OpenRaiser/Intern-Atlas huggingface dataset:
MedExpQA: Multilingual Benchmarking of Large Language Models for Medical Question Answering
Venue: arXiv cs.CL 2024
Year: 2024

Large Language Models (LLMs) have the potential of facilitating the development of Artificial Intelligence technology to assist medical experts for interactive decision support, which has been demonstrated by their competitive performances in Medical QA. However, while impressive, the required quality bar for medical applications remains far from being achieved. Currently, LLMs remain challenged by outdated knowledge and by their tendency to generate hallucinated content. Furthermore, most benchmarks to assess medical knowledge lack reference gold explanations which means that it is not possible to evaluate the reasoning of LLMs predictions. Finally, the situation is particularly grim if we consider benchmarking LLMs for languages other than English which remains, as far as we know, a totally neglected topic. In order to address these shortcomings, in this paper we present MedExpQA, the first multilingual benchmark based on medical exams to evaluate LLMs in Medical Question Answering. To the best of our knowledge, MedExpQA includes for the first time reference gold explanations written by medical doctors which can be leveraged to establish various gold-based upper-bounds for comparison with LLMs performance. Comprehensive multilingual experimentation using both the gold reference explanations and Retrieval Augmented Generation (RAG) approaches show that performance of LLMs still has large room for improvement, especially for languages other than English. Furthermore, and despite using state-of-the-art RAG methods, our results also demonstrate the difficulty of obtaining and integrating readily available medical knowledge that may positively impact results on downstream evaluations for Medical Question Answering. So far the benchmark is available in four languages, but we hope that this work may encourage further development to other languages.
KaMPIng: Flexible and (Near) Zero-Overhead C++ Bindings for MPI
Venue: arXiv cs.DC 2024
Year: 2024

The Message-Passing Interface (MPI) and C++ form the backbone of high-performance computing, but MPI only provides C and Fortran bindings. While this offers great language interoperability, high-level programming languages like C++ make software development quicker and less error-prone. We propose novel C++ language bindings that cover all abstraction levels from low-level MPI calls to convenient STL-style bindings, where most parameters are inferred from a small subset of parameters, by bringing named parameters to C++. This enables rapid prototyping and fine-tuning runtime behavior and memory management. A flexible type system and additional safety guarantees help to prevent programming errors. By exploiting C++'s template metaprogramming capabilities, this has (near) zero overhead, as only required code paths are generated at compile time. We demonstrate that our library is a strong foundation for a future distributed standard library using multiple application benchmarks, ranging from text-book sorting algorithms to phylogenetic interference.
OtterROS: Picking and Programming an Uncrewed Surface Vessel for Experimental Field Robotics Research with ROS 2
Venue: arXiv cs.RO 2024
Year: 2024

There exist a wide range of options for field robotics research using ground and aerial mobile robots, but there are comparatively few robust and research-ready uncrewed surface vessels (USVs). This workshop paper starts with a snapshot of USVs currently available to the research community and then describes "OtterROS", an open source ROS 2 solution for the Otter USV. Field experiments using OtterROS are described, which highlight the utility of the Otter USV and the benefits of using ROS 2 in aquatic robotics research. For those interested in USV research, the paper details recommended hardware to run OtterROS and includes an example ROS 2 package using OtterROS, removing unnecessary non-recurring engineering from field robotics research activities.
Case Study: Neural Network Malware Detection Verification for Feature and Image Datasets
Venue: arXiv cs.CR 2024
Year: 2024

Malware, or software designed with harmful intent, is an ever-evolving threat that can have drastic effects on both individuals and institutions. Neural network malware classification systems are key tools for combating these threats but are vulnerable to adversarial machine learning attacks. These attacks perturb input data to cause misclassification, bypassing protective systems. Existing defenses often rely on enhancing the training process, thereby increasing the model's robustness to these perturbations, which is quantified using verification. While training improvements are necessary, we propose focusing on the verification process used to evaluate improvements to training. As such, we present a case study that evaluates a novel verification domain that will help to ensure tangible safeguards against adversaries and provide a more reliable means of evaluating the robustness and effectiveness of anti-malware systems. To do so, we describe malware classification and two types of common malware datasets (feature and image datasets), demonstrate the certified robustness accuracy of malware classifiers using the Neural Network Verification (NNV) and Neural Network Enumeration (nnenum) tools, and outline the challenges and future considerations necessary for the improvement and refinement of the verification of malware classification. By evaluating this novel domain as a case study, we hope to increase its visibility, encourage further research and scrutiny, and ultimately enhance the resilience of digital systems against malicious attacks.
SwapAnything: Enabling Arbitrary Object Swapping in Personalized Visual Editing
Venue: arXiv cs.CV 2024
Year: 2024

