pwc-archive/papers-with-abstracts huggingface dataset:
Inference of dynamical gene regulatory networks from single-cell data with physics informed neural networks
Authors: Maria Mircea, Diego Garlaschelli, Stefan Semrau
Date: 2024-01-14 00:00:00

One of the main goals of developmental biology is to reveal the gene regulatory networks (GRNs) underlying the robust differentiation of multipotent progenitors into precisely specified cell types. Most existing methods to infer GRNs from experimental data have limited predictive power as the inferred GRNs merely reflect gene expression similarity or correlation. Here, we demonstrate, how physics-informed neural networks (PINNs) can be used to infer the parameters of predictive, dynamical GRNs that provide mechanistic understanding of biological processes. Specifically we study GRNs that exhibit bifurcation behavior and can therefore model cell differentiation. We show that PINNs outperform regular feed-forward neural networks on the parameter inference task and analyze two relevant experimental scenarios: 1. a system with cell communication for which gene expression trajectories are available and 2. snapshot measurements of a cell population in which cell communication is absent. Our analysis will inform the design of future experiments to be analyzed with PINNs and provides a starting point to explore this powerful class of neural network models further.
Efficient approximation of Earth Mover's Distance Based on Nearest Neighbor Search
Authors: Guangyu Meng, Ruyu Zhou, Liu Liu, Peixian Liang, Fang Liu, Danny Chen, Michael Niemier, X. Sharon Hu
Date: 2024-01-14 00:00:00
Tasks: GPU, image-classification, Image Classification

Earth Mover's Distance (EMD) is an important similarity measure between two distributions, used in computer vision and many other application domains. However, its exact calculation is computationally and memory intensive, which hinders its scalability and applicability for large-scale problems. Various approximate EMD algorithms have been proposed to reduce computational costs, but they suffer lower accuracy and may require additional memory usage or manual parameter tuning. In this paper, we present a novel approach, NNS-EMD, to approximate EMD using Nearest Neighbor Search (NNS), in order to achieve high accuracy, low time complexity, and high memory efficiency. The NNS operation reduces the number of data points compared in each NNS iteration and offers opportunities for parallel processing. We further accelerate NNS-EMD via vectorization on GPU, which is especially beneficial for large datasets. We compare NNS-EMD with both the exact EMD and state-of-the-art approximate EMD algorithms on image classification and retrieval tasks. We also apply NNS-EMD to calculate transport mapping and realize color transfer between images. NNS-EMD can be 44x to 135x faster than the exact EMD implementation, and achieves superior accuracy, speedup, and memory efficiency over existing approximate EMD methods.
PDE Generalization of In-Context Operator Networks: A Study on 1D Scalar Nonlinear Conservation Laws
Authors: Liu Yang, Stanley J. Osher
Date: 2024-01-14 00:00:00
Tasks: Operator learning

Can we build a single large model for a wide range of PDE-related scientific learning tasks? Can this model generalize to new PDEs, even of new forms, without any fine-tuning? In-context operator learning and the corresponding model In-Context Operator Networks (ICON) represent an initial exploration of these questions. The capability of ICON regarding the first question has been demonstrated previously. In this paper, we present a detailed methodology for solving PDE problems with ICON, and show how a single ICON model can make forward and reverse predictions for different equations with different strides, provided with appropriately designed data prompts. We show the positive evidence to the second question, i.e., ICON can generalize well to some PDEs with new forms without any fine-tuning. This is exemplified through a study on 1D scalar nonlinear conservation laws, a family of PDEs with temporal evolution. We also show how to broaden the range of problems that an ICON model can address, by transforming functions and equations to ICON's capability scope. We believe that the progress in this paper is a significant step towards the goal of training a foundation model for PDE-related tasks under the in-context operator learning framework.
Reliability and Interpretability in Science and Deep Learning
Authors: Luigi Scorzato
Date: 2024-01-14 00:00:00
Tasks: Deep Learning

