pwc-archive/papers-with-abstracts huggingface dataset:
A Hierarchical Training Paradigm for Antibody Structure-sequence Co-design
Date: 2023-10-30 00:00:00
Proceeding: NeurIPS 2023 11
Tasks: Specificity

Therapeutic antibodies are an essential and rapidly expanding drug modality. The binding specificity between antibodies and antigens is decided by complementarity-determining regions (CDRs) at the tips of these Y-shaped proteins. In this paper, we propose a hierarchical training paradigm (HTP) for the antibody sequence-structure co-design. HTP consists of four levels of training stages, each corresponding to a specific protein modality within a particular protein domain. Through carefully crafted tasks in different stages, HTP seamlessly and effectively integrates geometric graph neural networks (GNNs) with large-scale protein language models to excavate evolutionary information from not only geometric structures but also vast antibody and non-antibody sequence databases, which determines ligand binding pose and strength. Empirical experiments show that HTP sets the new state-of-the-art performance in the co-design problem as well as the fix-backbone design. Our research offers a hopeful path to unleash the potential of deep generative architectures and seeks to illuminate the way forward for the antibody sequence and structure co-design challenge.
Optimal Transport Model Distributional Robustness
Authors: Van-Anh Nguyen, Trung Le, Anh Tuan Bui, Thanh-Toan Do, Dinh Phung
Date: 2023-06-07 00:00:00
Proceeding: NeurIPS 2023 11
Tasks: model

Distributional robustness is a promising framework for training deep learning models that are less vulnerable to adversarial examples and data distribution shifts. Previous works have mainly focused on exploiting distributional robustness in the data space. In this work, we explore an optimal transport-based distributional robustness framework in model spaces. Specifically, we examine a model distribution within a Wasserstein ball centered on a given model distribution that maximizes the loss. We have developed theories that enable us to learn the optimal robust center model distribution. Interestingly, our developed theories allow us to flexibly incorporate the concept of sharpness awareness into training, whether it's a single model, ensemble models, or Bayesian Neural Networks, by considering specific forms of the center model distribution. These forms include a Dirac delta distribution over a single model, a uniform distribution over several models, and a general Bayesian Neural Network. Furthermore, we demonstrate that Sharpness-Aware Minimization (SAM) is a specific case of our framework when using a Dirac delta distribution over a single model, while our framework can be seen as a probabilistic extension of SAM. To validate the effectiveness of our framework in the aforementioned settings, we conducted extensive experiments, and the results reveal remarkable improvements compared to the baselines.
Evaluating the Robustness of Interpretability Methods through Explanation Invariance and Equivariance
Authors: Jonathan Crabbé, Mihaela van der Schaar
Date: 2023-04-13 00:00:00
Proceeding: NeurIPS 2023 11

Interpretability methods are valuable only if their explanations faithfully describe the explained model. In this work, we consider neural networks whose predictions are invariant under a specific symmetry group. This includes popular architectures, ranging from convolutional to graph neural networks. Any explanation that faithfully explains this type of model needs to be in agreement with this invariance property. We formalize this intuition through the notion of explanation invariance and equivariance by leveraging the formalism from geometric deep learning. Through this rigorous formalism, we derive (1) two metrics to measure the robustness of any interpretability method with respect to the model symmetry group; (2) theoretical robustness guarantees for some popular interpretability methods and (3) a systematic approach to increase the invariance of any interpretability method with respect to a symmetry group. By empirically measuring our metrics for explanations of models associated with various modalities and symmetry groups, we derive a set of 5 guidelines to allow users and developers of interpretability methods to produce robust explanations.
Polarized Online Discourse on Abortion: Frames and Hostile Expressions among Liberals and Conservatives
Authors: Ashwin Rao, Rong-Ching Chang, Qiankun Zhong, Kristina Lerman, Magdalena Wojcieszak
Date: 2023-11-28 00:00:00