Effective editing of personal content holds a pivotal role in enabling individuals to express their creativity, weaving captivating narratives within their visual stories, and elevate the overall quality and impact of their visual content. Therefore, in this work, we introduce SwapAnything, a novel framework that can swap any objects in an image with personalized concepts given by the reference, while keeping the context unchanged. Compared with existing methods for personalized subject swapping, SwapAnything has three unique advantages: (1) precise control of arbitrary objects and parts rather than the main subject, (2) more faithful preservation of context pixels, (3) better adaptation of the personalized concept to the image. First, we propose targeted variable swapping to apply region control over latent feature maps and swap masked variables for faithful context preservation and initial semantic concept swapping. Then, we introduce appearance adaptation, to seamlessly adapt the semantic concept into the original image in terms of target location, shape, style, and content during the image generation process. Extensive results on both human and automatic evaluation demonstrate significant improvements of our approach over baseline methods on personalized swapping. Furthermore, SwapAnything shows its precise and faithful swapping abilities across single object, multiple objects, partial object, and cross-domain swapping tasks. SwapAnything also achieves great performance on text-based swapping and tasks beyond swapping such as object insertion.
Dynamical stability and chaos in artificial neural network trajectories along training
Venue: arXiv cs.LG 2024
Year: 2024

The process of training an artificial neural network involves iteratively adapting its parameters so as to minimize the error of the network's prediction, when confronted with a learning task. This iterative change can be naturally interpreted as a trajectory in network space -- a time series of networks -- and thus the training algorithm (e.g. gradient descent optimization of a suitable loss function) can be interpreted as a dynamical system in graph space. In order to illustrate this interpretation, here we study the dynamical properties of this process by analyzing through this lens the network trajectories of a shallow neural network, and its evolution through learning a simple classification task. We systematically consider different ranges of the learning rate and explore both the dynamical and orbital stability of the resulting network trajectories, finding hints of regular and chaotic behavior depending on the learning rate regime. Our findings are put in contrast to common wisdom on convergence properties of neural networks and dynamical systems theory. This work also contributes to the cross-fertilization of ideas between dynamical systems theory, network theory and machine learning
Measuring Arbitrage Losses and Profitability of AMM Liquidity
Venue: arXiv cs.DC 2024
Year: 2024

This paper presents the results of a comprehensive empirical study of losses to arbitrageurs (following the formalization of loss-versus-rebalancing by [Milionis et al., 2022]) incurred by liquidity providers on automated market makers (AMMs). We show that those losses exceed the fees earned by liquidity providers across many of the largest AMM liquidity pools (on Uniswap). Remarkably, we also find that the Uniswap v2 pools are more profitable for passive LPs than their Uniswap v3 counterparts. We also investigate how arbitrage losses change with block times. As expected, arbitrage losses decrease when block production is faster. However, the rate of the decline varies significantly across different trading pairs. For instance, when comparing 100ms block times to Ethereum's current 12-second block times, the decrease in losses to arbitrageurs ranges between 20% to 70%, depending on the specific trading pair.
Slax: A Composable JAX Library for Rapid and Flexible Prototyping of Spiking Neural Networks
Venue: arXiv cs.NE 2024
Year: 2024

Recent advances to algorithms for training spiking neural networks (SNNs) often leverage their unique dynamics. While backpropagation through time (BPTT) with surrogate gradients dominate the field, a rich landscape of alternatives can situate algorithms across various points in the performance, bio-plausibility, and complexity landscape. Evaluating and comparing algorithms is currently a cumbersome and error-prone process, requiring them to be repeatedly re-implemented. We introduce Slax, a JAX-based library designed to accelerate SNN algorithm design, compatible with the broader JAX and Flax ecosystem. Slax provides optimized implementations of diverse training algorithms, allowing direct performance comparison. Its toolkit includes methods to visualize and debug algorithms through loss landscapes, gradient similarities, and other metrics of model behavior during training.
Towards Explainable Automated Neuroanatomy
Venue: arXiv cs.CV 2024
Year: 2024

We present a novel method for quantifying the microscopic structure of brain tissue. It is based on the automated recognition of interpretable features obtained by analyzing the shapes of cells. This contrasts with prevailing methods of brain anatomical analysis in two ways. First, contemporary methods use gray-scale values derived from smoothed version of the anatomical images, which dissipated valuable information from the texture of the images. Second, contemporary analysis uses the output of black-box Convolutional Neural Networks, while our system makes decisions based on interpretable features obtained by analyzing the shapes of individual cells. An important benefit of this open-box approach is that the anatomist can understand and correct the decisions made by the computer. Our proposed system can accurately localize and identify existing brain structures. This can be used to align and coregistar brains and will facilitate connectomic studies for reverse engineering of brain circuitry.
LLM-Augmented Retrieval: Enhancing Retrieval Models Through Language Models and Doc-Level Embedding
Venue: arXiv cs.IR 2024
Year: 2024

