pwc-archive/papers-with-abstracts huggingface dataset:
Decomposed Direct Preference Optimization for Structure-Based Drug Design
Authors: Xiwei Cheng, Xiangxin Zhou, Yuwei Yang, Yu Bao, Quanquan Gu
Date: 2024-07-19 00:00:00
Tasks: Drug Design

Diffusion models have achieved promising results for Structure-Based Drug Design (SBDD). Nevertheless, high-quality protein subpocket and ligand data are relatively scarce, which hinders the models' generation capabilities. Recently, Direct Preference Optimization (DPO) has emerged as a pivotal tool for aligning generative models with human preferences. In this paper, we propose DecompDPO, a structure-based optimization method aligns diffusion models with pharmaceutical needs using multi-granularity preference pairs. DecompDPO introduces decomposition into the optimization objectives and obtains preference pairs at the molecule or decomposed substructure level based on each objective's decomposability. Additionally, DecompDPO introduces a physics-informed energy term to ensure reasonable molecular conformations in the optimization results. Notably, DecompDPO can be effectively used for two main purposes: (1) fine-tuning pretrained diffusion models for molecule generation across various protein families, and (2) molecular optimization given a specific protein subpocket after generation. Extensive experiments on the CrossDocked2020 benchmark show that DecompDPO significantly improves model performance, achieving up to 95.2% Med. High Affinity and a 36.2% success rate for molecule generation, and 100% Med. High Affinity and a 52.1% success rate for molecular optimization.
Byzantine-tolerant distributed learning of finite mixture models
Authors: Qiong Zhang, Yan Shuo Tan, Jiahua Chen
Date: 2024-07-19 00:00:00

Traditional statistical methods need to be updated to work with modern distributed data storage paradigms. A common approach is the split-and-conquer framework, which involves learning models on local machines and averaging their parameter estimates. However, this does not work for the important problem of learning finite mixture models, because subpopulation indices on each local machine may be arbitrarily permuted (the "label switching problem"). Zhang and Chen (2022) proposed Mixture Reduction (MR) to address this issue, but MR remains vulnerable to Byzantine failure, whereby a fraction of local machines may transmit arbitrarily erroneous information. This paper introduces Distance Filtered Mixture Reduction (DFMR), a Byzantine tolerant adaptation of MR that is both computationally efficient and statistically sound. DFMR leverages the densities of local estimates to construct a robust filtering mechanism. By analysing the pairwise L2 distances between local estimates, DFMR identifies and removes severely corrupted local estimates while retaining the majority of uncorrupted ones. We provide theoretical justification for DFMR, proving its optimal convergence rate and asymptotic equivalence to the global maximum likelihood estimate under standard assumptions. Numerical experiments on simulated and real-world data validate the effectiveness of DFMR in achieving robust and accurate aggregation in the presence of Byzantine failure.
Truthfulness of Calibration Measures
Authors: Nika Haghtalab, Mingda Qiao, Kunhe Yang, Eric Zhao
Date: 2024-07-19 00:00:00
Tasks: Prediction

We initiate the study of the truthfulness of calibration measures in sequential prediction. A calibration measure is said to be truthful if the forecaster (approximately) minimizes the expected penalty by predicting the conditional expectation of the next outcome, given the prior distribution of outcomes. Truthfulness is an important property of calibration measures, ensuring that the forecaster is not incentivized to exploit the system with deliberate poor forecasts. This makes it an essential desideratum for calibration measures, alongside typical requirements, such as soundness and completeness. We conduct a taxonomy of existing calibration measures and their truthfulness. Perhaps surprisingly, we find that all of them are far from being truthful. That is, under existing calibration measures, there are simple distributions on which a polylogarithmic (or even zero) penalty is achievable, while truthful prediction leads to a polynomial penalty. Our main contribution is the introduction of a new calibration measure termed the Subsampled Smooth Calibration Error (SSCE) under which truthful prediction is optimal up to a constant multiplicative factor.
A Unified Confidence Sequence for Generalized Linear Models, with Applications to Bandits
Authors: Junghyun Lee, Se-Young Yun, Kwang-Sung Jun
Date: 2024-07-19 00:00:00
Tasks: LEMMA

