pwc-archive/papers-with-abstracts huggingface dataset:
QuickBind: A Light-Weight And Interpretable Molecular Docking Model
Authors: Wojtek Treyde, Seohyun Chris Kim, Nazim Bouatta, Mohammed AlQuraishi
Date: 2024-10-21 00:00:00
Tasks: Drug Discovery, Molecular Docking, Pose Prediction

Predicting a ligand's bound pose to a target protein is a key component of early-stage computational drug discovery. Recent developments in machine learning methods have focused on improving pose quality at the cost of model runtime. For high-throughput virtual screening applications, this exposes a capability gap that can be filled by moderately accurate but fast pose prediction. To this end, we developed QuickBind, a light-weight pose prediction algorithm. We assess QuickBind on widely used benchmarks and find that it provides an attractive trade-off between model accuracy and runtime. To facilitate virtual screening applications, we augment QuickBind with a binding affinity module and demonstrate its capabilities for multiple clinically-relevant drug targets. Finally, we investigate the mechanistic basis by which QuickBind makes predictions and find that it has learned key physicochemical properties of molecular docking, providing new insights into how machine learning models generate protein-ligand poses. By virtue of its simplicity, QuickBind can serve as both an effective virtual screening tool and a minimal test bed for exploring new model architectures and innovations. Model code and weights are available at https://github.com/aqlaboratory/QuickBind .
Evaluating the Performance of a D-Wave Quantum Annealing System for Feature Subset Selection in Software Defect Prediction
Authors: Ashis Kumar Mandal, Md Nadim, Chanchal K. Roy, Banani Roy, Kevin A. Schneider
Date: 2024-10-21 00:00:00
Tasks: Prediction

Predicting software defects early in the development process not only enhances the quality and reliability of the software but also decreases the cost of development. A wide range of machine learning techniques can be employed to create software defect prediction models, but the effectiveness and accuracy of these models are often influenced by the choice of appropriate feature subset. Since finding the optimal feature subset is computationally intensive, heuristic and metaheuristic approaches are commonly employed to identify near-optimal solutions within a reasonable time frame. Recently, the quantum computing paradigm quantum annealing (QA) has been deployed to find solutions to complex optimization problems. This opens up the possibility of addressing the feature subset selection problem with a QA machine. Although several strategies have been proposed for feature subset selection using a QA machine, little exploration has been done regarding the viability of a QA machine for feature subset selection in software defect prediction. This study investigates the potential of D-Wave QA system for this task, where we formulate a mutual information (MI)-based filter approach as an optimization problem and utilize a D-Wave Quantum Processing Unit (QPU) solver as a QA solver for feature subset selection. We evaluate the performance of this approach using multiple software defect datasets from the AEEM, JIRA, and NASA projects. We also utilize a D-Wave classical solver for comparative analysis. Our experimental results demonstrate that QA-based feature subset selection can enhance software defect prediction. Although the D-Wave QPU solver exhibits competitive prediction performance with the classical solver in software defect prediction, it significantly reduces the time required to identify the best feature subset compared to its classical counterpart.
Fair Bilevel Neural Network (FairBiNN): On Balancing fairness and accuracy via Stackelberg Equilibrium
Authors: Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, Amirarsalan Rajabi, Aida Tayebi, Ivan Garibay, Ozlem Ozmen Garibay
Date: 2024-10-21 00:00:00
Tasks: Bilevel Optimization, Fairness