Abortion has been one of the most divisive issues in the United States. Yet, missing is comprehensive longitudinal evidence on how political divides on abortion are reflected in public discourse over time, on a national scale, and in response to key events before and after the overturn of Roe v Wade. We analyze a corpus of over 3.5M tweets related to abortion over the span of one year (January 2022 to January 2023) from over 1.1M users. We estimate users' ideology and rely on state-of-the-art transformer-based classifiers to identify expressions of hostility and extract five prominent frames surrounding abortion. We use those data to examine (a) how prevalent were expressions of hostility (i.e., anger, toxic speech, insults, obscenities, and hate speech), (b) what frames liberals and conservatives used to articulate their positions on abortion, and (c) the prevalence of hostile expressions in liberals and conservative discussions of these frames. We show that liberals and conservatives largely mirrored each other's use of hostile expressions: as liberals used more hostile rhetoric, so did conservatives, especially in response to key events. In addition, the two groups used distinct frames and discussed them in vastly distinct contexts, suggesting that liberals and conservatives have differing perspectives on abortion. Lastly, frames favored by one side provoked hostile reactions from the other: liberals use more hostile expressions when addressing religion, fetal personhood, and exceptions to abortion bans, whereas conservatives use more hostile language when addressing bodily autonomy and women's health. This signals disrespect and derogation, which may further preclude understanding and exacerbate polarization.
DIN-SQL: Decomposed In-Context Learning of Text-to-SQL with Self-Correction
Authors: Mohammadreza Pourreza, Davood Rafiei
Date: 2023-04-21 00:00:00
Proceeding: NeurIPS 2023 11
Tasks: In-Context Learning, Text to SQL, Text-To-SQL

There is currently a significant gap between the performance of fine-tuned models and prompting approaches using Large Language Models (LLMs) on the challenging task of text-to-SQL, as evaluated on datasets such as Spider. To improve the performance of LLMs in the reasoning process, we study how decomposing the task into smaller sub-tasks can be effective. In particular, we show that breaking down the generation problem into sub-problems and feeding the solutions of those sub-problems into LLMs can be an effective approach for significantly improving their performance. Our experiments with three LLMs show that this approach consistently improves their simple few-shot performance by roughly 10%, pushing the accuracy of LLMs towards SOTA or surpassing it. On the holdout test set of Spider, the SOTA, in terms of execution accuracy, was 79.9 and the new SOTA at the time of this writing using our approach is 85.3. Our approach with in-context learning beats many heavily fine-tuned models by at least 5%. Additionally, when evaluated on the BIRD benchmark, our approach achieved an execution accuracy of 55.9%, setting a new SOTA on its holdout test set.
Onedata4Sci: Life science data management solution based on Onedata
Authors: Tomáš Svoboda, Tomáš Raček, Josef Handl, Jozef Sabo, Adrián Rošinec, Łukasz Opioła, Wojciech Jesionek, Milan Ešner, Markéta Pernisová, Natallia Madzia Valasevich, Aleš Křenek, Radka Svobodová
Date: 2023-11-28 00:00:00
Tasks: Management

Life-science experimental methods generate vast and ever-increasing volumes of data, which provide highly valuable research resources. However, management of these data is nontrivial and applicable software solutions are currently subject to intensive development. The solutions mainly fall into one of the two groups: general data management systems (e.g. Onedata, iRODS, B2SHARE, CERNBox) or very specialised data management solutions (e.g. solutions for biomolecular simulation data, biological imaging data, genomic data). To bridge this gap between them, we provide Onedata4Sci, a prototype data management solution, which is focused on the management of life science data and covers four key steps of the data life cycle, i.e. data acquisition, user access, computational processing and archiving. Onedata4Sci is based on the Onedata data management system. It is written in Python, fully containerised, with the support for processing the stored data in Kubernetes. The applicability of Onedata4Sci is shown in three distinct use cases -- plant imaging data, cellular imaging data, and cryo-electron microscopy data. Despite the use cases covering very different types of data and user patterns, Onedata4Sci demonstrated an ability to successfully handle all these conditions. Complete source codes of Onedata4Sci are available on GitHub (https://github.com/CERIT-SC/onedata4sci), and its documentation and manual for installation are also provided.
Leveraging Artificial Intelligence Technology for Mapping Research to Sustainable Development Goals: A Case Study
Authors: Hui Yin, Amir Aryani, Gavin Lambert, Marcus White, Luis Salvador-Carulla, Shazia Sadiq, Elvira Sojli, Jennifer Boddy, Greg Murray, Wing Wah Tham
Date: 2023-11-09 00:00:00
Tasks: TAG, text-classification, Text Classification

