pwc-archive/papers-with-abstracts huggingface dataset:
Rethinking model prototyping through the MedMNIST+ dataset collection
Authors: Sebastian Doerrich, Francesco Di Salvo, Julius Brockmann, Christian Ledig
Date: 2024-04-24 00:00:00
Tasks: Image Classification, Medical Image Classification, model

The integration of deep learning based systems in clinical practice is often impeded by challenges rooted in limited and heterogeneous medical datasets. In addition, the field has increasingly prioritized marginal performance gains on a few, narrowly scoped benchmarks over clinical applicability, slowing down meaningful algorithmic progress. This trend often results in excessive fine-tuning of existing methods on selected datasets rather than fostering clinically relevant innovations. In response, this work introduces a comprehensive benchmark for the MedMNIST+ dataset collection, designed to diversify the evaluation landscape across several imaging modalities, anatomical regions, classification tasks and sample sizes. We systematically reassess commonly used Convolutional Neural Networks (CNNs) and Vision Transformer (ViT) architectures across distinct medical datasets, training methodologies, and input resolutions to validate and refine existing assumptions about model effectiveness and development. Our findings suggest that computationally efficient training schemes and modern foundation models offer viable alternatives to costly end-to-end training. Additionally, we observe that higher image resolutions do not consistently improve performance beyond a certain threshold. This highlights the potential benefits of using lower resolutions, particularly in prototyping stages, to reduce computational demands without sacrificing accuracy. Notably, our analysis reaffirms the competitiveness of CNNs compared to ViTs, emphasizing the importance of comprehending the intrinsic capabilities of different architectures. Finally, by establishing a standardized evaluation framework, we aim to enhance transparency, reproducibility, and comparability within the MedMNIST+ dataset collection. Code is available at https://github.com/sdoerrich97/rethinking-model-prototyping-MedMNISTPlus .
An Empirical Study of Aegis
Authors: Daniel Saragih, Paridhi Goel, Tejas Balaji, Alyssa Li
Date: 2024-04-24 00:00:00
Tasks: Data Augmentation

Bit flipping attacks are one class of attacks on neural networks with numerous defense mechanisms invented to mitigate its potency. Due to the importance of ensuring the robustness of these defense mechanisms, we perform an empirical study on the Aegis framework. We evaluate the baseline mechanisms of Aegis on low-entropy data (MNIST), and we evaluate a pre-trained model with the mechanisms fine-tuned on MNIST. We also compare the use of data augmentation to the robustness training of Aegis, and how Aegis performs under other adversarial attacks, such as the generation of adversarial examples. We find that both the dynamic-exit strategy and robustness training of Aegis has some drawbacks. In particular, we see drops in accuracy when testing on perturbed data, and on adversarial examples, as compared to baselines. Moreover, we found that the dynamic exit-strategy loses its uniformity when tested on simpler datasets. The code for this project is available on GitHub.
BASS: Batched Attention-optimized Speculative Sampling
Authors: Haifeng Qian, Sujan Kumar Gonugondla, Sungsoo Ha, Mingyue Shang, Sanjay Krishna Gouda, Ramesh Nallapati, Sudipta Sengupta, Xiaofei Ma, Anoop Deoras
Date: 2024-04-24 00:00:00
Tasks: GPU, HumanEval

Speculative decoding has emerged as a powerful method to improve latency and throughput in hosting large language models. However, most existing implementations focus on generating a single sequence. Real-world generative AI applications often require multiple responses and how to perform speculative decoding in a batched setting while preserving its latency benefits poses non-trivial challenges. This paper describes a system of batched speculative decoding that sets a new state of the art in multi-sequence generation latency and that demonstrates superior GPU utilization as well as quality of generations within a time budget. For example, for a 7.8B-size model on a single A100 GPU and with a batch size of 8, each sequence is generated at an average speed of 5.8ms per token, the overall throughput being 1.1K tokens per second. These results represent state-of-the-art latency and a 2.15X speed-up over optimized regular decoding. Within a time budget that regular decoding does not finish, our system is able to generate sequences with HumanEval Pass@First of 43% and Pass@All of 61%, far exceeding what's feasible with single-sequence speculative decoding. Our peak GPU utilization during decoding reaches as high as 15.8%, more than 3X the highest of that of regular decoding and around 10X of single-sequence speculative decoding.
Bi-Mamba+: Bidirectional Mamba for Time Series Forecasting
Authors: Aobo Liang, Xingguo Jiang, Yan Sun, Xiaohou Shi, Ke Li
Date: 2024-04-24 00:00:00
Tasks: Computational Efficiency, Mamba, Time Series, Time Series Forecasting