In recent years, the question of the reliability of Machine Learning (ML) methods has acquired significant importance, and the analysis of the associated uncertainties has motivated a growing amount of research. However, most of these studies have applied standard error analysis to ML models, and in particular Deep Neural Network (DNN) models, which represent a rather significant departure from standard scientific modelling. It is therefore necessary to integrate the standard error analysis with a deeper epistemological analysis of the possible differences between DNN models and standard scientific modelling and the possible implications of these differences in the assessment of reliability. This article offers several contributions. First, it emphasises the ubiquitous role of model assumptions (both in ML and traditional Science) against the illusion of theory-free science. Secondly, model assumptions are analysed from the point of view of their (epistemic) complexity, which is shown to be language-independent. It is argued that the high epistemic complexity of DNN models hinders the estimate of their reliability and also their prospect of long-term progress. Some potential ways forward are suggested. Thirdly, this article identifies the close relation between a model's epistemic complexity and its interpretability, as introduced in the context of responsible AI. This clarifies in which sense, and to what extent, the lack of understanding of a model (black-box problem) impacts its interpretability in a way that is independent of individual skills. It also clarifies how interpretability is a precondition for assessing the reliability of any model, which cannot be based on statistical analysis alone. This article focuses on the comparison between traditional scientific models and DNN models. But, Random Forest and Logistic Regression models are also briefly considered.
Towards Engineering Fair and Equitable Software Systems for Managing Low-Altitude Airspace Authorizations
Authors: Usman Gohar, Michael C. Hunter, Agnieszka Marczak-Czajka, Robyn R. Lutz, Myra B. Cohen, Jane Cleland-Huang
Date: 2024-01-14 00:00:00
Tasks: Decision Making, Fairness, Management

Small Unmanned Aircraft Systems (sUAS) have gained widespread adoption across a diverse range of applications. This has introduced operational complexities within shared airspaces and an increase in reported incidents, raising safety concerns. In response, the U.S. Federal Aviation Administration (FAA) is developing a UAS Traffic Management (UTM) system to control access to airspace based on an sUAS's predicted ability to safely complete its mission. However, a fully automated system capable of swiftly approving or denying flight requests can be prone to bias and must consider safety, transparency, and fairness to diverse stakeholders. In this paper, we present an initial study that explores stakeholders' perspectives on factors that should be considered in an automated system. Results indicate flight characteristics and environmental conditions were perceived as most important but pilot and drone capabilities should also be considered. Further, several respondents indicated an aversion to any AI-supported automation, highlighting the need for full transparency in automated decision-making. Results provide a societal perspective on the challenges of automating UTM flight authorization decisions and help frame the ongoing design of a solution acceptable to the broader sUAS community.
Generative AI in EU Law: Liability, Privacy, Intellectual Property, and Cybersecurity
Authors: Claudio Novelli, Federico Casolari, Philipp Hacker, Giorgio Spedicato, Luciano Floridi
Date: 2024-01-14 00:00:00

The advent of Generative AI, particularly through Large Language Models (LLMs) like ChatGPT and its successors, marks a paradigm shift in the AI landscape. Advanced LLMs exhibit multimodality, handling diverse data formats, thereby broadening their application scope. However, the complexity and emergent autonomy of these models introduce challenges in predictability and legal compliance. This paper delves into the legal and regulatory implications of Generative AI and LLMs in the European Union context, analyzing aspects of liability, privacy, intellectual property, and cybersecurity. It critically examines the adequacy of the existing and proposed EU legislation, including the Artificial Intelligence Act (AIA) draft, in addressing the unique challenges posed by Generative AI in general and LLMs in particular. The paper identifies potential gaps and shortcomings in the legislative framework and proposes recommendations to ensure the safe and compliant deployment of generative models, ensuring they align with the EU's evolving digital landscape and legal standards.
Construction and Evaluation of Mandarin Multimodal Emotional Speech Database
Authors: Zhu Ting, Li Liangqi, Duan Shufei, Zhang Xueying, Xiao Zhongzhe, Jia Hairng, Liang Huizhi
Date: 2024-01-14 00:00:00