The persistent challenge of bias in machine learning models necessitates robust solutions to ensure parity and equal treatment across diverse groups, particularly in classification tasks. Current methods for mitigating bias often result in information loss and an inadequate balance between accuracy and fairness. To address this, we propose a novel methodology grounded in bilevel optimization principles. Our deep learning-based approach concurrently optimizes for both accuracy and fairness objectives, and under certain assumptions, achieving proven Pareto optimal solutions while mitigating bias in the trained model. Theoretical analysis indicates that the upper bound on the loss incurred by this method is less than or equal to the loss of the Lagrangian approach, which involves adding a regularization term to the loss function. We demonstrate the efficacy of our model primarily on tabular datasets such as UCI Adult and Heritage Health. When benchmarked against state-of-the-art fairness methods, our model exhibits superior performance, advancing fairness-aware machine learning solutions and bridging the accuracy-fairness gap. The implementation of FairBiNN is available on https://github.com/yazdanimehdi/FairBiNN.
Promoting cross-modal representations to improve multimodal foundation models for physiological signals
Authors: Ching Fang, Christopher Sandino, Behrooz Mahasseni, Juri Minxha, Hadi Pouransari, Erdrin Azemi, Ali Moin, Ellen Zippi
Date: 2024-10-21 00:00:00
Tasks: Contrastive Learning

Many healthcare applications are inherently multimodal, involving several physiological signals. As sensors for these signals become more common, improving machine learning methods for multimodal healthcare data is crucial. Pretraining foundation models is a promising avenue for success. However, methods for developing foundation models in healthcare are still in early exploration and it is unclear which pretraining strategies are most effective given the diversity of physiological signals. This is partly due to challenges in multimodal health data: obtaining data across many patients is difficult and costly, there is a lot of inter-subject variability, and modalities are often heterogeneously informative across downstream tasks. Here, we explore these challenges in the PhysioNet 2018 dataset. We use a masked autoencoding objective to pretrain a multimodal model. We show that the model learns representations that can be linearly probed for a diverse set of downstream tasks. We hypothesize that cross-modal reconstruction objectives are important for successful multimodal training, as they encourage the model to integrate information across modalities. We demonstrate that modality dropout in the input space improves performance across downstream tasks. We also find that late-fusion models pretrained with contrastive learning objectives are less effective across multiple tasks. Finally, we analyze the model's representations, showing that attention weights become more cross-modal and temporally aligned with our pretraining strategy. The learned embeddings also become more distributed in terms of the modalities encoded by each unit. Overall, our work demonstrates the utility of multimodal foundation models with health data, even across diverse physiological data sources. We further argue that explicit methods for inducing cross-modality may enhance multimodal pretraining strategies.
Integrating Reinforcement Learning with Foundation Models for Autonomous Robotics: Methods and Perspectives
Authors: Angelo Moroncelli, Vishal Soni, Asad Ali Shahid, Marco Maccarini, Marco Forgione, Dario Piga, Blerina Spahiu, Loris Roveda
Date: 2024-10-21 00:00:00
Tasks: Reinforcement Learning (RL)

Foundation models (FMs), large deep learning models pre-trained on vast, unlabeled datasets, exhibit powerful capabilities in understanding complex patterns and generating sophisticated outputs. However, they often struggle to adapt to specific tasks. Reinforcement learning (RL), which allows agents to learn through interaction and feedback, offers a compelling solution. Integrating RL with FMs enables these models to achieve desired outcomes and excel at particular tasks. Additionally, RL can be enhanced by leveraging the reasoning and generalization capabilities of FMs. This synergy is revolutionizing various fields, including robotics. FMs, rich in knowledge and generalization, provide robots with valuable information, while RL facilitates learning and adaptation through real-world interactions. This survey paper comprehensively explores this exciting intersection, examining how these paradigms can be integrated to advance robotic intelligence. We analyze the use of foundation models as action planners, the development of robotics-specific foundation models, and the mutual benefits of combining FMs with RL. Furthermore, we present a taxonomy of integration approaches, including large language models, vision-language models, diffusion models, and transformer-based RL models. We also explore how RL can utilize world representations learned from FMs to enhance robotic task execution. Our survey aims to synthesize current research and highlight key challenges in robotic reasoning and control, particularly in the context of integrating FMs and RL--two rapidly evolving technologies. By doing so, we seek to spark future research and emphasize critical areas that require further investigation to enhance robotics. We provide an updated collection of papers based on our taxonomy, accessible on our open-source project website at: https://github.com/clmoro/Robotics-RL-FMs-Integration.
Federated Communication-Efficient Multi-Objective Optimization
Authors: Baris Askin, Pranay Sharma, Gauri Joshi, Carlee Joe-Wong
Date: 2024-10-21 00:00:00

