension to a multidimensional setting of the thermodynamic integration, a technique developed in statistical physics. The method leverages the manifold hypothesis, estimating quantities within the intrinsic data manifold without defining an explicit coordinate map. It does not rely on any binning or space partitioning, but rather on the construction of a neighbourhood graph based on an adaptive bandwidth selection procedure. BMTI mitigates the limitations commonly associated with traditional nonparametric density estimators, effectively reconstructing smooth profiles even in high-dimensional embedding spaces. The method is tested on a variety of complex synthetic high-dimensional datasets, where it is shown to outperform traditional estimators, and is benchmarked on realistic datasets from the chemical physics literature.
The GeometricKernels Package: Heat and Matérn Kernels for Geometric Learning on Manifolds, Meshes, and Graphs
Authors: Peter Mostowsky, Vincent Dutordoir, Iskander Azangulov, Noémie Jaquier, Michael John Hutchinson, Aditya Ravuri, Leonel Rozo, Alexander Terenin, Viacheslav Borovitskiy
Date: 2024-07-10 00:00:00
Tasks: Gaussian Processes, Uncertainty Quantification

Kernels are a fundamental technical primitive in machine learning. In recent years, kernel-based methods such as Gaussian processes are becoming increasingly important in applications where quantifying uncertainty is of key interest. In settings that involve structured data defined on graphs, meshes, manifolds, or other related spaces, defining kernels with good uncertainty-quantification behavior, and computing their value numerically, is less straightforward than in the Euclidean setting. To address this difficulty, we present GeometricKernels, a software package which implements the geometric analogs of classical Euclidean squared exponential - also known as heat - and Mat\'ern kernels, which are widely-used in settings where uncertainty is of key interest. As a byproduct, we obtain the ability to compute Fourier-feature-type expansions, which are widely used in their own right, on a wide set of geometric spaces. Our implementation supports automatic differentiation in every major current framework simultaneously via a backend-agnostic design. In this companion paper to the package and its documentation, we outline the capabilities of the package and present an illustrated example of its interface. We also include a brief overview of the theory the package is built upon and provide some historic context in the appendix.
Smooth Like Butter: Evaluating Multi-Lattice Transitions in Property-Augmented Latent Spaces
Authors: Martha Baldwin, Nicholas A. Meisel, Christopher McComb
Date: 2024-07-10 00:00:00

Additive manufacturing has revolutionized structural optimization by enhancing component strength and reducing material requirements. One approach used to achieve these improvements is the application of multi-lattice structures, where the macro-scale performance relies on the detailed design of mesostructural lattice elements. Many current approaches to designing such structures use data-driven design to generate multi-lattice transition regions, making use of machine learning models that are informed solely by the geometry of the mesostructures. However, it remains unclear if the integration of mechanical properties into the dataset used to train such machine learning models would be beneficial beyond using geometric data alone. To address this issue, this work implements and evaluates a hybrid geometry/property Variational Autoencoder (VAE) for generating multi-lattice transition regions. In our study, we found that hybrid VAEs demonstrate enhanced performance in maintaining stiffness continuity through transition regions, indicating their suitability for design tasks requiring smooth mechanical properties.
Pareto Low-Rank Adapters: Efficient Multi-Task Learning with Preferences
Authors: Nikolaos Dimitriadis, Pascal Frossard, Francois Fleuret
Date: 2024-07-10 00:00:00
Tasks: Multi-Task Learning, Scene Understanding

Dealing with multi-task trade-offs during inference can be addressed via Pareto Front Learning (PFL) methods that parameterize the Pareto Front with a single model, contrary to traditional Multi-Task Learning (MTL) approaches that optimize for a single trade-off which has to be decided prior to training. However, recent PFL methodologies suffer from limited scalability, slow convergence and excessive memory requirements compared to MTL approaches while exhibiting inconsistent mappings from preference space to objective space. In this paper, we introduce PaLoRA, a novel parameter-efficient method that augments the original model with task-specific low-rank adapters and continuously parameterizes the Pareto Front in their convex hull. Our approach dedicates the original model and the adapters towards learning general and task-specific features, respectively. Additionally, we propose a deterministic sampling schedule of preference vectors that reinforces this division of labor, enabling faster convergence and scalability to real world networks. Our experimental results show that PaLoRA outperforms MTL and PFL baselines across various datasets, scales to large networks and provides a continuous parameterization of the Pareto Front, reducing the memory overhead $23.8-31.7$ times compared with competing PFL baselines in scene understanding benchmarks.
A Critical Review of Causal Reasoning Benchmarks for Large Language Models
Authors: Linying Yang, Vik Shirvaikar, Oscar Clivio, Fabian Falck
Date: 2024-07-10 00:00:00
Tasks: Causal Inference, counterfactual, Counterfactual Reasoning, Retrieval

