pwc-archive/papers-with-abstracts huggingface dataset:
PathoLM: Identifying pathogenicity from the DNA sequence through the Genome Foundation Model
Authors: Sajib Acharjee Dip, Uddip Acharjee Shuvo, Tran Chau, Haoqiu Song, Petra Choi, Xuan Wang, Liqing Zhang
Date: 2024-06-19 00:00:00
Tasks: Feature Engineering, Language Modelling, Specificity

Pathogen identification is pivotal in diagnosing, treating, and preventing diseases, crucial for controlling infections and safeguarding public health. Traditional alignment-based methods, though widely used, are computationally intense and reliant on extensive reference databases, often failing to detect novel pathogens due to their low sensitivity and specificity. Similarly, conventional machine learning techniques, while promising, require large annotated datasets and extensive feature engineering and are prone to overfitting. Addressing these challenges, we introduce PathoLM, a cutting-edge pathogen language model optimized for the identification of pathogenicity in bacterial and viral sequences. Leveraging the strengths of pre-trained DNA models such as the Nucleotide Transformer, PathoLM requires minimal data for fine-tuning, thereby enhancing pathogen detection capabilities. It effectively captures a broader genomic context, significantly improving the identification of novel and divergent pathogens. We developed a comprehensive data set comprising approximately 30 species of viruses and bacteria, including ESKAPEE pathogens, seven notably virulent bacterial strains resistant to antibiotics. Additionally, we curated a species classification dataset centered specifically on the ESKAPEE group. In comparative assessments, PathoLM dramatically outperforms existing models like DciPatho, demonstrating robust zero-shot and few-shot capabilities. Furthermore, we expanded PathoLM-Sp for ESKAPEE species classification, where it showed superior performance compared to other advanced deep learning methods, despite the complexities of the task.
Advancing Retail Data Science: Comprehensive Evaluation of Synthetic Data
Authors: Yu Xia, Chi-Hua Wang, Joshua Mabry, Guang Cheng
Date: 2024-06-19 00:00:00
Tasks: Demand Forecasting, Synthetic Data Generation

The evaluation of synthetic data generation is crucial, especially in the retail sector where data accuracy is paramount. This paper introduces a comprehensive framework for assessing synthetic retail data, focusing on fidelity, utility, and privacy. Our approach differentiates between continuous and discrete data attributes, providing precise evaluation criteria. Fidelity is measured through stability and generalizability. Stability ensures synthetic data accurately replicates known data distributions, while generalizability confirms its robustness in novel scenarios. Utility is demonstrated through the synthetic data's effectiveness in critical retail tasks such as demand forecasting and dynamic pricing, proving its value in predictive analytics and strategic planning. Privacy is safeguarded using Differential Privacy, ensuring synthetic data maintains a perfect balance between resembling training and holdout datasets without compromising security. Our findings validate that this framework provides reliable and scalable evaluation for synthetic retail data. It ensures high fidelity, utility, and privacy, making it an essential tool for advancing retail data science. This framework meets the evolving needs of the retail industry with precision and confidence, paving the way for future advancements in synthetic data methodologies.
Nutmeg and SPICE: Models and Data for Biomolecular Machine Learning
Authors: Peter Eastman, Benjamin P. Pritchard, John D. Chodera, Thomas E. Markland
Date: 2024-06-18 00:00:00

We describe version 2 of the SPICE dataset, a collection of quantum chemistry calculations for training machine learning potentials. It expands on the original dataset by adding much more sampling of chemical space and more data on non-covalent interactions. We train a set of potential energy functions called Nutmeg on it. They are based on the TensorNet architecture. They use a novel mechanism to improve performance on charged and polar molecules, injecting precomputed partial charges into the model to provide a reference for the large scale charge distribution. Evaluation of the new models shows they do an excellent job of reproducing energy differences between conformations, even on highly charged molecules or ones that are significantly larger than the molecules in the training set. They also produce stable molecular dynamics trajectories, and are fast enough to be useful for routine simulation of small molecules.
On instabilities in neural network-based physics simulators
Authors: Daniel Floryan
Date: 2024-06-18 00:00:00