We present a unified likelihood ratio-based confidence sequence (CS) for any (self-concordant) generalized linear model (GLM) that is guaranteed to be convex and numerically tight. We show that this is on par or improves upon known CSs for various GLMs, including Gaussian, Bernoulli, and Poisson. In particular, for the first time, our CS for Bernoulli has a $\mathrm{poly}(S)$-free radius where $S$ is the norm of the unknown parameter. Our first technical novelty is its derivation, which utilizes a time-uniform PAC-Bayesian bound with a uniform prior/posterior, despite the latter being a rather unpopular choice for deriving CSs. As a direct application of our new CS, we propose a simple and natural optimistic algorithm called OFUGLB, applicable to any generalized linear bandits (GLB; Filippi et al. (2010)). Our analysis shows that the celebrated optimistic approach simultaneously attains state-of-the-art regrets for various self-concordant (not necessarily bounded) GLBs, and even $\mathrm{poly}(S)$-free for bounded GLBs, including logistic bandits. The regret analysis, our second technical novelty, follows from combining our new CS with a new proof technique that completely avoids the previously widely used self-concordant control lemma (Faury et al., 2020, Lemma 9). Numerically, OFUGLB outperforms or is at par with prior algorithms for logistic bandits.
The Group Robustness is in the Details: Revisiting Finetuning under Spurious Correlations
Authors: Tyler LaBonte, John C. Hill, Xinchen Zhang, Vidya Muthukumar, Abhishek Kumar
Date: 2024-07-19 00:00:00

Modern machine learning models are prone to over-reliance on spurious correlations, which can often lead to poor performance on minority groups. In this paper, we identify surprising and nuanced behavior of finetuned models on worst-group accuracy via comprehensive experiments on four well-established benchmarks across vision and language tasks. We first show that the commonly used class-balancing techniques of mini-batch upsampling and loss upweighting can induce a decrease in worst-group accuracy (WGA) with training epochs, leading to performance no better than without class-balancing. While in some scenarios, removing data to create a class-balanced subset is more effective, we show this depends on group structure and propose a mixture method which can outperform both techniques. Next, we show that scaling pretrained models is generally beneficial for worst-group accuracy, but only in conjunction with appropriate class-balancing. Finally, we identify spectral imbalance in finetuning features as a potential source of group disparities -- minority group covariance matrices incur a larger spectral norm than majority groups once conditioned on the classes. Our results show more nuanced interactions of modern finetuned models with group robustness than was previously known. Our code is available at https://github.com/tmlabonte/revisiting-finetuning.
Neural topology optimization: the good, the bad, and the ugly
Authors: Suryanarayanan Manoj Sanu, Alejandro M. Aragon, Miguel A. Bessa
Date: 2024-07-19 00:00:00
Tasks: GPU, Misconceptions

Neural networks (NNs) hold great promise for advancing inverse design via topology optimization (TO), yet misconceptions about their application persist. This article focuses on neural topology optimization (neural TO), which leverages NNs to reparameterize the decision space and reshape the optimization landscape. While the method is still in its infancy, our analysis tools reveal critical insights into the NNs' impact on the optimization process. We demonstrate that the choice of NN architecture significantly influences the objective landscape and the optimizer's path to an optimum. Notably, NNs introduce non-convexities even in otherwise convex landscapes, potentially delaying convergence in convex problems but enhancing exploration for non-convex problems. This analysis lays the groundwork for future advancements by highlighting: 1) the potential of neural TO for non-convex problems and dedicated GPU hardware (the "good"), 2) the limitations in smooth landscapes (the "bad"), and 3) the complex challenge of selecting optimal NN architectures and hyperparameters for superior performance (the "ugly").
BRSR-OpGAN: Blind Radar Signal Restoration using Operational Generative Adversarial Network
Authors: Muhammad Uzair Zahid, Serkan Kiranyaz, Alper Yildirim, Moncef Gabbouj
Date: 2024-07-18 00:00:00
Tasks: Denoising, Generative Adversarial Network