Numerous benchmarks aim to evaluate the capabilities of Large Language Models (LLMs) for causal inference and reasoning. However, many of them can likely be solved through the retrieval of domain knowledge, questioning whether they achieve their purpose. In this review, we present a comprehensive overview of LLM benchmarks for causality. We highlight how recent benchmarks move towards a more thorough definition of causal reasoning by incorporating interventional or counterfactual reasoning. We derive a set of criteria that a useful benchmark or set of benchmarks should aim to satisfy. We hope this work will pave the way towards a general framework for the assessment of causal understanding in LLMs and the design of novel benchmarks.
A Self-organizing Interval Type-2 Fuzzy Neural Network for Multi-Step Time Series Prediction
Authors: Fulong Yao, Wanqing Zhao, Matthew Forshaw, Yang song
Date: 2024-07-10 00:00:00
Tasks: Prediction, Time Series, Time Series Prediction

Data uncertainty is inherent in many real-world applications and poses significant challenges for accurate time series predictions. The interval type 2 fuzzy neural network (IT2FNN) has shown exceptional performance in uncertainty modelling for single-step prediction tasks. However, extending it for multi-step ahead predictions introduces further issues in uncertainty handling as well as model interpretability and accuracy. To address these issues, this paper proposes a new selforganizing interval type-2 fuzzy neural network with multiple outputs (SOIT2FNN-MO). Differing from the traditional six-layer IT2FNN, a nine-layer network architecture is developed. First, a new co-antecedent layer and a modified consequent layer are devised to improve the interpretability of the fuzzy model for multi-step time series prediction problems. Second, a new link layer is created to improve the accuracy by building temporal connections between multi-step predictions. Third, a new transformation layer is designed to address the problem of the vanishing rule strength caused by high-dimensional inputs. Furthermore, a two-stage, self-organizing learning mechanism is developed to automatically extract fuzzy rules from data and optimize network parameters. Experimental results on chaotic and microgrid prediction problems demonstrate that SOIT2FNN-MO outperforms state-of-the-art methods, by achieving a better accuracy ranging from 1.6% to 30% depending on the level of noises in data. Additionally, the proposed model is more interpretable, offering deeper insights into the prediction process.
What's the score? Automated Denoising Score Matching for Nonlinear Diffusions
Authors: Raghav Singhal, Mark Goldstein, Rajesh Ranganath
Date: 2024-07-10 00:00:00
Tasks: Denoising

Reversing a diffusion process by learning its score forms the heart of diffusion-based generative modeling and for estimating properties of scientific systems. The diffusion processes that are tractable center on linear processes with a Gaussian stationary distribution. This limits the kinds of models that can be built to those that target a Gaussian prior or more generally limits the kinds of problems that can be generically solved to those that have conditionally linear score functions. In this work, we introduce a family of tractable denoising score matching objectives, called local-DSM, built using local increments of the diffusion process. We show how local-DSM melded with Taylor expansions enables automated training and score estimation with nonlinear diffusion processes. To demonstrate these ideas, we use automated-DSM to train generative models using non-Gaussian priors on challenging low dimensional distributions and the CIFAR10 image dataset. Additionally, we use the automated-DSM to learn the scores for nonlinear processes studied in statistical physics.
ICD Codes are Insufficient to Create Datasets for Machine Learning: An Evaluation Using All of Us Data for Coccidioidomycosis and Myocardial Infarction
Authors: Abigail E. Whitlock, Gondy Leroy, Fariba M. Donovan, John N. Galgiani
Date: 2024-07-10 00:00:00
Tasks: All

In medicine, machine learning (ML) datasets are often built using the International Classification of Diseases (ICD) codes. As new models are being developed, there is a need for larger datasets. However, ICD codes are intended for billing. We aim to determine how suitable ICD codes are for creating datasets to train ML models. We focused on a rare and common disease using the All of Us database. First, we compared the patient cohort created using ICD codes for Valley fever (coccidioidomycosis, CM) with that identified via serological confirmation. Second, we compared two similarly created patient cohorts for myocardial infarction (MI) patients. We identified significant discrepancies between these two groups, and the patient overlap was small. The CM cohort had 811 patients in the ICD-10 group, 619 patients in the positive-serology group, and 24 with both. The MI cohort had 14,875 patients in the ICD-10 group, 23,598 in the MI laboratory-confirmed group, and 6,531 in both. Demographics, rates of disease symptoms, and other clinical data varied across our case study cohorts.
Automating Weak Label Generation for Data Programming with Clinicians in the Loop
Authors: Jean Park, Sydney Pugh, Kaustubh Sridhar, Mengyu Liu, Navish Yarna, Ramneet Kaur, Souradeep Dutta, Elena Bernardis, Oleg Sokolsky, Insup Lee
Date: 2024-07-10 00:00:00
Tasks: Time Series