When neural networks are trained from data to simulate the dynamics of physical systems, they encounter a persistent challenge: the long-time dynamics they produce are often unphysical or unstable. We analyze the origin of such instabilities when learning linear dynamical systems, focusing on the training dynamics. We make several analytical findings which empirical observations suggest extend to nonlinear dynamical systems. First, the rate of convergence of the training dynamics is uneven and depends on the distribution of energy in the data. As a special case, the dynamics in directions where the data have no energy cannot be learned. Second, in the unlearnable directions, the dynamics produced by the neural network depend on the weight initialization, and common weight initialization schemes can produce unstable dynamics. Third, injecting synthetic noise into the data during training adds damping to the training dynamics and can stabilize the learned simulator, though doing so undesirably biases the learned dynamics. For each contributor to instability, we suggest mitigative strategies. We also highlight important differences between learning discrete-time and continuous-time dynamics, and discuss extensions to nonlinear systems.
Exact Community Recovery under Side Information: Optimality of Spectral Algorithms
Authors: Julia Gaudio, Nirmit Joshi
Date: 2024-06-18 00:00:00
Tasks: Stochastic Block Model

We study the problem of exact community recovery in general, two-community block models, in the presence of node-attributed $side$ $information$. We allow for a very general side information channel for node attributes, and for pairwise (edge) observations, consider both Bernoulli and Gaussian matrix models, capturing the Stochastic Block Model, Submatrix Localization, and $\mathbb{Z}_2$-Synchronization as special cases. A recent work of Dreveton et al. 2024 characterized the information-theoretic limit of a very general exact recovery problem with side information. In this paper, we show algorithmic achievability in the above important cases by designing a simple but optimal spectral algorithm that incorporates side information (when present) along with the eigenvectors of the pairwise observation matrix. Using the powerful tool of entrywise eigenvector analysis of Abbe et al. 2020, we show that our spectral algorithm can mimic the so called $genie$-$aided$ $estimators$, where the $i^{\mathrm{th}}$ genie-aided estimator optimally computes the estimate of the $i^{\mathrm{th}}$ label, when all remaining labels are revealed by a genie. This perspective provides a unified understanding of the optimality of spectral algorithms for various exact recovery problems in a recent line of work.
PIPPIN: Generating variable length full events from partons
Authors: Guillaume Quétant, John Andrew Raine, Matthew Leigh, Debajyoti Sengupta, Tobias Golling
Date: 2024-06-18 00:00:00

This paper presents a novel approach for directly generating full events at detector-level from parton-level information, leveraging cutting-edge machine learning techniques. To address the challenge of multiplicity variations between parton and reconstructed object spaces, we employ transformers, score-based models and normalizing flows. Our method tackles the inherent complexities of the stochastic transition between these two spaces and achieves remarkably accurate results. The combination of innovative techniques and the achieved accuracy demonstrates the potential of our approach in advancing the field and opens avenues for further exploration. This research contributes to the ongoing efforts in high-energy physics and generative modelling, providing a promising direction for enhanced precision in fast detector simulation.
Accelerated Stochastic Min-Max Optimization Based on Bias-corrected Momentum
Authors: Haoyuan Cai, Sulaiman A. Alghunaim, Ali H. Sayed
Date: 2024-06-18 00:00:00