Objective: Many studies on radar signal restoration in the literature focus on isolated restoration problems, such as denoising over a certain type of noise, while ignoring other types of artifacts. Additionally, these approaches usually assume a noisy environment with a limited set of fixed signal-to-noise ratio (SNR) levels. However, real-world radar signals are often corrupted by a blend of artifacts, including but not limited to unwanted echo, sensor noise, intentional jamming, and interference, each of which can vary in type, severity, and duration. This study introduces Blind Radar Signal Restoration using an Operational Generative Adversarial Network (BRSR-OpGAN), which uses a dual domain loss in the temporal and spectral domains. This approach is designed to improve the quality of radar signals, regardless of the diversity and intensity of the corruption. Methods: The BRSR-OpGAN utilizes 1D Operational GANs, which use a generative neuron model specifically optimized for blind restoration of corrupted radar signals. This approach leverages GANs' flexibility to adapt dynamically to a wide range of artifact characteristics. Results: The proposed approach has been extensively evaluated using a well-established baseline and a newly curated extended dataset called the Blind Radar Signal Restoration (BRSR) dataset. This dataset was designed to simulate real-world conditions and includes a variety of artifacts, each varying in severity. The evaluation shows an average SNR improvement over 15.1 dB and 14.3 dB for the baseline and BRSR datasets, respectively. Finally, even on resource-constrained platforms, the proposed approach can be applied in real-time.
Event-Triggered Reinforcement Learning Based Joint Resource Allocation for Ultra-Reliable Low-Latency V2X Communications
Authors: Nasir Khan, Sinem Coleri
Date: 2024-07-18 00:00:00
Tasks: Deep Reinforcement Learning

Future 6G-enabled vehicular networks face the challenge of ensuring ultra-reliable low-latency communication (URLLC) for delivering safety-critical information in a timely manner. Existing resource allocation schemes for vehicle-to-everything (V2X) communication systems primarily rely on traditional optimization-based algorithms. However, these methods often fail to guarantee the strict reliability and latency requirements of URLLC applications in dynamic vehicular environments due to the high complexity and communication overhead of the solution methodologies. This paper proposes a novel deep reinforcement learning (DRL) based framework for the joint power and block length allocation to minimize the worst-case decoding-error probability in the finite block length (FBL) regime for a URLLC-based downlink V2X communication system. The problem is formulated as a non-convex mixed-integer nonlinear programming problem (MINLP). Initially, an algorithm grounded in optimization theory is developed based on deriving the joint convexity of the decoding error probability in the block length and transmit power variables within the region of interest. Subsequently, an efficient event-triggered DRL-based algorithm is proposed to solve the joint optimization problem. Incorporating event-triggered learning into the DRL framework enables assessing whether to initiate the DRL process, thereby reducing the number of DRL process executions while maintaining reasonable reliability performance. Simulation results demonstrate that the proposed event-triggered DRL scheme can achieve 95% of the performance of the joint optimization scheme while reducing the DRL executions by up to 24% for different network settings.
Unmasking Social Bots: How Confident Are We?
Authors: James Giroux, Ariyarathne Gangani, Alexander C. Nwala, Cristiano Fanelli
Date: 2024-07-18 00:00:00
Tasks: Decision Making

Social bots remain a major vector for spreading disinformation on social media and a menace to the public. Despite the progress made in developing multiple sophisticated social bot detection algorithms and tools, bot detection remains a challenging, unsolved problem that is fraught with uncertainty due to the heterogeneity of bot behaviors, training data, and detection algorithms. Detection models often disagree on whether to label the same account as bot or human-controlled. However, they do not provide any measure of uncertainty to indicate how much we should trust their results. We propose to address both bot detection and the quantification of uncertainty at the account level - a novel feature of this research. This dual focus is crucial as it allows us to leverage additional information related to the quantified uncertainty of each prediction, thereby enhancing decision-making and improving the reliability of bot classifications. Specifically, our approach facilitates targeted interventions for bots when predictions are made with high confidence and suggests caution (e.g., gathering more data) when predictions are uncertain.
EggNet: An Evolving Graph-based Graph Attention Network for Particle Track Reconstruction
Authors: Paolo Calafiura, Jay Chan, Loic Delabrouille, Brandon Wang
Date: 2024-07-18 00:00:00
Tasks: Edge Classification, Graph Attention