Large Deep Neural Networks (DNNs) are often data hungry and need high-quality labeled data in copious amounts for learning to converge. This is a challenge in the field of medicine since high quality labeled data is often scarce. Data programming has been the ray of hope in this regard, since it allows us to label unlabeled data using multiple weak labeling functions. Such functions are often supplied by a domain expert. Data-programming can combine multiple weak labeling functions and suggest labels better than simple majority voting over the different functions. However, it is not straightforward to express such weak labeling functions, especially in high-dimensional settings such as images and time-series data. What we propose in this paper is a way to bypass this issue, using distance functions. In high-dimensional spaces, it is easier to find meaningful distance metrics which can generalize across different labeling tasks. We propose an algorithm that queries an expert for labels of a few representative samples of the dataset. These samples are carefully chosen by the algorithm to capture the distribution of the dataset. The labels assigned by the expert on the representative subset induce a labeling on the full dataset, thereby generating weak labels to be used in the data programming pipeline. In our medical time series case study, labeling a subset of 50 to 130 out of 3,265 samples showed 17-28% improvement in accuracy and 13-28% improvement in F1 over the baseline using clinician-defined labeling functions. In our medical image case study, labeling a subset of about 50 to 120 images from 6,293 unlabeled medical images using our approach showed significant improvement over the baseline method, Snuba, with an increase of approximately 5-15% in accuracy and 12-19% in F1 score.
Identification and Estimation of the Bi-Directional MR with Some Invalid Instruments
Authors: Feng Xie, Zhen Yao, Lin Xie, Yan Zeng, Zhi Geng
Date: 2024-07-10 00:00:00
Tasks: valid

We consider the challenging problem of estimating causal effects from purely observational data in the bi-directional Mendelian randomization (MR), where some invalid instruments, as well as unmeasured confounding, usually exist. To address this problem, most existing methods attempt to find proper valid instrumental variables (IVs) for the target causal effect by expert knowledge or by assuming that the causal model is a one-directional MR model. As such, in this paper, we first theoretically investigate the identification of the bi-directional MR from observational data. In particular, we provide necessary and sufficient conditions under which valid IV sets are correctly identified such that the bi-directional MR model is identifiable, including the causal directions of a pair of phenotypes (i.e., the treatment and outcome). Moreover, based on the identification theory, we develop a cluster fusion-like method to discover valid IV sets and estimate the causal effects of interest. We theoretically demonstrate the correctness of the proposed algorithm. Experimental results show the effectiveness of our method for estimating causal effects in bi-directional MR.
Token-Mol 1.0: Tokenized drug design with large language model
Authors: Jike Wang, Rui Qin, Mingyang Wang, Meijing Fang, Yangyang Zhang, Yuchen Zhu, Qun Su, Qiaolin Gou, Chao Shen, Odin Zhang, Zhenxing Wu, Dejun Jiang, Xujun Zhang, Huifeng Zhao, Xiaozhe Wan, Zhourui Wu, Liwei Liu, Yu Kang, Chang-Yu Hsieh, Tingjun Hou
Date: 2024-07-10 00:00:00
Tasks: Drug Design, Drug Discovery, Language Modeling, Language Modelling, Large Language Model, Molecular Property Prediction, Property Prediction, regression, Reinforcement Learning (RL)

Significant interests have recently risen in leveraging sequence-based large language models (LLMs) for drug design. However, most current applications of LLMs in drug discovery lack the ability to comprehend three-dimensional (3D) structures, thereby limiting their effectiveness in tasks that explicitly involve molecular conformations. In this study, we introduced Token-Mol, a token-only 3D drug design model. This model encodes all molecular information, including 2D and 3D structures, as well as molecular property data, into tokens, which transforms classification and regression tasks in drug discovery into probabilistic prediction problems, thereby enabling learning through a unified paradigm. Token-Mol is built on the transformer decoder architecture and trained using random causal masking techniques. Additionally, we proposed the Gaussian cross-entropy (GCE) loss function to overcome the challenges in regression tasks, significantly enhancing the capacity of LLMs to learn continuous numerical values. Through a combination of fine-tuning and reinforcement learning (RL), Token-Mol achieves performance comparable to or surpassing existing task-specific methods across various downstream tasks, including pocket-based molecular generation, conformation generation, and molecular property prediction. Compared to existing molecular pre-trained models, Token-Mol exhibits superior proficiency in handling a wider range of downstream tasks essential for drug design. Notably, our approach improves regression task accuracy by approximately 30% compared to similar token-only methods. Token-Mol overcomes the precision limitations of token-only models and has the potential to integrate seamlessly with general models such as ChatGPT, paving the way for the development of a universal artificial intelligence drug design model that facilitates rapid and high-quality drug design by experts.