A multi-modal emotional speech Mandarin database including articulatory kinematics, acoustics, glottal and facial micro-expressions is designed and established, which is described in detail from the aspects of corpus design, subject selection, recording details and data processing. Where signals are labeled with discrete emotion labels (neutral, happy, pleasant, indifferent, angry, sad, grief) and dimensional emotion labels (pleasure, arousal, dominance). In this paper, the validity of dimension annotation is verified by statistical analysis of dimension annotation data. The SCL-90 scale data of annotators are verified and combined with PAD annotation data for analysis, so as to explore the internal relationship between the outlier phenomenon in annotation and the psychological state of annotators. In order to verify the speech quality and emotion discrimination of the database, this paper uses 3 basic models of SVM, CNN and DNN to calculate the recognition rate of these seven emotions. The results show that the average recognition rate of seven emotions is about 82% when using acoustic data alone. When using glottal data alone, the average recognition rate is about 72%. Using kinematics data alone, the average recognition rate also reaches 55.7%. Therefore, the database is of high quality and can be used as an important source for speech analysis research, especially for the task of multimodal emotional speech analysis.
ELLA-V: Stable Neural Codec Language Modeling with Alignment-guided Sequence Reordering
Authors: Yakun Song, Zhuo Chen, Xiaofei Wang, Ziyang Ma, Xie Chen
Date: 2024-01-14 00:00:00
Tasks: Audio Generation, Language Modeling, Language Modelling, text-to-speech, Text to Speech

The language model (LM) approach based on acoustic and linguistic prompts, such as VALL-E, has achieved remarkable progress in the field of zero-shot audio generation. However, existing methods still have some limitations: 1) repetitions, transpositions, and omissions in the output synthesized speech due to limited alignment constraints between audio and phoneme tokens; 2) challenges of fine-grained control over the synthesized speech with autoregressive (AR) language model; 3) infinite silence generation due to the nature of AR-based decoding, especially under the greedy strategy. To alleviate these issues, we propose ELLA-V, a simple but efficient LM-based zero-shot text-to-speech (TTS) framework, which enables fine-grained control over synthesized audio at the phoneme level. The key to ELLA-V is interleaving sequences of acoustic and phoneme tokens, where phoneme tokens appear ahead of the corresponding acoustic tokens. The experimental findings reveal that our model outperforms VALL-E in terms of accuracy and delivers more stable results using both greedy and sampling-based decoding strategies. The code of ELLA-V will be open-sourced after cleanups. Audio samples are available at https://ereboas.github.io/ELLAV/.
Small LLMs Are Weak Tool Learners: A Multi-LLM Agent
Authors: Weizhou Shen, Chenliang Li, Hongzhan Chen, Ming Yan, Xiaojun Quan, Hehong Chen, Ji Zhang, Fei Huang
Date: 2024-01-14 00:00:00
Tasks: Language Modelling, Large Language Model, Task Planning

Large Language Model (LLM) agents significantly extend the capabilities of standalone LLMs, empowering them to interact with external tools (e.g., APIs, functions) and complete various tasks in a self-directed fashion. The challenge of tool use demands that LLMs not only understand user queries and generate answers accurately but also excel in task planning, tool invocation, and result summarization. While traditional works focus on training a single LLM with all these capabilities, performance limitations become apparent, particularly with smaller models. To overcome these challenges, we propose a novel approach that decomposes the aforementioned capabilities into a planner, caller, and summarizer. Each component is implemented by a single LLM that focuses on a specific capability and collaborates with others to accomplish the task. This modular framework facilitates individual updates and the potential use of smaller LLMs for building each capability. To effectively train this framework, we introduce a two-stage training paradigm. First, we fine-tune a backbone LLM on the entire dataset without discriminating sub-tasks, providing the model with a comprehensive understanding of the task. Second, the fine-tuned LLM is used to instantiate the planner, caller, and summarizer respectively, which are continually fine-tuned on respective sub-tasks. Evaluation across various tool-use benchmarks illustrates that our proposed multi-LLM framework surpasses the traditional single-LLM approach, highlighting its efficacy and advantages in tool learning.
MapGPT: Map-Guided Prompting with Adaptive Path Planning for Vision-and-Language Navigation
Authors: Jiaqi Chen, Bingqian Lin, ran Xu, Zhenhua Chai, Xiaodan Liang, Kwan-Yee K. Wong
Date: 2024-01-14 00:00:00
Tasks: Decision Making, Vision and Language Navigation