We study a federated version of multi-objective optimization (MOO), where a single model is trained to optimize multiple objective functions. MOO has been extensively studied in the centralized setting but is less explored in federated or distributed settings. We propose FedCMOO, a novel communication-efficient federated multi-objective optimization (FMOO) algorithm that improves the error convergence performance of the model compared to existing approaches. Unlike prior works, the communication cost of FedCMOO does not scale with the number of objectives, as each client sends a single aggregated gradient to the central server. We provide a convergence analysis of the proposed method for smooth and non-convex objective functions under milder assumptions than in prior work. In addition, we introduce a variant of FedCMOO that allows users to specify a preference over the objectives in terms of a desired ratio of the final objective values. Through extensive experiments, we demonstrate the superiority of our proposed method over baseline approaches.
Refusal-Trained LLMs Are Easily Jailbroken As Browser Agents
Authors: Priyanshu Kumar, Elaine Lau, Saranya Vijayakumar, Tu Trinh, Scale Red Team, Elaine Chang, Vaughn Robinson, Sean Hendryx, Shuyan Zhou, Matt Fredrikson, Summer Yue, Zifan Wang
Date: 2024-10-11 00:00:00
Tasks: Chatbot, Red Teaming

For safety reasons, large language models (LLMs) are trained to refuse harmful user instructions, such as assisting dangerous activities. We study an open question in this work: does the desired safety refusal, typically enforced in chat contexts, generalize to non-chat and agentic use cases? Unlike chatbots, LLM agents equipped with general-purpose tools, such as web browsers and mobile devices, can directly influence the real world, making it even more crucial to refuse harmful instructions. In this work, we primarily focus on red-teaming browser agents, LLMs that manipulate information via web browsers. To this end, we introduce Browser Agent Red teaming Toolkit (BrowserART), a comprehensive test suite designed specifically for red-teaming browser agents. BrowserART is consist of 100 diverse browser-related harmful behaviors (including original behaviors and ones sourced from HarmBench [Mazeika et al., 2024] and AirBench 2024 [Zeng et al., 2024b]) across both synthetic and real websites. Our empirical study on state-of-the-art browser agents reveals that, while the backbone LLM refuses harmful instructions as a chatbot, the corresponding agent does not. Moreover, attack methods designed to jailbreak refusal-trained LLMs in the chat settings transfer effectively to browser agents. With human rewrites, GPT-4o and o1-preview-based browser agents attempted 98 and 63 harmful behaviors (out of 100), respectively. We publicly release BrowserART and call on LLM developers, policymakers, and agent developers to collaborate on improving agent safety
LEGO-Learn: Label-Efficient Graph Open-Set Learning
Authors: Haoyan Xu, Kay Liu, Zhengtao Yao, Philip S. Yu, Mengyuan Li, Kaize Ding, Yue Zhao
Date: 2024-10-21 00:00:00
Tasks: Node Classification, Open Set Learning, Out of Distribution (OOD) Detection