Lower-bound analyses for nonconvex strongly-concave minimax optimization problems have shown that stochastic first-order algorithms require at least $\mathcal{O}(\varepsilon^{-4})$ oracle complexity to find an $\varepsilon$-stationary point. Some works indicate that this complexity can be improved to $\mathcal{O}(\varepsilon^{-3})$ when the loss gradient is Lipschitz continuous. The question of achieving enhanced convergence rates under distinct conditions, remains unresolved. In this work, we address this question for optimization problems that are nonconvex in the minimization variable and strongly concave or Polyak-Lojasiewicz (PL) in the maximization variable. We introduce novel bias-corrected momentum algorithms utilizing efficient Hessian-vector products. We establish convergence conditions and demonstrate a lower iteration complexity of $\mathcal{O}(\varepsilon^{-3})$ for the proposed algorithms. The effectiveness of the method is validated through applications to robust logistic regression using real-world datasets.
Sharp detection of low-dimensional structure in probability measures via dimensional logarithmic Sobolev inequalities
Authors: Matthew T. C. Li, Tiangang Cui, Fengyi Li, Youssef Marzouk, Olivier Zahm
Date: 2024-06-18 00:00:00
Tasks: Dimensionality Reduction

Identifying low-dimensional structure in high-dimensional probability measures is an essential pre-processing step for efficient sampling. We introduce a method for identifying and approximating a target measure $\pi$ as a perturbation of a given reference measure $\mu$ along a few significant directions of $\mathbb{R}^{d}$. The reference measure can be a Gaussian or a nonlinear transformation of a Gaussian, as commonly arising in generative modeling. Our method extends prior work on minimizing majorizations of the Kullback--Leibler divergence to identify optimal approximations within this class of measures. Our main contribution unveils a connection between the \emph{dimensional} logarithmic Sobolev inequality (LSI) and approximations with this ansatz. Specifically, when the target and reference are both Gaussian, we show that minimizing the dimensional LSI is equivalent to minimizing the KL divergence restricted to this ansatz. For general non-Gaussian measures, the dimensional LSI produces majorants that uniformly improve on previous majorants for gradient-based dimension reduction. We further demonstrate the applicability of this analysis to the squared Hellinger distance, where analogous reasoning shows that the dimensional Poincar\'e inequality offers improved bounds.
ABNet: Attention BarrierNet for Safe and Scalable Robot Learning
Authors: Wei Xiao, Tsun-Hsuan Wang, Daniela Rus
Date: 2024-06-18 00:00:00
Tasks: Autonomous Driving, Robot Manipulation

Safe learning is central to AI-enabled robots where a single failure may lead to catastrophic results. Barrier-based method is one of the dominant approaches for safe robot learning. However, this method is not scalable, hard to train, and tends to generate unstable signals under noisy inputs that are challenging to be deployed for robots. To address these challenges, we propose a novel Attention BarrierNet (ABNet) that is scalable to build larger foundational safe models in an incremental manner. Each head of BarrierNet in the ABNet could learn safe robot control policies from different features and focus on specific part of the observation. In this way, we do not need to one-shotly construct a large model for complex tasks, which significantly facilitates the training of the model while ensuring its stable output. Most importantly, we can still formally prove the safety guarantees of the ABNet. We demonstrate the strength of ABNet in 2D robot obstacle avoidance, safe robot manipulation, and vision-based end-to-end autonomous driving, with results showing much better robustness and guarantees over existing models.
$k$-Submodular Interdiction Problems under Distributional Risk-Receptiveness and Robustness: Application to Machine Learning
Authors: Seonghun Park, Manish Bansal
Date: 2024-06-18 00:00:00
Tasks: feature selection

We study submodular optimization in adversarial context, applicable to machine learning problems such as feature selection using data susceptible to uncertainties and attacks. We focus on Stackelberg games between an attacker (or interdictor) and a defender where the attacker aims to minimize the defender's objective of maximizing a $k$-submodular function. We allow uncertainties arising from the success of attacks and inherent data noise, and address challenges due to incomplete knowledge of the probability distribution of random parameters. Specifically, we introduce Distributionally Robust $k$-Submodular Interdiction Problem (DRO $k$-SIP) and Distributionally Risk-Receptive $k$-Submodular Interdiction Problem (DRR $k$-SIP) along with finitely convergent exact algorithms for solving them. When solving the DRO $k$-SIP, the attacker optimizes their expected payoff with respect to the worst-case probability distribution within the ambiguity set, and thereby have robust attack strategies despite distributional ambiguity. In contrast, the DRR $k$-SIP identifies attacker strategies with the best-case probability distribution, and identifies critical vulnerabilities for the defender. The optimal values derived from both DRO $k$-SIP and DRR $k$-SIP offer a confidence interval-like range for the expected value of the defender's objective function, capturing distributional ambiguity. We conduct computational experiments on instances of feature selection and sensor placement problems, using Wisconsin breast cancer data and synthetic data, respectively.
Data Plagiarism Index: Characterizing the Privacy Risk of Data-Copying in Tabular Generative Models
Authors: Joshua Ward, Chi-Hua Wang, Guang Cheng
Date: 2024-06-18 00:00:00
Tasks: Fairness, Inference Attack, Membership Inference Attack

