OpenRaiser/Intern-Atlas huggingface dataset:
Ammonia-Net: A Multi-task Joint Learning Model for Multi-class Segmentation and Classification in Tooth-marked Tongue Diagnosis
Venue: arXiv cs.CV 2023
Year: 2023

In Traditional Chinese Medicine, the tooth marks on the tongue, stemming from prolonged dental pressure, serve as a crucial indicator for assessing qi (yang) deficiency, which is intrinsically linked to visceral health. Manual diagnosis of tooth-marked tongue solely relies on experience. Nonetheless, the diversity in shape, color, and type of tooth marks poses a challenge to diagnostic accuracy and consistency. To address these problems, herein we propose a multi-task joint learning model named Ammonia-Net. This model employs a convolutional neural network-based architecture, specifically designed for multi-class segmentation and classification of tongue images. Ammonia-Net performs semantic segmentation of tongue images to identify tongue and tooth marks. With the assistance of segmentation output, it classifies the images into the desired number of classes: healthy tongue, light tongue, moderate tongue, and severe tongue. As far as we know, this is the first attempt to apply the semantic segmentation results of tooth marks for tooth-marked tongue classification. To train Ammonia-Net, we collect 856 tongue images from 856 subjects. After a number of extensive experiments, the experimental results show that the proposed model achieves 99.06% accuracy in the two-class classification task of tooth-marked tongue identification and 80.02%. As for the segmentation task, mIoU for tongue and tooth marks amounts to 71.65%.
FASER: Binary Code Similarity Search through the use of Intermediate Representations
Venue: arXiv cs.CR 2023
Year: 2023

Being able to identify functions of interest in cross-architecture software is useful whether you are analysing for malware, securing the software supply chain or conducting vulnerability research. Cross-Architecture Binary Code Similarity Search has been explored in numerous studies and has used a wide range of different data sources to achieve its goals. The data sources typically used draw on common structures derived from binaries such as function control flow graphs or binary level call graphs, the output of the disassembly process or the outputs of a dynamic analysis approach. One data source which has received less attention is binary intermediate representations. Binary Intermediate representations possess two interesting properties: they are cross architecture by their very nature and encode the semantics of a function explicitly to support downstream usage. Within this paper we propose Function as a String Encoded Representation (FASER) which combines long document transformers with the use of intermediate representations to create a model capable of cross architecture function search without the need for manual feature engineering, pre-training or a dynamic analysis step. We compare our approach against a series of baseline approaches for two tasks; A general function search task and a targeted vulnerability search task. Our approach demonstrates strong performance across both tasks, performing better than all baseline approaches.
PeaTMOSS: Mining Pre-Trained Models in Open-Source Software
Venue: arXiv cs.SE 2023
Year: 2023

Developing and training deep learning models is expensive, so software engineers have begun to reuse pre-trained deep learning models (PTMs) and fine-tune them for downstream tasks. Despite the wide-spread use of PTMs, we know little about the corresponding software engineering behaviors and challenges. To enable the study of software engineering with PTMs, we present the PeaTMOSS dataset: Pre-Trained Models in Open-Source Software. PeaTMOSS has three parts: a snapshot of (1) 281,638 PTMs, (2) 27,270 open-source software repositories that use PTMs, and (3) a mapping between PTMs and the projects that use them. We challenge PeaTMOSS miners to discover software engineering practices around PTMs. A demo and link to the full dataset are available at: https://github.com/PurdueDualityLab/PeaTMOSS-Demos.
Evaluating Self-Supervised Speech Representations for Indigenous American Languages
Venue: arXiv cs.CL 2023
Year: 2023

The application of self-supervision to speech representation learning has garnered significant interest in recent years, due to its scalability to large amounts of unlabeled data. However, much progress, both in terms of pre-training and downstream evaluation, has remained concentrated in monolingual models that only consider English. Few models consider other languages, and even fewer consider indigenous ones. In our submission to the New Language Track of the ASRU 2023 ML-SUPERB Challenge, we present an ASR corpus for Quechua, an indigenous South American Language. We benchmark the efficacy of large SSL models on Quechua, along with 6 other indigenous languages such as Guarani and Bribri, on low-resource ASR. Our results show surprisingly strong performance by state-of-the-art SSL models, showing the potential generalizability of large-scale models to real-world data.
BrickStARt: Enabling In-situ Design and Tangible Exploration for Personal Fabrication using Mixed Reality
Venue: arXiv cs.HC 2023
Year: 2023