Long-term time series forecasting (LTSF) provides longer insights into future trends and patterns. Over the past few years, deep learning models especially Transformers have achieved advanced performance in LTSF tasks. However, LTSF faces inherent challenges such as long-term dependencies capturing and sparse semantic characteristics. Recently, a new state space model (SSM) named Mamba is proposed. With the selective capability on input data and the hardware-aware parallel computing algorithm, Mamba has shown great potential in balancing predicting performance and computational efficiency compared to Transformers. To enhance Mamba's ability to preserve historical information in a longer range, we design a novel Mamba+ block by adding a forget gate inside Mamba to selectively combine the new features with the historical features in a complementary manner. Furthermore, we apply Mamba+ both forward and backward and propose Bi-Mamba+, aiming to promote the model's ability to capture interactions among time series elements. Additionally, multivariate time series data in different scenarios may exhibit varying emphasis on intra- or inter-series dependencies. Therefore, we propose a series-relation-aware decider that controls the utilization of channel-independent or channel-mixing tokenization strategy for specific datasets. Extensive experiments on 8 real-world datasets show that our model achieves more accurate predictions compared with state-of-the-art methods.
ChEX: Interactive Localization and Region Description in Chest X-rays
Authors: Philip Müller, Georgios Kaissis, Daniel Rueckert
Date: 2024-04-24 00:00:00

Report generation models offer fine-grained textual interpretations of medical images like chest X-rays, yet they often lack interactivity (i.e. the ability to steer the generation process through user queries) and localized interpretability (i.e. visually grounding their predictions), which we deem essential for future adoption in clinical practice. While there have been efforts to tackle these issues, they are either limited in their interactivity by not supporting textual queries or fail to also offer localized interpretability. Therefore, we propose a novel multitask architecture and training paradigm integrating textual prompts and bounding boxes for diverse aspects like anatomical regions and pathologies. We call this approach the Chest X-Ray Explainer (ChEX). Evaluations across a heterogeneous set of 9 chest X-ray tasks, including localized image interpretation and report generation, showcase its competitiveness with SOTA models while additional analysis demonstrates ChEX's interactive capabilities. Code: https://github.com/philip-mueller/chex
Exploring Machine Learning Algorithms for Infection Detection Using GC-IMS Data: A Preliminary Study
Authors: Christos Sardianos, Chrysostomos Symvoulidis, Matthias Schlögl, Iraklis Varlamis, Georgios Th. Papadopoulos
Date: 2024-04-24 00:00:00
Tasks: Diagnostic, Management

The developing field of enhanced diagnostic techniques in the diagnosis of infectious diseases, constitutes a crucial domain in modern healthcare. By utilizing Gas Chromatography-Ion Mobility Spectrometry (GC-IMS) data and incorporating machine learning algorithms into one platform, our research aims to tackle the ongoing issue of precise infection identification. Inspired by these difficulties, our goals consist of creating a strong data analytics process, enhancing machine learning (ML) models, and performing thorough validation for clinical applications. Our research contributes to the emerging field of advanced diagnostic technologies by integrating Gas Chromatography-Ion Mobility Spectrometry (GC-IMS) data and machine learning algorithms within a unified Laboratory Information Management System (LIMS) platform. Preliminary trials demonstrate encouraging levels of accuracy when employing various ML algorithms to differentiate between infected and non-infected samples. Continuing endeavors are currently concentrated on enhancing the effectiveness of the model, investigating techniques to clarify its functioning, and incorporating many types of data to further support the early detection of diseases.
CompilerDream: Learning a Compiler World Model for General Code Optimization
Authors: Chaoyi Deng, Jialong Wu, Ningya Feng, Jianmin Wang, Mingsheng Long
Date: 2024-04-24 00:00:00
Tasks: Diversity, Model-based Reinforcement Learning, reinforcement-learning, Value prediction, Zero-shot Generalization