Embodied agents equipped with GPT as their brains have exhibited extraordinary decision-making and generalization abilities across various tasks. However, existing zero-shot agents for vision-and-language navigation (VLN) only prompt GPT-4 to select potential locations within localized environments, without constructing an effective "global-view" for the agent to understand the overall environment. In this work, we present a novel map-guided GPT-based agent, dubbed MapGPT, which introduces an online linguistic-formed map to encourage global exploration. Specifically, we build an online map and incorporate it into the prompts that include node information and topological relationships, to help GPT understand the spatial environment. Benefiting from this design, we further propose an adaptive planning mechanism to assist the agent in performing multi-step path planning based on a map, systematically exploring multiple candidate nodes or sub-goals step by step. Extensive experiments demonstrate that our MapGPT is applicable to both GPT-4 and GPT-4V, achieving state-of-the-art zero-shot performance on R2R and REVERIE simultaneously (~10% and ~12% improvements in SR), and showcasing the newly emergent global thinking and path planning abilities of the GPT.
Small Language Model Can Self-correct
Authors: Haixia Han, Jiaqing Liang, Jie Shi, Qianyu He, Yanghua Xiao
Date: 2024-01-14 00:00:00
Tasks: Language Modeling, Language Modelling, model, Small Language Model

Generative Language Models (LMs) such as ChatGPT have exhibited remarkable performance across various downstream tasks. Nevertheless, one of their most prominent drawbacks is generating inaccurate or false information with a confident tone. Previous studies have devised sophisticated pipelines and prompts to induce large LMs to exhibit the capability for self-correction. However, large LMs are explicitly prompted to verify and modify its answers separately rather than completing all steps spontaneously like humans. Moreover, these complex prompts are extremely challenging for small LMs to follow. In this paper, we introduce the \underline{I}ntrinsic \underline{S}elf-\underline{C}orrection (ISC) in generative language models, aiming to correct the initial output of LMs in a self-triggered manner, even for those small LMs with 6 billion parameters. Specifically, we devise a pipeline for constructing self-correction data and propose Partial Answer Masking (PAM), aiming to endow the model with the capability for intrinsic self-correction through fine-tuning. We conduct experiments using LMs with parameters sizes ranging from 6 billion to 13 billion in two tasks, including commonsense reasoning and factual knowledge reasoning. Our experiments demonstrate that the outputs generated using ISC outperform those generated without self-correction. We believe that the output quality of even small LMs can be further improved by empowering them with the ability to intrinsic self-correct.
Semi-Supervised Semantic Segmentation using Redesigned Self-Training for White Blood Cells
Authors: Vinh Quoc Luu, Duy Khanh Le, Huy Thanh Nguyen, Minh Thanh Nguyen, Thinh Tien Nguyen, Vinh Quang Dinh
Date: 2024-01-14 00:00:00
Tasks: Segmentation, Semantic Segmentation, Semi-Supervised Semantic Segmentation

Artificial Intelligence (AI) in healthcare, especially in white blood cell cancer diagnosis, is hindered by two primary challenges: the lack of large-scale labeled datasets for white blood cell (WBC) segmentation and outdated segmentation methods. These challenges inhibit the development of more accurate and modern techniques to diagnose cancer relating to white blood cells. To address the first challenge, a semi-supervised learning framework should be devised to efficiently capitalize on the scarcity of the dataset available. In this work, we address this issue by proposing a novel self-training pipeline with the incorporation of FixMatch. Self-training is a technique that utilizes the model trained on labeled data to generate pseudo-labels for the unlabeled data and then re-train on both of them. FixMatch is a consistency-regularization algorithm to enforce the model's robustness against variations in the input image. We discover that by incorporating FixMatch in the self-training pipeline, the performance improves in the majority of cases. Our performance achieved the best performance with the self-training scheme with consistency on DeepLab-V3 architecture and ResNet-50, reaching 90.69%, 87.37%, and 76.49% on Zheng 1, Zheng 2, and LISC datasets, respectively.
SpineCLUE: Automatic Vertebrae Identification Using Contrastive Learning and Uncertainty Estimation
Authors: Sheng Zhang, Minheng Chen, Junxian Wu, Ziyue Zhang, Tonglong Li, Cheng Xue, Youyong Kong
Date: 2024-01-14 00:00:00
Tasks: Contrastive Learning