How can we train graph-based models to recognize unseen classes while keeping labeling costs low? Graph open-set learning (GOL) and out-of-distribution (OOD) detection aim to address this challenge by training models that can accurately classify known, in-distribution (ID) classes while identifying and handling previously unseen classes during inference. It is critical for high-stakes, real-world applications where models frequently encounter unexpected data, including finance, security, and healthcare. However, current GOL methods assume access to many labeled ID samples, which is unrealistic for large-scale graphs due to high annotation costs. In this paper, we propose LEGO-Learn (Label-Efficient Graph Open-set Learning), a novel framework that tackles open-set node classification on graphs within a given label budget by selecting the most informative ID nodes. LEGO-Learn employs a GNN-based filter to identify and exclude potential OOD nodes and then select highly informative ID nodes for labeling using the K-Medoids algorithm. To prevent the filter from discarding valuable ID examples, we introduce a classifier that differentiates between the C known ID classes and an additional class representing OOD nodes (hence, a C+1 classifier). This classifier uses a weighted cross-entropy loss to balance the removal of OOD nodes while retaining informative ID nodes. Experimental results on four real-world datasets demonstrate that LEGO-Learn significantly outperforms leading methods, with up to a 6.62% improvement in ID classification accuracy and a 7.49% increase in AUROC for OOD detection.
Large Language Models in Computer Science Education: A Systematic Literature Review
Authors: Nishat Raihan, Mohammed Latif Siddiq, Joanna C. S. Santos, Marcos Zampieri
Date: 2024-10-21 00:00:00
Tasks: Code Generation, Systematic Literature Review, Text Generation

Large language models (LLMs) are becoming increasingly better at a wide range of Natural Language Processing tasks (NLP), such as text generation and understanding. Recently, these models have extended their capabilities to coding tasks, bridging the gap between natural languages (NL) and programming languages (PL). Foundational models such as the Generative Pre-trained Transformer (GPT) and LLaMA series have set strong baseline performances in various NL and PL tasks. Additionally, several models have been fine-tuned specifically for code generation, showing significant improvements in code-related applications. Both foundational and fine-tuned models are increasingly used in education, helping students write, debug, and understand code. We present a comprehensive systematic literature review to examine the impact of LLMs in computer science and computer engineering education. We analyze their effectiveness in enhancing the learning experience, supporting personalized education, and aiding educators in curriculum development. We address five research questions to uncover insights into how LLMs contribute to educational outcomes, identify challenges, and suggest directions for future research.
LEADS: Lightweight Embedded Assisted Driving System
Authors: Tianhao Fu, Querobin Mascarenhas, Andrew Forti
Date: 2024-10-23 00:00:00

With the rapid development of electric vehicles, formula races that face high school and university students have become more popular than ever as the threshold for design and manufacturing has been lowered. In many cases, we see teams inspired by or directly using toolkits and technologies inherited from standardized commercial vehicles. These architectures are usually overly complicated for amateur applications like the races. In order to improve the efficiency and simplify the development of instrumentation, control, and analysis systems, we propose LEADS (Lightweight Embedded Assisted Driving System), a dedicated solution for such scenarios.
Robust and Minimally Invasive Watermarking for EaaS
Authors: Zongqi Wang, Baoyuan Wu, Jingyuan Deng, Yujiu Yang
Date: 2024-10-23 00:00:00
Tasks: Model extraction

Embeddings as a Service (EaaS) is emerging as a crucial role in AI applications. Unfortunately, EaaS is vulnerable to model extraction attacks, highlighting the urgent need for copyright protection. Although some preliminary works propose applying embedding watermarks to protect EaaS, recent research reveals that these watermarks can be easily removed. Hence, it is crucial to inject robust watermarks resistant to watermark removal attacks. Existing watermarking methods typically inject a target embedding into embeddings through linear interpolation when the text contains triggers. However, this mechanism results in each watermarked embedding having the same component, which makes the watermark easy to identify and eliminate. Motivated by this, in this paper, we propose a novel embedding-specific watermarking (ESpeW) mechanism to offer robust copyright protection for EaaS. Our approach involves injecting unique, yet readily identifiable watermarks into each embedding. Watermarks inserted by ESpeW are designed to maintain a significant distance from one another and to avoid sharing common components, thus making it significantly more challenging to remove the watermarks. Moreover, ESpeW is minimally invasive, as it reduces the impact on embeddings to less than 1\%, setting a new milestone in watermarking for EaaS. Extensive experiments on four popular datasets demonstrate that ESpeW can even watermark successfully against a highly aggressive removal strategy without sacrificing the quality of embeddings.
ALTA: Compiler-Based Analysis of Transformers
Authors: Peter Shaw, James Cohan, Jacob Eisenstein, Kenton Lee, Jonathan Berant, Kristina Toutanova
Date: 2024-10-23 00:00:00

