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Mar 11

Making the Most of your Model: Methods for Finetuning and Applying Pretrained Transformers

This thesis provides methods and analysis of models which make progress on this goal. The techniques outlined are task agnostic, and should provide benefit when used with nearly any transformer LM. We introduce two new finetuning methods which add new capabilities to the models they are used on. The first adds a recurrence mechanism, which removes the fixed-window sized constraint and improves the efficiency of a transformer decoder. The second allows masked language models (MLMs) to be used for initialization of both the encoder and decoder of a non-autoregressive sequence-to-sequence transformer, opening up generative applications of models which were previously only used for natural language understanding tasks. We also introduce two new techniques for improving the quality of predictions of any transformer decoder without additional finetuning. One, hidden state optimization, can be applied to any transformer decoder to improve the quality of predictions at inference time, especially for few-shot classification. The other, conditional beam search, allows practitioners to search for natural language generation (NLG) model outputs with high likelihood while conditioning on the event that the output is not degenerate (e.g. empty, repetitive, etc.). Finally, we provide theoretical and empirical insights on the divergence of model-likelihood and output quality which has widely been observed in prior work. These insights apply to any model which represents a distribution over text, and apply to language models which are not transformers or even autoregressive. We argue that the NLP community has, to some extent, misunderstood the implications of these findings, and encourage a point of view which has more nuance.

DaViT: Dual Attention Vision Transformers

In this work, we introduce Dual Attention Vision Transformers (DaViT), a simple yet effective vision transformer architecture that is able to capture global context while maintaining computational efficiency. We propose approaching the problem from an orthogonal angle: exploiting self-attention mechanisms with both "spatial tokens" and "channel tokens". With spatial tokens, the spatial dimension defines the token scope, and the channel dimension defines the token feature dimension. With channel tokens, we have the inverse: the channel dimension defines the token scope, and the spatial dimension defines the token feature dimension. We further group tokens along the sequence direction for both spatial and channel tokens to maintain the linear complexity of the entire model. We show that these two self-attentions complement each other: (i) since each channel token contains an abstract representation of the entire image, the channel attention naturally captures global interactions and representations by taking all spatial positions into account when computing attention scores between channels; (ii) the spatial attention refines the local representations by performing fine-grained interactions across spatial locations, which in turn helps the global information modeling in channel attention. Extensive experiments show our DaViT achieves state-of-the-art performance on four different tasks with efficient computations. Without extra data, DaViT-Tiny, DaViT-Small, and DaViT-Base achieve 82.8%, 84.2%, and 84.6% top-1 accuracy on ImageNet-1K with 28.3M, 49.7M, and 87.9M parameters, respectively. When we further scale up DaViT with 1.5B weakly supervised image and text pairs, DaViT-Gaint reaches 90.4% top-1 accuracy on ImageNet-1K. Code is available at https://github.com/dingmyu/davit.

Biases in Expected Goals Models Confound Finishing Ability

Expected Goals (xG) has emerged as a popular tool for evaluating finishing skill in soccer analytics. It involves comparing a player's cumulative xG with their actual goal output, where consistent overperformance indicates strong finishing ability. However, the assessment of finishing skill in soccer using xG remains contentious due to players' difficulty in consistently outperforming their cumulative xG. In this paper, we aim to address the limitations and nuances surrounding the evaluation of finishing skill using xG statistics. Specifically, we explore three hypotheses: (1) the deviation between actual and expected goals is an inadequate metric due to the high variance of shot outcomes and limited sample sizes, (2) the inclusion of all shots in cumulative xG calculation may be inappropriate, and (3) xG models contain biases arising from interdependencies in the data that affect skill measurement. We found that sustained overperformance of cumulative xG requires both high shot volumes and exceptional finishing, including all shot types can obscure the finishing ability of proficient strikers, and that there is a persistent bias that makes the actual and expected goals closer for excellent finishers than it really is. Overall, our analysis indicates that we need more nuanced quantitative approaches for investigating a player's finishing ability, which we achieved using a technique from AI fairness to learn an xG model that is calibrated for multiple subgroups of players. As a concrete use case, we show that (1) the standard biased xG model underestimates Messi's GAX by 17% and (2) Messi's GAX is 27% higher than the typical elite high-shot-volume attacker, indicating that Messi is even a more exceptional finisher than people commonly believed.