Vertebrae identification in arbitrary fields-of-view plays a crucial role in diagnosing spine disease. Most spine CT contain only local regions, such as the neck, chest, and abdomen. Therefore, identification should not depend on specific vertebrae or a particular number of vertebrae being visible. Existing methods at the spine-level are unable to meet this challenge. In this paper, we propose a three-stage method to address the challenges in 3D CT vertebrae identification at vertebrae-level. By sequentially performing the tasks of vertebrae localization, segmentation, and identification, the anatomical prior information of the vertebrae is effectively utilized throughout the process. Specifically, we introduce a dual-factor density clustering algorithm to acquire localization information for individual vertebra, thereby facilitating subsequent segmentation and identification processes. In addition, to tackle the issue of interclass similarity and intra-class variability, we pre-train our identification network by using a supervised contrastive learning method. To further optimize the identification results, we estimated the uncertainty of the classification network and utilized the message fusion module to combine the uncertainty scores, while aggregating global information about the spine. Our method achieves state-of-the-art results on the VerSe19 and VerSe20 challenge benchmarks. Additionally, our approach demonstrates outstanding generalization performance on an collected dataset containing a wide range of abnormal cases.
BET: Explaining Deep Reinforcement Learning through The Error-Prone Decisions
Authors: Xiao Liu, Jie Zhao, Wubing Chen, Mao Tan, Yongxing Su
Date: 2024-01-14 00:00:00
Tasks: Decision Making, Deep Reinforcement Learning, reinforcement-learning, Reinforcement Learning, Starcraft, Starcraft II

Despite the impressive capabilities of Deep Reinforcement Learning (DRL) agents in many challenging scenarios, their black-box decision-making process significantly limits their deployment in safety-sensitive domains. Several previous self-interpretable works focus on revealing the critical states of the agent's decision. However, they cannot pinpoint the error-prone states. To address this issue, we propose a novel self-interpretable structure, named Backbone Extract Tree (BET), to better explain the agent's behavior by identify the error-prone states. At a high level, BET hypothesizes that states in which the agent consistently executes uniform decisions exhibit a reduced propensity for errors. To effectively model this phenomenon, BET expresses these states within neighborhoods, each defined by a curated set of representative states. Therefore, states positioned at a greater distance from these representative benchmarks are more prone to error. We evaluate BET in various popular RL environments and show its superiority over existing self-interpretable models in terms of explanation fidelity. Furthermore, we demonstrate a use case for providing explanations for the agents in StarCraft II, a sophisticated multi-agent cooperative game. To the best of our knowledge, we are the first to explain such a complex scenarios using a fully transparent structure.
Stabilizing Sharpness-aware Minimization Through A Simple Renormalization Strategy
Authors: Chengli Tan, Jiangshe Zhang, Junmin Liu, Yicheng Wang, Yunda Hao
Date: 2024-01-14 00:00:00
Tasks: Learning Theory

Recently, sharpness-aware minimization (SAM) has attracted much attention because of its surprising effectiveness in improving generalization performance. However, compared to stochastic gradient descent (SGD), it is more prone to getting stuck at the saddle points, which as a result may lead to performance degradation. To address this issue, we propose a simple renormalization strategy, dubbed Stable SAM (SSAM), so that the gradient norm of the descent step maintains the same as that of the ascent step. Our strategy is easy to implement and flexible enough to integrate with SAM and its variants, almost at no computational cost. With elementary tools from convex optimization and learning theory, we also conduct a theoretical analysis of sharpness-aware training, revealing that compared to SGD, the effectiveness of SAM is only assured in a limited regime of learning rate. In contrast, we show how SSAM extends this regime of learning rate and then it can consistently perform better than SAM with the minor modification. Finally, we demonstrate the improved performance of SSAM on several representative data sets and tasks.