The number of publications related to the Sustainable Development Goals (SDGs) continues to grow. These publications cover a diverse spectrum of research, from humanities and social sciences to engineering and health. Given the imperative of funding bodies to monitor outcomes and impacts, linking publications to relevant SDGs is critical but remains time-consuming and difficult given the breadth and complexity of the SDGs. A publication may relate to several goals (interconnection feature of goals), and therefore require multidisciplinary knowledge to tag accurately. Machine learning approaches are promising and have proven particularly valuable for tasks such as manual data labeling and text classification. In this study, we employed over 82,000 publications from an Australian university as a case study. We utilized a similarity measure to map these publications onto Sustainable Development Goals (SDGs). Additionally, we leveraged the OpenAI GPT model to conduct the same task, facilitating a comparative analysis between the two approaches. Experimental results show that about 82.89% of the results obtained by the similarity measure overlap (at least one tag) with the outputs of the GPT model. The adopted model (similarity measure) can complement GPT model for SDG classification. Furthermore, deep learning methods, which include the similarity measure used here, are more accessible and trusted for dealing with sensitive data without the use of commercial AI services or the deployment of expensive computing resources to operate large language models. Our study demonstrates how a crafted combination of the two methods can achieve reliable results for mapping research to the SDGs.
Localization of a Passive Source with a Sensor Network based Experimental Molecular Communication Platform
Authors: Fatih Gulec, Damla Yagmur Koda, Baris Atakan, Andrew W. Eckford
Date: 2023-11-28 00:00:00

In a practical molecular communication scenario such as monitoring air pollutants released from an unknown source, it is essential to estimate the location of the molecular transmitter (TX). This paper presents a novel Sensor Network-based Localization Algorithm (SNCLA) for passive transmission by using a novel experimental platform which mainly comprises a clustered sensor network (SN) with $24$ sensor nodes and evaporating ethanol molecules as the passive TX. In SNCLA, a Gaussian plume model is employed to derive the location estimator. The parameters such as transmitted mass, wind velocity, detection time, and actual concentration are calculated or estimated from the measured signals via the SN to be employed as the input for the location estimator. The numerical results show that the performance of SNCLA is better for stronger winds in the medium. Our findings show that evaporated molecules do not propagate homogeneously through the SN due to the presence of the wind. In addition, our statistical analysis based on the measured experimental data shows that the sensed signals by the SN have a log-normal distribution, while the additive noise follows a Student's t-distribution in contrast to the Gaussian assumption in the literature.
Information Design in Multi-Agent Reinforcement Learning
Authors: Yue Lin, Wenhao Li, Hongyuan Zha, Baoxiang Wang
Date: 2023-05-08 00:00:00
Proceeding: NeurIPS 2023 11
Tasks: Multi-agent Reinforcement Learning, reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL)

Reinforcement learning (RL) is inspired by the way human infants and animals learn from the environment. The setting is somewhat idealized because, in actual tasks, other agents in the environment have their own goals and behave adaptively to the ego agent. To thrive in those environments, the agent needs to influence other agents so their actions become more helpful and less harmful. Research in computational economics distills two ways to influence others directly: by providing tangible goods (mechanism design) and by providing information (information design). This work investigates information design problems for a group of RL agents. The main challenges are two-fold. One is the information provided will immediately affect the transition of the agent trajectories, which introduces additional non-stationarity. The other is the information can be ignored, so the sender must provide information that the receiver is willing to respect. We formulate the Markov signaling game, and develop the notions of signaling gradient and the extended obedience constraints that address these challenges. Our algorithm is efficient on various mixed-motive tasks and provides further insights into computational economics. Our code is publicly available at https://github.com/YueLin301/InformationDesignMARL.
Maximize to Explore: One Objective Function Fusing Estimation, Planning, and Exploration
Authors: Zhihan Liu, Miao Lu, Wei Xiong, Han Zhong, Hao Hu, Shenao Zhang, Sirui Zheng, Zhuoran Yang, Zhaoran Wang
Date: 2023-05-29 00:00:00
Proceeding: NeurIPS 2023 11
Tasks: MuJoCo