Track reconstruction is a crucial task in particle experiments and is traditionally very computationally expensive due to its combinatorial nature. Recently, graph neural networks (GNNs) have emerged as a promising approach that can improve scalability. Most of these GNN-based methods, including the edge classification (EC) and the object condensation (OC) approach, require an input graph that needs to be constructed beforehand. In this work, we consider a one-shot OC approach that reconstructs particle tracks directly from a set of hits (point cloud) by recursively applying graph attention networks with an evolving graph structure. This approach iteratively updates the graphs and can better facilitate the message passing across each graph. Preliminary studies on the TrackML dataset show better track performance compared to the methods that require a fixed input graph.
Crafting Efficient Fine-Tuning Strategies for Large Language Models
Authors: Michael Oliver, Guan Wang
Date: 2024-07-18 00:00:00
Tasks: Attribute, Attribute Extraction, Hyperparameter Optimization

This paper addresses the challenges of efficiently fine-tuning large language models (LLMs) by exploring data efficiency and hyperparameter optimization. We investigate the minimum data required for effective fine-tuning and propose a novel hyperparameter optimization method that leverages early-stage model performance. Our experiments demonstrate that fine-tuning with as few as 200 samples can improve model accuracy from 70\% to 88\% in a product attribute extraction task. We identify a saturation point of approximately 6,500 samples, beyond which additional data yields diminishing returns. Our proposed bayesian hyperparameter optimization method, which evaluates models at 20\% of total training time, correlates strongly with final model performance, with 4 out of 5 top early-stage models remaining in the top 5 at completion. This approach led to a 2\% improvement in accuracy over baseline models when evaluated on an independent test set. These findings offer actionable insights for practitioners, potentially reducing computational load and dependency on extensive datasets while enhancing overall performance of fine-tuned LLMs.
Data-Algorithm-Architecture Co-Optimization for Fair Neural Networks on Skin Lesion Dataset
Authors: Yi Sheng, Junhuan Yang, Jinyang Li, James Alaina, Xiaowei Xu, Yiyu Shi, Jingtong Hu, Weiwen Jiang, Lei Yang
Date: 2024-07-18 00:00:00
Tasks: AutoML, Data Augmentation, Fairness, Neural Architecture Search

As Artificial Intelligence (AI) increasingly integrates into our daily lives, fairness has emerged as a critical concern, particularly in medical AI, where datasets often reflect inherent biases due to social factors like the underrepresentation of marginalized communities and socioeconomic barriers to data collection. Traditional approaches to mitigating these biases have focused on data augmentation and the development of fairness-aware training algorithms. However, this paper argues that the architecture of neural networks, a core component of Machine Learning (ML), plays a crucial role in ensuring fairness. We demonstrate that addressing fairness effectively requires a holistic approach that simultaneously considers data, algorithms, and architecture. Utilizing Automated ML (AutoML) technology, specifically Neural Architecture Search (NAS), we introduce a novel framework, BiaslessNAS, designed to achieve fair outcomes in analyzing skin lesion datasets. BiaslessNAS incorporates fairness considerations at every stage of the NAS process, leading to the identification of neural networks that are not only more accurate but also significantly fairer. Our experiments show that BiaslessNAS achieves a 2.55% increase in accuracy and a 65.50% improvement in fairness compared to traditional NAS methods, underscoring the importance of integrating fairness into neural network architecture for better outcomes in medical AI applications.
Attention in SRAM on Tenstorrent Grayskull
Authors: Moritz Thüning
Date: 2024-07-18 00:00:00
Tasks: CPU, GPU