3D printers enable end-users to design and fabricate unique physical artifacts but maintain an increased entry barrier and friction. End users must design tangible artifacts through intangible media away from the main problem space (ex-situ) and transfer spatial requirements to an abstract software environment. To allow users to evaluate dimensions, balance, or fit early and in-situ, we developed BrickStARt, a design tool using tangible construction blocks paired with a mixed-reality headset. Users assemble a physical block model at the envisioned location of the fabricated artifact. Designs can be tested tangibly, refined, and digitally post-processed, remaining continuously in-situ. We implemented BrickStARt using a Magic Leap headset and present walkthroughs, highlighting novel interactions for 3D design. In a user study (n=16), first-time 3D modelers succeeded more often using BrickStARt than Tinkercad. Our results suggest that BrickStARt provides an accessible and explorative process while facilitating quick, tangible design iterations that allow users to detect physics-related issues (e.g., clearance) early on.
MathCoder: Seamless Code Integration in LLMs for Enhanced Mathematical Reasoning
Venue: arXiv cs.CL 2023
Year: 2023

The recently released GPT-4 Code Interpreter has demonstrated remarkable proficiency in solving challenging math problems, primarily attributed to its ability to seamlessly reason with natural language, generate code, execute code, and continue reasoning based on the execution output. In this paper, we present a method to fine-tune open-source language models, enabling them to use code for modeling and deriving math equations and, consequently, enhancing their mathematical reasoning abilities. We propose a method of generating novel and high-quality datasets with math problems and their code-based solutions, referred to as MathCodeInstruct. Each solution interleaves natural language, code, and execution results. We also introduce a customized supervised fine-tuning and inference approach. This approach yields the MathCoder models, a family of models capable of generating code-based solutions for solving challenging math problems. Impressively, the MathCoder models achieve state-of-the-art scores among open-source LLMs on the MATH (45.2%) and GSM8K (83.9%) datasets, substantially outperforming other open-source alternatives. Notably, the MathCoder model not only surpasses ChatGPT-3.5 and PaLM-2 on GSM8K and MATH but also outperforms GPT-4 on the competition-level MATH dataset. The dataset and models will be released at https://github.com/mathllm/MathCoder.
Logical Languages Accepted by Transformer Encoders with Hard Attention
Venue: arXiv cs.FL 2023
Year: 2023

We contribute to the study of formal languages that can be recognized by transformer encoders. We focus on two self-attention mechanisms: (1) UHAT (Unique Hard Attention Transformers) and (2) AHAT (Average Hard Attention Transformers). UHAT encoders are known to recognize only languages inside the circuit complexity class ${\sf AC}^0$, i.e., accepted by a family of poly-sized and depth-bounded boolean circuits with unbounded fan-ins. On the other hand, AHAT encoders can recognize languages outside ${\sf AC}^0$), but their expressive power still lies within the bigger circuit complexity class ${\sf TC}^0$, i.e., ${\sf AC}^0$-circuits extended by majority gates. We first show a negative result that there is an ${\sf AC}^0$-language that cannot be recognized by an UHAT encoder. On the positive side, we show that UHAT encoders can recognize a rich fragment of ${\sf AC}^0$-languages, namely, all languages definable in first-order logic with arbitrary unary numerical predicates. This logic, includes, for example, all regular languages from ${\sf AC}^0$. We then show that AHAT encoders can recognize all languages of our logic even when we enrich it with counting terms. We apply these results to derive new results on the expressive power of UHAT and AHAT up to permutation of letters (a.k.a. Parikh images).
Contextualized Structural Self-supervised Learning for Ontology Matching
Venue: arXiv cs.LG 2023
Year: 2023

Ontology matching (OM) entails the identification of semantic relationships between concepts within two or more knowledge graphs (KGs) and serves as a critical step in integrating KGs from various sources. Recent advancements in deep OM models have harnessed the power of transformer-based language models and the advantages of knowledge graph embedding. Nevertheless, these OM models still face persistent challenges, such as a lack of reference alignments, runtime latency, and unexplored different graph structures within an end-to-end framework. In this study, we introduce a novel self-supervised learning OM framework with input ontologies, called LaKERMap. This framework capitalizes on the contextual and structural information of concepts by integrating implicit knowledge into transformers. Specifically, we aim to capture multiple structural contexts, encompassing both local and global interactions, by employing distinct training objectives. To assess our methods, we utilize the Bio-ML datasets and tasks. The findings from our innovative approach reveal that LaKERMap surpasses state-of-the-art systems in terms of alignment quality and inference time. Our models and codes are available here: https://github.com/ellenzhuwang/lakermap.
On Repairing Natural Language to SQL Queries
Venue: arXiv cs.DB 2023
Year: 2023