Recently embedding-based retrieval or dense retrieval have shown state of the art results, compared with traditional sparse or bag-of-words based approaches. This paper introduces a model-agnostic doc-level embedding framework through large language model (LLM) augmentation. In addition, it also improves some important components in the retrieval model training process, such as negative sampling, loss function, etc. By implementing this LLM-augmented retrieval framework, we have been able to significantly improve the effectiveness of widely-used retriever models such as Bi-encoders (Contriever, DRAGON) and late-interaction models (ColBERTv2), thereby achieving state-of-the-art results on LoTTE datasets and BEIR datasets.
Softmax Attention with Constant Cost per Token
Venue: arXiv cs.LG 2024
Year: 2024

We propose a simple modification to the conventional attention mechanism applied by Transformers: Instead of quantifying pairwise query-key similarity with scaled dot-products, we quantify it with the logarithms of scaled dot-products of exponentials. Our modification linearizes attention with exponential kernel feature maps, whose corresponding feature function is infinite dimensional. We show that our modification is expressible as a composition of log-sums of exponentials, with a latent space of constant size, enabling application with constant time and space complexity per token. We implement our modification, verify that it works in practice, and conclude that it is a promising alternative to conventional attention.
Localizing Moments of Actions in Untrimmed Videos of Infants with Autism Spectrum Disorder
Venue: arXiv cs.CV 2024
Year: 2024

Autism Spectrum Disorder (ASD) presents significant challenges in early diagnosis and intervention, impacting children and their families. With prevalence rates rising, there is a critical need for accessible and efficient screening tools. Leveraging machine learning (ML) techniques, in particular Temporal Action Localization (TAL), holds promise for automating ASD screening. This paper introduces a self-attention based TAL model designed to identify ASD-related behaviors in infant videos. Unlike existing methods, our approach simplifies complex modeling and emphasizes efficiency, which is essential for practical deployment in real-world scenarios. Importantly, this work underscores the importance of developing computer vision methods capable of operating in naturilistic environments with little equipment control, addressing key challenges in ASD screening. This study is the first to conduct end-to-end temporal action localization in untrimmed videos of infants with ASD, offering promising avenues for early intervention and support. We report baseline results of behavior detection using our TAL model. We achieve 70% accuracy for look face, 79% accuracy for look object, 72% for smile and 65% for vocalization.
Towards Improved Semiconductor Defect Inspection for high-NA EUVL based on SEMI-SuperYOLO-NAS
Venue: arXiv cs.CV 2024
Year: 2024

Due to potential pitch reduction, the semiconductor industry is adopting High-NA EUVL technology. However, its low depth of focus presents challenges for High Volume Manufacturing. To address this, suppliers are exploring thinner photoresists and new underlayers/hardmasks. These may suffer from poor SNR, complicating defect detection. Vision-based ML algorithms offer a promising solution for semiconductor defect inspection. However, developing a robust ML model across various image resolutions without explicit training remains a challenge for nano-scale defect inspection. This research's goal is to propose a scale-invariant ADCD framework capable to upscale images, addressing this issue. We propose an improvised ADCD framework as SEMI-SuperYOLO-NAS, which builds upon the baseline YOLO-NAS architecture. This framework integrates a SR assisted branch to aid in learning HR features by the defect detection backbone, particularly for detecting nano-scale defect instances from LR images. Additionally, the SR-assisted branch can recursively generate upscaled images from their corresponding downscaled counterparts, enabling defect detection inference across various image resolutions without requiring explicit training. Moreover, we investigate improved data augmentation strategy aimed at generating diverse and realistic training datasets to enhance model performance. We have evaluated our proposed approach using two original FAB datasets obtained from two distinct processes and captured using two different imaging tools. Finally, we demonstrate zero-shot inference for our model on a new, originating from a process condition distinct from the training dataset and possessing different Pitch characteristics. Experimental validation demonstrates that our proposed ADCD framework aids in increasing the throughput of imaging tools for defect inspection by reducing the required image pixel resolutions.
Rapid and Precise Topological Comparison with Merge Tree Neural Networks
Venue: arXiv cs.LG 2024
Year: 2024