The promise of tabular generative models is to produce realistic synthetic data that can be shared and safely used without dangerous leakage of information from the training set. In evaluating these models, a variety of methods have been proposed to measure the tendency to copy data from the training dataset when generating a sample. However, these methods suffer from either not considering data-copying from a privacy threat perspective, not being motivated by recent results in the data-copying literature or being difficult to make compatible with the high dimensional, mixed type nature of tabular data. This paper proposes a new similarity metric and Membership Inference Attack called Data Plagiarism Index (DPI) for tabular data. We show that DPI evaluates a new intuitive definition of data-copying and characterizes the corresponding privacy risk. We show that the data-copying identified by DPI poses both privacy and fairness threats to common, high performing architectures; underscoring the necessity for more sophisticated generative modeling techniques to mitigate this issue.
Additive regularization schedule for neural architecture search
Authors: Mark Potanin, Kirill Vayser, Vadim Strijov
Date: 2024-06-18 00:00:00
Tasks: Efficient Neural Network, Neural Architecture Search

Neural network structures have a critical impact on the accuracy and stability of forecasting. Neural architecture search procedures help design an optimal neural network according to some loss function, which represents a set of quality criteria. This paper investigates the problem of neural network structure optimization. It proposes a way to construct a loss function, which contains a set of additive elements. Each element is called the regularizer. It corresponds to some part of the neural network structure and represents a criterion to optimize. The optimization procedure changes the structure in iterations. To optimize various parts of the structure, the procedure changes the set of regularizers according to some schedule. The authors propose a way to construct the additive regularization schedule. By comparing regularized models with non-regularized ones for a collection of datasets the computational experiments show that the proposed method finds efficient neural network structure and delivers accurate networks of low complexity.
Reinforcement Learning for Corporate Bond Trading: A Sell Side Perspective
Authors: Samuel Atkins, Ali Fathi, Sammy Assefa
Date: 2024-06-18 00:00:00
Tasks: reinforcement-learning, Reinforcement Learning

A corporate bond trader in a typical sell side institution such as a bank provides liquidity to the market participants by buying/selling securities and maintaining an inventory. Upon receiving a request for a buy/sell price quote (RFQ), the trader provides a quote by adding a spread over a \textit{prevalent market price}. For illiquid bonds, the market price is harder to observe, and traders often resort to available benchmark bond prices (such as MarketAxess, Bloomberg, etc.). In \cite{Bergault2023ModelingLI}, the concept of \textit{Fair Transfer Price} for an illiquid corporate bond was introduced which is derived from an infinite horizon stochastic optimal control problem (for maximizing the trader's expected P\&L, regularized by the quadratic variation). In this paper, we consider the same optimization objective, however, we approach the estimation of an optimal bid-ask spread quoting strategy in a data driven manner and show that it can be learned using Reinforcement Learning. Furthermore, we perform extensive outcome analysis to examine the reasonableness of the trained agent's behavior.
How to Compute the Probability of a Word
Authors: Tiago Pimentel, Clara Meister
Date: 2024-06-20 00:00:00
Tasks: Sentence