In online reinforcement learning (online RL), balancing exploration and exploitation is crucial for finding an optimal policy in a sample-efficient way. To achieve this, existing sample-efficient online RL algorithms typically consist of three components: estimation, planning, and exploration. However, in order to cope with general function approximators, most of them involve impractical algorithmic components to incentivize exploration, such as optimization within data-dependent level-sets or complicated sampling procedures. To address this challenge, we propose an easy-to-implement RL framework called \textit{Maximize to Explore} (\texttt{MEX}), which only needs to optimize \emph{unconstrainedly} a single objective that integrates the estimation and planning components while balancing exploration and exploitation automatically. Theoretically, we prove that \texttt{MEX} achieves a sublinear regret with general function approximations for Markov decision processes (MDP) and is further extendable to two-player zero-sum Markov games (MG). Meanwhile, we adapt deep RL baselines to design practical versions of \texttt{MEX}, in both model-free and model-based manners, which can outperform baselines by a stable margin in various MuJoCo environments with sparse rewards. Compared with existing sample-efficient online RL algorithms with general function approximations, \texttt{MEX} achieves similar sample efficiency while enjoying a lower computational cost and is more compatible with modern deep RL methods.
Language Models can Solve Computer Tasks
Authors: Geunwoo Kim, Pierre Baldi, Stephen Mcaleer
Date: 2023-03-30 00:00:00
Proceeding: NeurIPS 2023 11
Tasks: Language Modelling, Large Language Model, Reinforcement Learning (RL)

Agents capable of carrying out general tasks on a computer can improve efficiency and productivity by automating repetitive tasks and assisting in complex problem-solving. Ideally, such agents should be able to solve new computer tasks presented to them through natural language commands. However, previous approaches to this problem require large amounts of expert demonstrations and task-specific reward functions, both of which are impractical for new tasks. In this work, we show that a pre-trained large language model (LLM) agent can execute computer tasks guided by natural language using a simple prompting scheme where the agent Recursively Criticizes and Improves its output (RCI). The RCI approach significantly outperforms existing LLM methods for automating computer tasks and surpasses supervised learning (SL) and reinforcement learning (RL) approaches on the MiniWoB++ benchmark. We compare multiple LLMs and find that RCI with the InstructGPT-3+RLHF LLM is state-of-the-art on MiniWoB++, using only a handful of demonstrations per task rather than tens of thousands, and without a task-specific reward function. Furthermore, we demonstrate RCI prompting's effectiveness in enhancing LLMs' reasoning abilities on a suite of natural language reasoning tasks, outperforming chain of thought (CoT) prompting with external feedback. We find that RCI combined with CoT performs better than either separately. Our code can be found here: https://github.com/posgnu/rci-agent.
IODeep: an IOD for the introduction of deep learning in the DICOM standard
Authors: Salvatore Contino, Luca Cruciata, Orazio Gambino, Roberto Pirrone
Date: 2023-11-10 00:00:00
Tasks: Diagnostic, Federated Learning, Image Segmentation, Semantic Segmentation