Merge trees are a valuable tool in the scientific visualization of scalar fields; however, current methods for merge tree comparisons are computationally expensive, primarily due to the exhaustive matching between tree nodes. To address this challenge, we introduce the Merge Tree Neural Network (MTNN), a learned neural network model designed for merge tree comparison. The MTNN enables rapid and high-quality similarity computation. We first demonstrate how to train graph neural networks, which emerged as effective encoders for graphs, in order to produce embeddings of merge trees in vector spaces for efficient similarity comparison. Next, we formulate the novel MTNN model that further improves the similarity comparisons by integrating the tree and node embeddings with a new topological attention mechanism. We demonstrate the effectiveness of our model on real-world data in different domains and examine our model's generalizability across various datasets. Our experimental analysis demonstrates our approach's superiority in accuracy and efficiency. In particular, we speed up the prior state-of-the-art by more than $100\times$ on the benchmark datasets while maintaining an error rate below $0.1\%$.
Design of Transit-Centric Multimodal Urban Mobility System with Autonomous Mobility-on-Demand
Venue: arXiv cs.SI 2024
Year: 2024

This paper addresses the pressing challenge of urban mobility in the context of growing urban populations, changing demand patterns for urban mobility, and emerging technologies like Mobility-on-Demand (MoD) platforms and Autonomous Vehicle (AV). As urban areas swell and demand pattern changes, the integration of Autonomous Mobility-on-Demand (AMoD) systems with existing public transit (PT) networks presents great opportunities to enhancing urban mobility. We propose a novel optimization framework for solving the Transit-Centric Multimodal Urban Mobility with Autonomous Mobility-on-Demand (TCMUM-AMoD) at scale. The system operator (public transit agency) determines the network design and frequency settings of the PT network, fleet sizing and allocations of AMoD system, and the pricing for using the multimodal system with the goal of minimizing passenger disutility. Passengers' mode and route choice behaviors are modeled explicitly using discrete choice models. A first-order approximation algorithm is introduced to solve the problem at scale. Using a case study in Chicago, we showcase the potential to optimize urban mobility across different demand scenarios. To our knowledge, ours is the first paper to jointly optimize transit network design, fleet sizing, and pricing for the multimodal mobility system while considering passengers' mode and route choices.
ClusterRadar: an Interactive Web-Tool for the Multi-Method Exploration of Spatial Clusters Over Time
Venue: arXiv cs.HC 2024
Year: 2024

Spatial cluster analysis, the detection of localized patterns of similarity in geospatial data, has a wide-range of applications for scientific discovery and practical decision making. One way to detect spatial clusters is by using local indicators of spatial association, such as Local Moran's I or Getis-Ord Gi*. However, different indicators tend to produce substantially different results due to their distinct operational characteristics. Choosing a suitable method or comparing results from multiple methods is a complex task. Furthermore, spatial clusters are dynamic and it is often useful to track their evolution over time, which adds an additional layer of complexity. ClusterRadar is a web-tool designed to address these analytical challenges. The tool allows users to easily perform spatial clustering and analyze the results in an interactive environment, uniquely prioritizing temporal analysis and the comparison of multiple methods. The tool's interactive dashboard presents several visualizations, each offering a distinct perspective of the temporal and methodological aspects of the spatial clustering results. ClusterRadar has several features designed to maximize its utility to a broad user-base, including support for various geospatial formats, and a fully in-browser execution environment to preserve the privacy of sensitive data. Feedback from a varied set of researchers suggests ClusterRadar's potential for enhancing the temporal analysis of spatial clusters.
WILBUR: Adaptive In-Context Learning for Robust and Accurate Web Agents
Venue: arXiv cs.CL 2024
Year: 2024

In the realm of web agent research, achieving both generalization and accuracy remains a challenging problem. Due to high variance in website structure, existing approaches often fail. Moreover, existing fine-tuning and in-context learning techniques fail to generalize across multiple websites. We introduce Wilbur, an approach that uses a differentiable ranking model and a novel instruction synthesis technique to optimally populate a black-box large language model's prompt with task demonstrations from previous runs. To maximize end-to-end success rates, we also propose an intelligent backtracking mechanism that learns and recovers from its mistakes. Finally, we show that our ranking model can be trained on data from a generative auto-curriculum which samples representative goals from an LLM, runs the agent, and automatically evaluates it, with no manual annotation. Wilbur achieves state-of-the-art results on the WebVoyager benchmark, beating text-only models by 8% overall, and up to 36% on certain websites. On the same benchmark, Wilbur is within 5% of a strong multi-modal model despite only receiving textual inputs, and further analysis reveals a substantial number of failures are due to engineering challenges of operating the web.