Effective code optimization in compilers is crucial for computer and software engineering. The success of these optimizations primarily depends on the selection and ordering of the optimization passes applied to the code. While most compilers rely on a fixed sequence of optimization passes, current methods to find the optimal sequence either employ impractically slow search algorithms or learning methods that struggle to generalize to code unseen during training. We introduce CompilerDream, a model-based reinforcement learning approach to general code optimization. CompilerDream comprises a compiler world model that accurately simulates the intrinsic properties of optimization passes and an agent trained on this model to produce effective optimization strategies. By training on a large-scale program dataset, CompilerDream is equipped to serve as a general code optimizer across various application scenarios and source-code languages. Our extensive experiments first highlight CompilerDream's strong optimization capabilities for autotuning, where it leads the CompilerGym leaderboard. More importantly, the zero-shot generalization ability of large-scale trained compiler world model and agent, excels across diverse datasets, surpassing LLVM's built-in optimizations and other state-of-the-art methods in both settings of value prediction and end-to-end code optimization.
Collaborative Heterogeneous Causal Inference Beyond Meta-analysis
Authors: Tianyu Guo, Sai Praneeth Karimireddy, Michael I. Jordan
Date: 2024-04-24 00:00:00
Tasks: Causal Inference, Density Estimation, Federated Learning

Collaboration between different data centers is often challenged by heterogeneity across sites. To account for the heterogeneity, the state-of-the-art method is to re-weight the covariate distributions in each site to match the distribution of the target population. Nevertheless, this method could easily fail when a certain site couldn't cover the entire population. Moreover, it still relies on the concept of traditional meta-analysis after adjusting for the distribution shift. In this work, we propose a collaborative inverse propensity score weighting estimator for causal inference with heterogeneous data. Instead of adjusting the distribution shift separately, we use weighted propensity score models to collaboratively adjust for the distribution shift. Our method shows significant improvements over the methods based on meta-analysis when heterogeneity increases. To account for the vulnerable density estimation, we further discuss the double machine method and show the possibility of using nonparametric density estimation with d<8 and a flexible machine learning method to guarantee asymptotic normality. We propose a federated learning algorithm to collaboratively train the outcome model while preserving privacy. Using synthetic and real datasets, we demonstrate the advantages of our method.
Generalizing the SINDy approach with nested neural networks
Authors: Camilla Fiorini, Clément Flint, Louis Fostier, Emmanuel Franck, Reyhaneh Hashemi, Victor Michel-Dansac, Wassim Tenachi
Date: 2024-04-24 00:00:00
Tasks: regression, Symbolic Regression

Symbolic Regression (SR) is a widely studied field of research that aims to infer symbolic expressions from data. A popular approach for SR is the Sparse Identification of Nonlinear Dynamical Systems (SINDy) framework, which uses sparse regression to identify governing equations from data. This study introduces an enhanced method, Nested SINDy, that aims to increase the expressivity of the SINDy approach thanks to a nested structure. Indeed, traditional symbolic regression and system identification methods often fail with complex systems that cannot be easily described analytically. Nested SINDy builds on the SINDy framework by introducing additional layers before and after the core SINDy layer. This allows the method to identify symbolic representations for a wider range of systems, including those with compositions and products of functions. We demonstrate the ability of the Nested SINDy approach to accurately find symbolic expressions for simple systems, such as basic trigonometric functions, and sparse (false but accurate) analytical representations for more complex systems. Our results highlight Nested SINDy's potential as a tool for symbolic regression, surpassing the traditional SINDy approach in terms of expressivity. However, we also note the challenges in the optimization process for Nested SINDy and suggest future research directions, including the designing of a more robust methodology for the optimization process. This study proves that Nested SINDy can effectively discover symbolic representations of dynamical systems from data, offering new opportunities for understanding complex systems through data-driven methods.
MD-NOMAD: Mixture density nonlinear manifold decoder for emulating stochastic differential equations and uncertainty propagation
Authors: Akshay Thakur, Souvik Chakraborty
Date: 2024-04-24 00:00:00
Tasks: Decoder, Operator learning