Data analysts use SQL queries to access and manipulate data on their databases. However, these queries are often challenging to write, and small mistakes can lead to unexpected data output. Recent work has explored several ways to automatically synthesize queries based on a user-provided specification. One promising technique called text-to-SQL consists of the user providing a natural language description of the intended behavior and the database's schema. Even though text-to-SQL tools are becoming more accurate, there are still many instances where they fail to produce the correct query. In this paper, we analyze when text-to-SQL tools fail to return the correct query and show that it is often the case that the returned query is close to a correct query. We propose to repair these failing queries using a mutation-based approach that is agnostic to the text-to-SQL tool being used. We evaluate our approach on two recent text-to-SQL tools, RAT-SQL and SmBoP, and show that our approach can repair a significant number of failing queries.
Consistency Regularization Improves Placenta Segmentation in Fetal EPI MRI Time Series
Venue: arXiv cs.CV 2023
Year: 2023

The placenta plays a crucial role in fetal development. Automated 3D placenta segmentation from fetal EPI MRI holds promise for advancing prenatal care. This paper proposes an effective semi-supervised learning method for improving placenta segmentation in fetal EPI MRI time series. We employ consistency regularization loss that promotes consistency under spatial transformation of the same image and temporal consistency across nearby images in a time series. The experimental results show that the method improves the overall segmentation accuracy and provides better performance for outliers and hard samples. The evaluation also indicates that our method improves the temporal coherency of the prediction, which could lead to more accurate computation of temporal placental biomarkers. This work contributes to the study of the placenta and prenatal clinical decision-making. Code is available at https://github.com/firstmover/cr-seg.
Automatic and Human-AI Interactive Text Generation
Venue: arXiv cs.CL 2023
Year: 2023

In this tutorial, we focus on text-to-text generation, a class of natural language generation (NLG) tasks, that takes a piece of text as input and then generates a revision that is improved according to some specific criteria (e.g., readability or linguistic styles), while largely retaining the original meaning and the length of the text. This includes many useful applications, such as text simplification, paraphrase generation, style transfer, etc. In contrast to text summarization and open-ended text completion (e.g., story), the text-to-text generation tasks we discuss in this tutorial are more constrained in terms of semantic consistency and targeted language styles. This level of control makes these tasks ideal testbeds for studying the ability of models to generate text that is both semantically adequate and stylistically appropriate. Moreover, these tasks are interesting from a technical standpoint, as they require complex combinations of lexical and syntactical transformations, stylistic control, and adherence to factual knowledge, -- all at once. With a special focus on text simplification and revision, this tutorial aims to provide an overview of the state-of-the-art natural language generation research from four major aspects -- Data, Models, Human-AI Collaboration, and Evaluation -- and to discuss and showcase a few significant and recent advances: (1) the use of non-retrogressive approaches; (2) the shift from fine-tuning to prompting with large language models; (3) the development of new learnable metric and fine-grained human evaluation framework; (4) a growing body of studies and datasets on non-English languages; (5) the rise of HCI+NLP+Accessibility interdisciplinary research to create real-world writing assistant systems.
Information Geometry for the Working Information Theorist
Venue: arXiv cs.IT 2023
Year: 2023

Information geometry is a study of statistical manifolds, that is, spaces of probability distributions from a geometric perspective. Its classical information-theoretic applications relate to statistical concepts such as Fisher information, sufficient statistics, and efficient estimators. Today, information geometry has emerged as an interdisciplinary field that finds applications in diverse areas such as radar sensing, array signal processing, quantum physics, deep learning, and optimal transport. This article presents an overview of essential information geometry to initiate an information theorist, who may be unfamiliar with this exciting area of research. We explain the concepts of divergences on statistical manifolds, generalized notions of distances, orthogonality, and geodesics, thereby paving the way for concrete applications and novel theoretical investigations. We also highlight some recent information-geometric developments, which are of interest to the broader information theory community.
Trustworthy Formal Natural Language Specifications
Venue: arXiv cs.PL 2023
Year: 2023

Interactive proof assistants are computer programs carefully constructed to check a human-designed proof of a mathematical claim with high confidence in the implementation. However, this only validates truth of a formal claim, which may have been mistranslated from a claim made in natural language. This is especially problematic when using proof assistants to formally verify the correctness of software with respect to a natural language specification. The translation from informal to formal remains a challenging, time-consuming process that is difficult to audit for correctness. This paper shows that it is possible to build support for specifications written in expressive subsets of natural language, within existing proof assistants, consistent with the principles used to establish trust and auditability in proof assistants themselves. We implement a means to provide specifications in a modularly extensible formal subset of English, and have them automatically translated into formal claims, entirely within the Lean proof assistant. Our approach is extensible (placing no permanent restrictions on grammatical structure), modular (allowing information about new words to be distributed alongside libraries), and produces proof certificates explaining how each word was interpreted and how the sentence's structure was used to compute the meaning. We apply our prototype to the translation of various English descriptions of formal specifications from a popular textbook into Lean formalizations; all can be translated correctly with a modest lexicon with only minor modifications related to lexicon size.
RTDK-BO: High Dimensional Bayesian Optimization with Reinforced Transformer Deep kernels
Venue: arXiv cs.LG 2023
Year: 2023