COPILOT: Human-Environment Collision Prediction and Localization from Egocentric Videos

The ability to forecast human-environment collisions from egocentric observations is vital to enable collision avoidance in applications such as VR, AR, and wearable assistive robotics. In this work, we introduce the challenging problem of predicting collisions in diverse environments from multi-view egocentric videos captured from body-mounted cameras. Solving this problem requires a generalizable perception system that can classify which human body joints will collide and estimate a collision region heatmap to localize collisions in the environment. To achieve this, we propose a transformer-based model called COPILOT to perform collision prediction and localization simultaneously, which accumulates information across multi-view inputs through a novel 4D space-time-viewpoint attention mechanism. To train our model and enable future research on this task, we develop a synthetic data generation framework that produces egocentric videos of virtual humans moving and colliding within diverse 3D environments. This framework is then used to establish a large-scale dataset consisting of 8.6M egocentric RGBD frames. Extensive experiments show that COPILOT generalizes to unseen synthetic as well as real-world scenes. We further demonstrate COPILOT outputs are useful for downstream collision avoidance through simple closed-loop control. Please visit our project webpage at https://sites.google.com/stanford.edu/copilot.

Multi-Track Timeline Control for Text-Driven 3D Human Motion Generation

Recent advances in generative modeling have led to promising progress on synthesizing 3D human motion from text, with methods that can generate character animations from short prompts and specified durations. However, using a single text prompt as input lacks the fine-grained control needed by animators, such as composing multiple actions and defining precise durations for parts of the motion. To address this, we introduce the new problem of timeline control for text-driven motion synthesis, which provides an intuitive, yet fine-grained, input interface for users. Instead of a single prompt, users can specify a multi-track timeline of multiple prompts organized in temporal intervals that may overlap. This enables specifying the exact timings of each action and composing multiple actions in sequence or at overlapping intervals. To generate composite animations from a multi-track timeline, we propose a new test-time denoising method. This method can be integrated with any pre-trained motion diffusion model to synthesize realistic motions that accurately reflect the timeline. At every step of denoising, our method processes each timeline interval (text prompt) individually, subsequently aggregating the predictions with consideration for the specific body parts engaged in each action. Experimental comparisons and ablations validate that our method produces realistic motions that respect the semantics and timing of given text prompts. Our code and models are publicly available at https://mathis.petrovich.fr/stmc.

How Effective Are Neural Networks for Fixing Security Vulnerabilities

Security vulnerability repair is a difficult task that is in dire need of automation. Two groups of techniques have shown promise: (1) large code language models (LLMs) that have been pre-trained on source code for tasks such as code completion, and (2) automated program repair (APR) techniques that use deep learning (DL) models to automatically fix software bugs. This paper is the first to study and compare Java vulnerability repair capabilities of LLMs and DL-based APR models. The contributions include that we (1) apply and evaluate five LLMs (Codex, CodeGen, CodeT5, PLBART and InCoder), four fine-tuned LLMs, and four DL-based APR techniques on two real-world Java vulnerability benchmarks (Vul4J and VJBench), (2) design code transformations to address the training and test data overlapping threat to Codex, (3) create a new Java vulnerability repair benchmark VJBench, and its transformed version VJBench-trans and (4) evaluate LLMs and APR techniques on the transformed vulnerabilities in VJBench-trans. Our findings include that (1) existing LLMs and APR models fix very few Java vulnerabilities. Codex fixes 10.2 (20.4%), the most number of vulnerabilities. (2) Fine-tuning with general APR data improves LLMs' vulnerability-fixing capabilities. (3) Our new VJBench reveals that LLMs and APR models fail to fix many Common Weakness Enumeration (CWE) types, such as CWE-325 Missing cryptographic step and CWE-444 HTTP request smuggling. (4) Codex still fixes 8.3 transformed vulnerabilities, outperforming all the other LLMs and APR models on transformed vulnerabilities. The results call for innovations to enhance automated Java vulnerability repair such as creating larger vulnerability repair training data, tuning LLMs with such data, and applying code simplification transformation to facilitate vulnerability repair.