We propose a new programming language called ALTA and a compiler that can map ALTA programs to Transformer weights. ALTA is inspired by RASP, a language proposed by Weiss et al. (2021), and Tracr (Lindner et al., 2023), a compiler from RASP programs to Transformer weights. ALTA complements and extends this prior work, offering the ability to express loops and to compile programs to Universal Transformers, among other advantages. ALTA allows us to constructively show how Transformers can represent length-invariant algorithms for computing parity and addition, as well as a solution to the SCAN benchmark of compositional generalization tasks, without requiring intermediate scratchpad decoding steps. We also propose tools to analyze cases where the expressibility of an algorithm is established, but end-to-end training on a given training set fails to induce behavior consistent with the desired algorithm. To this end, we explore training from ALTA execution traces as a more fine-grained supervision signal. This enables additional experiments and theoretical analyses relating the learnability of various algorithms to data availability and modeling decisions, such as positional encodings. We make the ALTA framework -- language specification, symbolic interpreter, and weight compiler -- available to the community to enable further applications and insights.
Leveraging Skills from Unlabeled Prior Data for Efficient Online Exploration
Authors: Max Wilcoxson, Qiyang Li, Kevin Frans, Sergey Levine
Date: 2024-10-23 00:00:00
Tasks: Efficient Exploration, Reinforcement Learning (RL)

Unsupervised pretraining has been transformative in many supervised domains. However, applying such ideas to reinforcement learning (RL) presents a unique challenge in that fine-tuning does not involve mimicking task-specific data, but rather exploring and locating the solution through iterative self-improvement. In this work, we study how unlabeled prior trajectory data can be leveraged to learn efficient exploration strategies. While prior data can be used to pretrain a set of low-level skills, or as additional off-policy data for online RL, it has been unclear how to combine these ideas effectively for online exploration. Our method SUPE (Skills from Unlabeled Prior data for Exploration) demonstrates that a careful combination of these ideas compounds their benefits. Our method first extracts low-level skills using a variational autoencoder (VAE), and then pseudo-relabels unlabeled trajectories using an optimistic reward model, transforming prior data into high-level, task-relevant examples. Finally, SUPE uses these transformed examples as additional off-policy data for online RL to learn a high-level policy that composes pretrained low-level skills to explore efficiently. We empirically show that SUPE reliably outperforms prior strategies, successfully solving a suite of long-horizon, sparse-reward tasks. Code: https://github.com/rail-berkeley/supe.
TP-Eval: Tap Multimodal LLMs' Potential in Evaluation by Customizing Prompts
Authors: Yuxuan Xie, Tianhua Li, Wenqi Shao, Kaipeng Zhang
Date: 2024-10-23 00:00:00

Recently, multimodal large language models (MLLMs) have received much attention for their impressive capabilities. The evaluation of MLLMs is becoming critical to analyzing attributes of MLLMs and providing valuable insights. However, current benchmarks overlook the problem of prompt sensitivity - minor prompt variations may lead to significant performance fluctuations. Thus, inappropriate prompts may obscure the models' capabilities, underestimating the models' performance. Moreover, different models have different preferences for different prompts, and thus, using the same prompt for all models will cause evaluation bias. This paper analyzes this deficiency in existing benchmarks and further introduces a new evaluation framework named TP-Eval, which introduces a prompt customization method to reduce evaluation biases and tap models' potential. TP-Eval will rewrite the original prompts to different customized prompts for different models. In particular, we propose some well-designed modules for prompt customization tailored to the scenario of MLLM evaluation. Extensive experiments demonstrate the effectiveness of our approach to uncovering models' capabilities, and TP-Eval should benefit the community in developing more comprehensive and convincing MLLM evaluation benchmarks.