We propose a neural operator framework, termed mixture density nonlinear manifold decoder (MD-NOMAD), for stochastic simulators. Our approach leverages an amalgamation of the pointwise operator learning neural architecture nonlinear manifold decoder (NOMAD) with mixture density-based methods to estimate conditional probability distributions for stochastic output functions. MD-NOMAD harnesses the ability of probabilistic mixture models to estimate complex probability and the high-dimensional scalability of pointwise neural operator NOMAD. We conduct empirical assessments on a wide array of stochastic ordinary and partial differential equations and present the corresponding results, which highlight the performance of the proposed framework.
Gradformer: Graph Transformer with Exponential Decay
Authors: Chuang Liu, Zelin Yao, Yibing Zhan, Xueqi Ma, Shirui Pan, Wenbin Hu
Date: 2024-04-24 00:00:00
Tasks: Graph Classification, Graph Neural Network, Inductive Bias

Graph Transformers (GTs) have demonstrated their advantages across a wide range of tasks. However, the self-attention mechanism in GTs overlooks the graph's inductive biases, particularly biases related to structure, which are crucial for the graph tasks. Although some methods utilize positional encoding and attention bias to model inductive biases, their effectiveness is still suboptimal analytically. Therefore, this paper presents Gradformer, a method innovatively integrating GT with the intrinsic inductive bias by applying an exponential decay mask to the attention matrix. Specifically, the values in the decay mask matrix diminish exponentially, correlating with the decreasing node proximities within the graph structure. This design enables Gradformer to retain its ability to capture information from distant nodes while focusing on the graph's local details. Furthermore, Gradformer introduces a learnable constraint into the decay mask, allowing different attention heads to learn distinct decay masks. Such an design diversifies the attention heads, enabling a more effective assimilation of diverse structural information within the graph. Extensive experiments on various benchmarks demonstrate that Gradformer consistently outperforms the Graph Neural Network and GT baseline models in various graph classification and regression tasks. Additionally, Gradformer has proven to be an effective method for training deep GT models, maintaining or even enhancing accuracy compared to shallow models as the network deepens, in contrast to the significant accuracy drop observed in other GT models.Codes are available at \url{https://github.com/LiuChuang0059/Gradformer}.
ViViDex: Learning Vision-based Dexterous Manipulation from Human Videos
Authors: Zerui Chen, ShiZhe Chen, Etienne Arlaud, Ivan Laptev, Cordelia Schmid
Date: 2024-04-24 00:00:00

In this work, we aim to learn a unified vision-based policy for multi-fingered robot hands to manipulate a variety of objects in diverse poses. Though prior work has shown benefits of using human videos for policy learning, performance gains have been limited by the noise in estimated trajectories. Moreover, reliance on privileged object information such as ground-truth object states further limits the applicability in realistic scenarios. To address these limitations, we propose a new framework ViViDex to improve vision-based policy learning from human videos. It first uses reinforcement learning with trajectory guided rewards to train state-based policies for each video, obtaining both visually natural and physically plausible trajectories from the video. We then rollout successful episodes from state-based policies and train a unified visual policy without using any privileged information. We propose coordinate transformation to further enhance the visual point cloud representation, and compare behavior cloning and diffusion policy for the visual policy training. Experiments both in simulation and on the real robot demonstrate that ViViDex outperforms state-of-the-art approaches on three dexterous manipulation tasks.
Deep Learning for Accelerated and Robust MRI Reconstruction: a Review
Authors: Reinhard Heckel, Mathews Jacob, Akshay Chaudhari, Or Perlman, Efrat Shimron
Date: 2024-04-24 00:00:00
Tasks: Deep Learning, Diagnostic, MRI Reconstruction