The LHCb ultra-fast simulation option, Lamarr: design and validation

Detailed detector simulation is the major consumer of CPU resources at LHCb, having used more than 90% of the total computing budget during Run 2 of the Large Hadron Collider at CERN. As data is collected by the upgraded LHCb detector during Run 3 of the LHC, larger requests for simulated data samples are necessary, and will far exceed the pledged resources of the experiment, even with existing fast simulation options. An evolution of technologies and techniques to produce simulated samples is mandatory to meet the upcoming needs of analysis to interpret signal versus background and measure efficiencies. In this context, we propose Lamarr, a Gaudi-based framework designed to offer the fastest solution for the simulation of the LHCb detector. Lamarr consists of a pipeline of modules parameterizing both the detector response and the reconstruction algorithms of the LHCb experiment. Most of the parameterizations are made of Deep Generative Models and Gradient Boosted Decision Trees trained on simulated samples or alternatively, where possible, on real data. Embedding Lamarr in the general LHCb Gauss Simulation framework allows combining its execution with any of the available generators in a seamless way. Lamarr has been validated by comparing key reconstructed quantities with Detailed Simulation. Good agreement of the simulated distributions is obtained with two-order-of-magnitude speed-up of the simulation phase.

On the application of Large Language Models for language teaching and assessment technology

The recent release of very large language models such as PaLM and GPT-4 has made an unprecedented impact in the popular media and public consciousness, giving rise to a mixture of excitement and fear as to their capabilities and potential uses, and shining a light on natural language processing research which had not previously received so much attention. The developments offer great promise for education technology, and in this paper we look specifically at the potential for incorporating large language models in AI-driven language teaching and assessment systems. We consider several research areas and also discuss the risks and ethical considerations surrounding generative AI in education technology for language learners. Overall we find that larger language models offer improvements over previous models in text generation, opening up routes toward content generation which had not previously been plausible. For text generation they must be prompted carefully and their outputs may need to be reshaped before they are ready for use. For automated grading and grammatical error correction, tasks whose progress is checked on well-known benchmarks, early investigations indicate that large language models on their own do not improve on state-of-the-art results according to standard evaluation metrics. For grading it appears that linguistic features established in the literature should still be used for best performance, and for error correction it may be that the models can offer alternative feedback styles which are not measured sensitively with existing methods. In all cases, there is work to be done to experiment with the inclusion of large language models in education technology for language learners, in order to properly understand and report on their capacities and limitations, and to ensure that foreseeable risks such as misinformation and harmful bias are mitigated.

Learning Support and Trivial Prototypes for Interpretable Image Classification

Prototypical part network (ProtoPNet) methods have been designed to achieve interpretable classification by associating predictions with a set of training prototypes, which we refer to as trivial prototypes because they are trained to lie far from the classification boundary in the feature space. Note that it is possible to make an analogy between ProtoPNet and support vector machine (SVM) given that the classification from both methods relies on computing similarity with a set of training points (i.e., trivial prototypes in ProtoPNet, and support vectors in SVM). However, while trivial prototypes are located far from the classification boundary, support vectors are located close to this boundary, and we argue that this discrepancy with the well-established SVM theory can result in ProtoPNet models with inferior classification accuracy. In this paper, we aim to improve the classification of ProtoPNet with a new method to learn support prototypes that lie near the classification boundary in the feature space, as suggested by the SVM theory. In addition, we target the improvement of classification results with a new model, named ST-ProtoPNet, which exploits our support prototypes and the trivial prototypes to provide more effective classification. Experimental results on CUB-200-2011, Stanford Cars, and Stanford Dogs datasets demonstrate that ST-ProtoPNet achieves state-of-the-art classification accuracy and interpretability results. We also show that the proposed support prototypes tend to be better localised in the object of interest rather than in the background region.