Language models (LMs) estimate a probability distribution over strings in a natural language; these distributions are crucial for computing perplexity and surprisal in linguistics research. While we are usually concerned with measuring these values for words, most LMs operate over subwords. Despite seemingly straightforward, accurately computing probabilities over one unit given probabilities over the other requires care. Indeed, we show here that many recent linguistic studies have been incorrectly computing these values. This paper derives the correct methods for computing word probabilities, highlighting issues when relying on language models that use beginning-of-word (bow)-marking tokenisers, e.g., the GPT family. Empirically, we show that correcting the widespread bug in probability computations affects measured outcomes in sentence comprehension and lexical optimisation analyses.
xCOMET-lite: Bridging the Gap Between Efficiency and Quality in Learned MT Evaluation Metrics
Authors: Daniil Larionov, Mikhail Seleznyov, Vasiliy Viskov, Alexander Panchenko, Steffen Eger
Date: 2024-06-20 00:00:00
Tasks: Machine Translation, Quantization

State-of-the-art trainable machine translation evaluation metrics like xCOMET achieve high correlation with human judgment but rely on large encoders (up to 10.7B parameters), making them computationally expensive and inaccessible to researchers with limited resources. To address this issue, we investigate whether the knowledge stored in these large encoders can be compressed while maintaining quality. We employ distillation, quantization, and pruning techniques to create efficient xCOMET alternatives and introduce a novel data collection pipeline for efficient black-box distillation. Our experiments show that, using quantization, xCOMET can be compressed up to three times with no quality degradation. Additionally, through distillation, we create an 278M-sized xCOMET-lite metric, which has only 2.6% of xCOMET-XXL parameters, but retains 92.1% of its quality. Besides, it surpasses strong small-scale metrics like COMET-22 and BLEURT-20 on the WMT22 metrics challenge dataset by 6.4%, despite using 50% fewer parameters. All code, dataset, and models are available online at https://github.com/NL2G/xCOMET-lite.
Unmasking Database Vulnerabilities: Zero-Knowledge Schema Inference Attacks in Text-to-SQL Systems
Authors: Đorđe Klisura, Anthony Rios
Date: 2024-06-20 00:00:00
Tasks: Language Modelling, Text to SQL, Text-To-SQL

Text-to-SQL systems empower users to interact with databases using natural language, automatically translating queries into executable SQL code. However, their reliance on database schema information for SQL generation exposes them to significant security vulnerabilities, particularly schema inference attacks that can lead to unauthorized data access or manipulation. In this paper, we introduce a novel zero-knowledge framework for reconstructing the underlying database schema of text-to-SQL models without any prior knowledge of the database. Our approach systematically probes text-to-SQL models with specially crafted questions and leverages a surrogate GPT-4 model to interpret the outputs, effectively uncovering hidden schema elements -- including tables, columns, and data types. We demonstrate that our method achieves high accuracy in reconstructing table names, with F1 scores of up to .99 for generative models and .78 for fine-tuned models, underscoring the severity of schema leakage risks. Furthermore, we propose a simple protection mechanism for generative models and empirically show its limitations in mitigating these attacks.
Investigating Mysteries of CoT-Augmented Distillation
Authors: Somin Wadhwa, Silvio Amir, Byron C. Wallace
Date: 2024-06-20 00:00:00
Tasks: Question Answering

Eliciting "chain of thought" (CoT) rationales -- sequences of token that convey a "reasoning" process -- has been shown to consistently improve LLM performance on tasks like question answering. More recent efforts have shown that such rationales can also be used for model distillation: Including CoT sequences (elicited from a large "teacher" model) in addition to target labels when fine-tuning a small student model yields (often substantial) improvements. In this work we ask: Why and how does this additional training signal help in model distillation? We perform ablations to interrogate this, and report some potentially surprising results. Specifically: (1) Placing CoT sequences after labels (rather than before) realizes consistently better downstream performance -- this means that no student "reasoning" is necessary at test time to realize gains. (2) When rationales are appended in this way, they need not be coherent reasoning sequences to yield improvements; performance increases are robust to permutations of CoT tokens, for example. In fact, (3) a small number of key tokens are sufficient to achieve improvements equivalent to those observed when full rationales are used in model distillation.