Deep learning (DL) has recently emerged as a pivotal technology for enhancing magnetic resonance imaging (MRI), a critical tool in diagnostic radiology. This review paper provides a comprehensive overview of recent advances in DL for MRI reconstruction. It focuses on DL approaches and architectures designed to improve image quality, accelerate scans, and address data-related challenges. These include end-to-end neural networks, pre-trained networks, generative models, and self-supervised methods. The paper also discusses the role of DL in optimizing acquisition protocols, enhancing robustness against distribution shifts, and tackling subtle bias. Drawing on the extensive literature and practical insights, it outlines current successes, limitations, and future directions for leveraging DL in MRI reconstruction, while emphasizing the potential of DL to significantly impact clinical imaging practices.
Long-term Off-Policy Evaluation and Learning
Authors: Yuta Saito, Himan Abdollahpouri, Jesse Anderton, Ben Carterette, Mounia Lalmas
Date: 2024-04-24 00:00:00
Tasks: Off-policy evaluation

Short- and long-term outcomes of an algorithm often differ, with damaging downstream effects. A known example is a click-bait algorithm, which may increase short-term clicks but damage long-term user engagement. A possible solution to estimate the long-term outcome is to run an online experiment or A/B test for the potential algorithms, but it takes months or even longer to observe the long-term outcomes of interest, making the algorithm selection process unacceptably slow. This work thus studies the problem of feasibly yet accurately estimating the long-term outcome of an algorithm using only historical and short-term experiment data. Existing approaches to this problem either need a restrictive assumption about the short-term outcomes called surrogacy or cannot effectively use short-term outcomes, which is inefficient. Therefore, we propose a new framework called Long-term Off-Policy Evaluation (LOPE), which is based on reward function decomposition. LOPE works under a more relaxed assumption than surrogacy and effectively leverages short-term rewards to substantially reduce the variance. Synthetic experiments show that LOPE outperforms existing approaches particularly when surrogacy is severely violated and the long-term reward is noisy. In addition, real-world experiments on large-scale A/B test data collected on a music streaming platform show that LOPE can estimate the long-term outcome of actual algorithms more accurately than existing feasible methods.
Neural Proto-Language Reconstruction
Authors: Chenxuan Cui, Ying Chen, Qinxin Wang, David R. Mortensen
Date: 2024-04-24 00:00:00
Tasks: Data Augmentation, Machine Translation, Translation

Proto-form reconstruction has been a painstaking process for linguists. Recently, computational models such as RNN and Transformers have been proposed to automate this process. We take three different approaches to improve upon previous methods, including data augmentation to recover missing reflexes, adding a VAE structure to the Transformer model for proto-to-language prediction, and using a neural machine translation model for the reconstruction task. We find that with the additional VAE structure, the Transformer model has a better performance on the WikiHan dataset, and the data augmentation step stabilizes the training.
Augmented CARDS: A machine learning approach to identifying triggers of climate change misinformation on Twitter
Authors: Cristian Rojas, Frank Algra-Maschio, Mark Andrejevic, Travis Coan, John Cook, Yuan-Fang Li
Date: 2024-04-24 00:00:00
Tasks: Misinformation

Misinformation about climate change poses a significant threat to societal well-being, prompting the urgent need for effective mitigation strategies. However, the rapid proliferation of online misinformation on social media platforms outpaces the ability of fact-checkers to debunk false claims. Automated detection of climate change misinformation offers a promising solution. In this study, we address this gap by developing a two-step hierarchical model, the Augmented CARDS model, specifically designed for detecting contrarian climate claims on Twitter. Furthermore, we apply the Augmented CARDS model to five million climate-themed tweets over a six-month period in 2022. We find that over half of contrarian climate claims on Twitter involve attacks on climate actors or conspiracy theories. Spikes in climate contrarianism coincide with one of four stimuli: political events, natural events, contrarian influencers, or convinced influencers. Implications for automated responses to climate misinformation are discussed.