Bayesian Optimization (BO), guided by Gaussian process (GP) surrogates, has proven to be an invaluable technique for efficient, high-dimensional, black-box optimization, a critical problem inherent to many applications such as industrial design and scientific computing. Recent contributions have introduced reinforcement learning (RL) to improve the optimization performance on both single function optimization and \textit{few-shot} multi-objective optimization. However, even few-shot techniques fail to exploit similarities shared between closely related objectives. In this paper, we combine recent developments in Deep Kernel Learning (DKL) and attention-based Transformer models to improve the modeling powers of GP surrogates with meta-learning. We propose a novel method for improving meta-learning BO surrogates by incorporating attention mechanisms into DKL, empowering the surrogates to adapt to contextual information gathered during the BO process. We combine this Transformer Deep Kernel with a learned acquisition function trained with continuous Soft Actor-Critic Reinforcement Learning to aid in exploration. This Reinforced Transformer Deep Kernel (RTDK-BO) approach yields state-of-the-art results in continuous high-dimensional optimization problems.
Multitask Learning for Time Series Data with 2D Convolution
Venue: arXiv cs.LG 2023
Year: 2023

Multitask learning (MTL) aims to develop a unified model that can handle a set of closely related tasks simultaneously. By optimizing the model across multiple tasks, MTL generally surpasses its non-MTL counterparts in terms of generalizability. Although MTL has been extensively researched in various domains such as computer vision, natural language processing, and recommendation systems, its application to time series data has received limited attention. In this paper, we investigate the application of MTL to the time series classification (TSC) problem. However, when we integrate the state-of-the-art 1D convolution-based TSC model with MTL, the performance of the TSC model actually deteriorates. By comparing the 1D convolution-based models with the Dynamic Time Warping (DTW) distance function, it appears that the underwhelming results stem from the limited expressive power of the 1D convolutional layers. To overcome this challenge, we propose a novel design for a 2D convolution-based model that enhances the model's expressiveness. Leveraging this advantage, our proposed method outperforms competing approaches on both the UCR Archive and an industrial transaction TSC dataset.
ILSH: The Imperial Light-Stage Head Dataset for Human Head View Synthesis
Venue: arXiv cs.CV 2023
Year: 2023

This paper introduces the Imperial Light-Stage Head (ILSH) dataset, a novel light-stage-captured human head dataset designed to support view synthesis academic challenges for human heads. The ILSH dataset is intended to facilitate diverse approaches, such as scene-specific or generic neural rendering, multiple-view geometry, 3D vision, and computer graphics, to further advance the development of photo-realistic human avatars. This paper details the setup of a light-stage specifically designed to capture high-resolution (4K) human head images and describes the process of addressing challenges (preprocessing, ethical issues) in collecting high-quality data. In addition to the data collection, we address the split of the dataset into train, validation, and test sets. Our goal is to design and support a fair view synthesis challenge task for this novel dataset, such that a similar level of performance can be maintained and expected when using the test set, as when using the validation set. The ILSH dataset consists of 52 subjects captured using 24 cameras with all 82 lighting sources turned on, resulting in a total of 1,248 close-up head images, border masks, and camera pose pairs.
Gradient Descent Provably Solves Nonlinear Tomographic Reconstruction
Venue: arXiv cs.CV 2023
Year: 2023

In computed tomography (CT), the forward model consists of a linear Radon transform followed by an exponential nonlinearity based on the attenuation of light according to the Beer-Lambert Law. Conventional reconstruction often involves inverting this nonlinearity as a preprocessing step and then solving a convex inverse problem. However, this nonlinear measurement preprocessing required to use the Radon transform is poorly conditioned in the vicinity of high-density materials, such as metal. This preprocessing makes CT reconstruction methods numerically sensitive and susceptible to artifacts near high-density regions. In this paper, we study a technique where the signal is directly reconstructed from raw measurements through the nonlinear forward model. Though this optimization is nonconvex, we show that gradient descent provably converges to the global optimum at a geometric rate, perfectly reconstructing the underlying signal with a near minimal number of random measurements. We also prove similar results in the under-determined setting where the number of measurements is significantly smaller than the dimension of the signal. This is achieved by enforcing prior structural information about the signal through constraints on the optimization variables. We illustrate the benefits of direct nonlinear CT reconstruction with cone-beam CT experiments on synthetic and real 3D volumes. We show that this approach reduces metal artifacts compared to a commercial reconstruction of a human skull with metal dental crowns.