Background and Objective: In recent years, Artificial Intelligence (AI) and in particular Deep Neural Networks (DNN) became a relevant research topic in biomedical image segmentation due to the availability of more and more data sets along with the establishment of well known competitions. Despite the popularity of DNN based segmentation on the research side, these techniques are almost unused in the daily clinical practice even if they could support effectively the physician during the diagnostic process. Apart from the issues related to the explainability of the predictions of a neural model, such systems are not integrated in the diagnostic workflow, and a standardization of their use is needed to achieve this goal. Methods: This paper presents IODeep a new DICOM Information Object Definition (IOD) aimed at storing both the weights and the architecture of a DNN already trained on a particular image dataset that is labeled as regards the acquisition modality, the anatomical region, and the disease under investigation. Results: The IOD architecture is presented along with a DNN selection algorithm from the PACS server based on the labels outlined above, and a simple PACS viewer purposely designed for demonstrating the effectiveness of the DICOM integration, while no modifications are required on the PACS server side. Also a service based architecture in support of the entire workflow has been implemented. Conclusion: IODeep ensures full integration of a trained AI model in a DICOM infrastructure, and it is also enables a scenario where a trained model can be either fine-tuned with hospital data or trained in a federated learning scheme shared by different hospitals. In this way AI models can be tailored to the real data produced by a Radiology ward thus improving the physician decision making process. Source code is freely available at https://github.com/CHILab1/IODeep.git
Plug-and-Play Stability for Intracortical Brain-Computer Interfaces: A One-Year Demonstration of Seamless Brain-to-Text Communication
Authors: Chaofei Fan, Nick Hahn, Foram Kamdar, Donald Avansino, Guy H. Wilson, Leigh Hochberg, Krishna V. Shenoy, Jaimie M. Henderson, Francis R. Willett
Date: 2023-11-06 00:00:00
Proceeding: NeurIPS 2023 11
Tasks: Decoder

Intracortical brain-computer interfaces (iBCIs) have shown promise for restoring rapid communication to people with neurological disorders such as amyotrophic lateral sclerosis (ALS). However, to maintain high performance over time, iBCIs typically need frequent recalibration to combat changes in the neural recordings that accrue over days. This requires iBCI users to stop using the iBCI and engage in supervised data collection, making the iBCI system hard to use. In this paper, we propose a method that enables self-recalibration of communication iBCIs without interrupting the user. Our method leverages large language models (LMs) to automatically correct errors in iBCI outputs. The self-recalibration process uses these corrected outputs ("pseudo-labels") to continually update the iBCI decoder online. Over a period of more than one year (403 days), we evaluated our Continual Online Recalibration with Pseudo-labels (CORP) framework with one clinical trial participant. CORP achieved a stable decoding accuracy of 93.84% in an online handwriting iBCI task, significantly outperforming other baseline methods. Notably, this is the longest-running iBCI stability demonstration involving a human participant. Our results provide the first evidence for long-term stabilization of a plug-and-play, high-performance communication iBCI, addressing a major barrier for the clinical translation of iBCIs.
Human-in-the-Loop Optimization for Deep Stimulus Encoding in Visual Prostheses
Authors: Jacob Granley, Tristan Fauvel, Matthew Chalk, Michael Beyeler
Date: 2023-06-16 00:00:00
Proceeding: NeurIPS 2023 11
Tasks: Bayesian Optimization

Neuroprostheses show potential in restoring lost sensory function and enhancing human capabilities, but the sensations produced by current devices often seem unnatural or distorted. Exact placement of implants and differences in individual perception lead to significant variations in stimulus response, making personalized stimulus optimization a key challenge. Bayesian optimization could be used to optimize patient-specific stimulation parameters with limited noisy observations, but is not feasible for high-dimensional stimuli. Alternatively, deep learning models can optimize stimulus encoding strategies, but typically assume perfect knowledge of patient-specific variations. Here we propose a novel, practically feasible approach that overcomes both of these fundamental limitations. First, a deep encoder network is trained to produce optimal stimuli for any individual patient by inverting a forward model mapping electrical stimuli to visual percepts. Second, a preferential Bayesian optimization strategy utilizes this encoder to optimize patient-specific parameters for a new patient, using a minimal number of pairwise comparisons between candidate stimuli. We demonstrate the viability of this approach on a novel, state-of-the-art visual prosthesis model. We show that our approach quickly learns a personalized stimulus encoder, leads to dramatic improvements in the quality of restored vision, and is robust to noisy patient feedback and misspecifications in the underlying forward model. Overall, our results suggest that combining the strengths of deep learning and Bayesian optimization could significantly improve the perceptual experience of patients fitted with visual prostheses and may prove a viable solution for a range of neuroprosthetic technologies.