Soft-NMS -- Improving Object Detection With One Line of Code

Non-maximum suppression is an integral part of the object detection pipeline. First, it sorts all detection boxes on the basis of their scores. The detection box M with the maximum score is selected and all other detection boxes with a significant overlap (using a pre-defined threshold) with M are suppressed. This process is recursively applied on the remaining boxes. As per the design of the algorithm, if an object lies within the predefined overlap threshold, it leads to a miss. To this end, we propose Soft-NMS, an algorithm which decays the detection scores of all other objects as a continuous function of their overlap with M. Hence, no object is eliminated in this process. Soft-NMS obtains consistent improvements for the coco-style mAP metric on standard datasets like PASCAL VOC 2007 (1.7% for both R-FCN and Faster-RCNN) and MS-COCO (1.3% for R-FCN and 1.1% for Faster-RCNN) by just changing the NMS algorithm without any additional hyper-parameters. Using Deformable-RFCN, Soft-NMS improves state-of-the-art in object detection from 39.8% to 40.9% with a single model. Further, the computational complexity of Soft-NMS is the same as traditional NMS and hence it can be efficiently implemented. Since Soft-NMS does not require any extra training and is simple to implement, it can be easily integrated into any object detection pipeline. Code for Soft-NMS is publicly available on GitHub (http://bit.ly/2nJLNMu).

INDUS: Effective and Efficient Language Models for Scientific Applications

Large language models (LLMs) trained on general domain corpora showed remarkable results on natural language processing (NLP) tasks. However, previous research demonstrated LLMs trained using domain-focused corpora perform better on specialized tasks. Inspired by this pivotal insight, we developed INDUS, a comprehensive suite of LLMs tailored for the Earth science, biology, physics, heliophysics, planetary sciences and astrophysics domains and trained using curated scientific corpora drawn from diverse data sources. The suite of models include: (1) an encoder model trained using domain-specific vocabulary and corpora to address natural language understanding tasks, (2) a contrastive-learning-based general text embedding model trained using a diverse set of datasets drawn from multiple sources to address information retrieval tasks and (3) smaller versions of these models created using knowledge distillation techniques to address applications which have latency or resource constraints. We also created three new scientific benchmark datasets namely, CLIMATE-CHANGE-NER (entity-recognition), NASA-QA (extractive QA) and NASA-IR (IR) to accelerate research in these multi-disciplinary fields. Finally, we show that our models outperform both general-purpose encoders (RoBERTa) and existing domain-specific encoders (SciBERT) on these new tasks as well as existing benchmark tasks in the domains of interest.

PeaTMOSS: A Dataset and Initial Analysis of Pre-Trained Models in Open-Source Software

The development and training of deep learning models have become increasingly costly and complex. Consequently, software engineers are adopting pre-trained models (PTMs) for their downstream applications. The dynamics of the PTM supply chain remain largely unexplored, signaling a clear need for structured datasets that document not only the metadata but also the subsequent applications of these models. Without such data, the MSR community cannot comprehensively understand the impact of PTM adoption and reuse. This paper presents the PeaTMOSS dataset, which comprises metadata for 281,638 PTMs and detailed snapshots for all PTMs with over 50 monthly downloads (14,296 PTMs), along with 28,575 open-source software repositories from GitHub that utilize these models. Additionally, the dataset includes 44,337 mappings from 15,129 downstream GitHub repositories to the 2,530 PTMs they use. To enhance the dataset's comprehensiveness, we developed prompts for a large language model to automatically extract model metadata, including the model's training datasets, parameters, and evaluation metrics. Our analysis of this dataset provides the first summary statistics for the PTM supply chain, showing the trend of PTM development and common shortcomings of PTM package documentation. Our example application reveals inconsistencies in software licenses across PTMs and their dependent projects. PeaTMOSS lays the foundation for future research, offering rich opportunities to investigate the PTM supply chain. We outline mining opportunities on PTMs, their downstream usage, and cross-cutting questions.