When implementations of the Transformer's self-attention layer utilize SRAM instead of DRAM, they can achieve significant speedups. The Tenstorrent Grayskull architecture provides a large SRAM, distributed across a grid of cores. This work presents a fused kernel for Grayskull, that exclusively utilizes its large SRAM by combining matrix multiplication, attention score scaling and Softmax operations. Additionally, a dedicated Softmax kernel utilizing the SRAM and a CPU implementation serving as a baseline are presented. The Softmax operation consumes most of the runtime in the computation of attention weights from queries and keys on Grayskull. The speedup of the dedicated Softmax kernel compared to the CPU implementation is up to $10 \times$, and the Softmax implementation inside the fused kernel is approximately $1.8 \times$ faster than the dedicated Softmax kernel. The time and memory complexity of all implementations is quadratic in sequence length. Currently, the Grayskull e150 is approximately $30 \times$ cheaper for the general public than an Nvidia H100 PCIe (a state-of-the-art GPU) and offers approximately $1.5 \times$ more SRAM.
Privacy-preserving gradient-based fair federated learning
Authors: Janis Adamek, Moritz Schulze Darup
Date: 2024-07-18 00:00:00
Tasks: Collaborative Fairness, Fairness, Federated Learning, Privacy Preserving

Federated learning (FL) schemes allow multiple participants to collaboratively train neural networks without the need to directly share the underlying data.However, in early schemes, all participants eventually obtain the same model. Moreover, the aggregation is typically carried out by a third party, who obtains combined gradients or weights, which may reveal the model. These downsides underscore the demand for fair and privacy-preserving FL schemes. Here, collaborative fairness asks for individual model quality depending on the individual data contribution. Privacy is demanded with respect to any kind of data outsourced to the third party. Now, there already exist some approaches aiming for either fair or privacy-preserving FL and a few works even address both features. In our paper, we build upon these seminal works and present a novel, fair and privacy-preserving FL scheme. Our approach, which mainly relies on homomorphic encryption, stands out for exclusively using local gradients. This increases the usability in comparison to state-of-the-art approaches and thereby opens the door to applications in control.
Optimal high-precision shadow estimation
Authors: Sitan Chen, Jerry Li, Allen Liu
Date: 2024-07-18 00:00:00
Tasks: Dimensionality Reduction

We give the first tight sample complexity bounds for shadow tomography and classical shadows in the regime where the target error is below some sufficiently small inverse polynomial in the dimension of the Hilbert space. Formally we give a protocol that, given any $m\in\mathbb{N}$ and $\epsilon \le O(d^{-12})$, measures $O(\log(m)/\epsilon^2)$ copies of an unknown mixed state $\rho\in\mathbb{C}^{d\times d}$ and outputs a classical description of $\rho$ which can then be used to estimate any collection of $m$ observables to within additive accuracy $\epsilon$. Previously, even for the simpler task of shadow tomography -- where the $m$ observables are known in advance -- the best known rates either scaled benignly but suboptimally in all of $m, d, \epsilon$, or scaled optimally in $\epsilon, m$ but had additional polynomial factors in $d$ for general observables. Intriguingly, we also show via dimensionality reduction, that we can rescale $\epsilon$ and $d$ to reduce to the regime where $\epsilon \le O(d^{-1/2})$. Our algorithm draws upon representation-theoretic tools recently developed in the context of full state tomography.
Quantum Natural Stochastic Pairwise Coordinate Descent
Authors: Mohammad Aamir Sohail, Mohsen Heidari, S. Sandeep Pradhan
Date: 2024-07-18 00:00:00
Tasks: Computational Efficiency, Quantum Machine Learning

Variational quantum algorithms, optimized using gradient-based methods, often exhibit sub-optimal convergence performance due to their dependence on Euclidean geometry. Quantum natural gradient descent (QNGD) is a more efficient method that incorporates the geometry of the state space via a quantum information metric. However, QNGD is computationally intensive and suffers from high sample complexity. In this work, we formulate a novel quantum information metric and construct an unbiased estimator for this metric using single-shot measurements. We develop a quantum optimization algorithm that leverages the geometry of the state space via this estimator while avoiding full-state tomography, as in conventional techniques. We provide the convergence analysis of the algorithm under mild conditions. Furthermore, we provide experimental results that demonstrate the better sample complexity and faster convergence of our algorithm compared to the state-of-the-art approaches. Our results illustrate the algorithm's ability to avoid saddle points and local minima.