PTMTorrent: A Dataset for Mining Open-source Pre-trained Model Packages

Due to the cost of developing and training deep learning models from scratch, machine learning engineers have begun to reuse pre-trained models (PTMs) and fine-tune them for downstream tasks. PTM registries known as "model hubs" support engineers in distributing and reusing deep learning models. PTM packages include pre-trained weights, documentation, model architectures, datasets, and metadata. Mining the information in PTM packages will enable the discovery of engineering phenomena and tools to support software engineers. However, accessing this information is difficult - there are many PTM registries, and both the registries and the individual packages may have rate limiting for accessing the data. We present an open-source dataset, PTMTorrent, to facilitate the evaluation and understanding of PTM packages. This paper describes the creation, structure, usage, and limitations of the dataset. The dataset includes a snapshot of 5 model hubs and a total of 15,913 PTM packages. These packages are represented in a uniform data schema for cross-hub mining. We describe prior uses of this data and suggest research opportunities for mining using our dataset. The PTMTorrent dataset (v1) is available at: https://app.globus.org/file-manager?origin_id=55e17a6e-9d8f-11ed-a2a2-8383522b48d9&origin_path=%2F~%2F. Our dataset generation tools are available on GitHub: https://doi.org/10.5281/zenodo.7570357.

Challenges and Practices of Deep Learning Model Reengineering: A Case Study on Computer Vision

Many engineering organizations are reimplementing and extending deep neural networks from the research community. We describe this process as deep learning model reengineering. Deep learning model reengineering - reusing, reproducing, adapting, and enhancing state-of-the-art deep learning approaches - is challenging for reasons including under-documented reference models, changing requirements, and the cost of implementation and testing. In addition, individual engineers may lack expertise in software engineering, yet teams must apply knowledge of software engineering and deep learning to succeed. Prior work has examined on DL systems from a "product" view, examining defects from projects regardless of the engineers' purpose. Our study is focused on reengineering activities from a "process" view, and focuses on engineers specifically engaged in the reengineering process. Our goal is to understand the characteristics and challenges of deep learning model reengineering. We conducted a case study of this phenomenon, focusing on the context of computer vision. Our results draw from two data sources: defects reported in open-source reeengineering projects, and interviews conducted with open-source project contributors and the leaders of a reengineering team. Our results describe how deep learning-based computer vision techniques are reengineered, analyze the distribution of defects in this process, and discuss challenges and practices. Integrating our quantitative and qualitative data, we proposed a novel reengineering workflow. Our findings inform several future directions, including: measuring additional unknown aspects of model reengineering; standardizing engineering practices to facilitate reengineering; and developing tools to support model reengineering and model reuse.

An Empirical Study of Pre-Trained Model Reuse in the Hugging Face Deep Learning Model Registry

Deep Neural Networks (DNNs) are being adopted as components in software systems. Creating and specializing DNNs from scratch has grown increasingly difficult as state-of-the-art architectures grow more complex. Following the path of traditional software engineering, machine learning engineers have begun to reuse large-scale pre-trained models (PTMs) and fine-tune these models for downstream tasks. Prior works have studied reuse practices for traditional software packages to guide software engineers towards better package maintenance and dependency management. We lack a similar foundation of knowledge to guide behaviors in pre-trained model ecosystems. In this work, we present the first empirical investigation of PTM reuse. We interviewed 12 practitioners from the most popular PTM ecosystem, Hugging Face, to learn the practices and challenges of PTM reuse. From this data, we model the decision-making process for PTM reuse. Based on the identified practices, we describe useful attributes for model reuse, including provenance, reproducibility, and portability. Three challenges for PTM reuse are missing attributes, discrepancies between claimed and actual performance, and model risks. We substantiate these identified challenges with systematic measurements in the Hugging Face ecosystem. Our work informs future directions on optimizing deep learning ecosystems by automated measuring useful attributes and potential attacks, and envision future research on infrastructure and standardization for model registries.

On the Opportunities and Risks of Foundation Models

AI is undergoing a paradigm shift with the rise of models (e.g., BERT, DALL-E, GPT-3) that are trained on broad data at scale and are adaptable to a wide range of downstream tasks. We call these models foundation models to underscore their critically central yet incomplete character. This report provides a thorough account of the opportunities and risks of foundation models, ranging from their capabilities (e.g., language, vision, robotics, reasoning, human interaction) and technical principles(e.g., model architectures, training procedures, data, systems, security, evaluation, theory) to their applications (e.g., law, healthcare, education) and societal impact (e.g., inequity, misuse, economic and environmental impact, legal and ethical considerations). Though foundation models are based on standard deep learning and transfer learning, their scale results in new emergent capabilities,and their effectiveness across so many tasks incentivizes homogenization. Homogenization provides powerful leverage but demands caution, as the defects of the foundation model are inherited by all the adapted models downstream. Despite the impending widespread deployment of foundation models, we currently lack a clear understanding of how they work, when they fail, and what they are even capable of due to their emergent properties. To tackle these questions, we believe much of the critical research on foundation models will require deep interdisciplinary collaboration commensurate with their fundamentally sociotechnical nature.

An Experience Report on Machine Learning Reproducibility: Guidance for Practitioners and TensorFlow Model Garden Contributors

Machine learning techniques are becoming a fundamental tool for scientific and engineering progress. These techniques are applied in contexts as diverse as astronomy and spam filtering. However, correctly applying these techniques requires careful engineering. Much attention has been paid to the technical potential; relatively little attention has been paid to the software engineering process required to bring research-based machine learning techniques into practical utility. Technology companies have supported the engineering community through machine learning frameworks such as TensorFLow and PyTorch, but the details of how to engineer complex machine learning models in these frameworks have remained hidden. To promote best practices within the engineering community, academic institutions and Google have partnered to launch a Special Interest Group on Machine Learning Models (SIGMODELS) whose goal is to develop exemplary implementations of prominent machine learning models in community locations such as the TensorFlow Model Garden (TFMG). The purpose of this report is to define a process for reproducing a state-of-the-art machine learning model at a level of quality suitable for inclusion in the TFMG. We define the engineering process and elaborate on each step, from paper analysis to model release. We report on our experiences implementing the YOLO model family with a team of 26 student researchers, share the tools we developed, and describe the lessons we learned along the way.

The Chandra Source Catalog

The Chandra Source Catalog (CSC) is a general purpose virtual X-ray astrophysics facility that provides access to a carefully selected set of generally useful quantities for individual X-ray sources, and is designed to satisfy the needs of a broad-based group of scientists, including those who may be less familiar with astronomical data analysis in the X-ray regime. The first release of the CSC includes information about 94,676 distinct X-ray sources detected in a subset of public ACIS imaging observations from roughly the first eight years of the Chandra mission. This release of the catalog includes point and compact sources with observed spatial extents <~ 30''. The catalog (1) provides access to the best estimates of the X-ray source properties for detected sources, with good scientific fidelity, and directly supports scientific analysis using the individual source data; (2) facilitates analysis of a wide range of statistical properties for classes of X-ray sources; and (3) provides efficient access to calibrated observational data and ancillary data products for individual X-ray sources, so that users can perform detailed further analysis using existing tools. The catalog includes real X-ray sources detected with flux estimates that are at least 3 times their estimated 1 sigma uncertainties in at least one energy band, while maintaining the number of spurious sources at a level of <~ 1 false source per field for a 100 ks observation. For each detected source, the CSC provides commonly tabulated quantities, including source position, extent, multi-band fluxes, hardness ratios, and variability statistics, derived from the observations in which the source is detected. In addition to these traditional catalog elements, for each X-ray source the CSC includes an extensive set of file-based data products that can be manipulated interactively.

Selection Function of Clusters in Dark Energy Survey Year 3 Data from Cross-Matching with South Pole Telescope Detections

Galaxy clusters selected based on overdensities of galaxies in photometric surveys provide the largest cluster samples. Yet modeling the selection function of such samples is complicated by non-cluster members projected along the line of sight (projection effects) and the potential detection of unvirialized objects (contamination). We empirically constrain the magnitude of these effects by cross-matching galaxy clusters selected in the Dark Energy survey data with the \rdmpr, algorithm with significant detections in three South Pole Telescope surveys (SZ, pol-ECS, pol-500d). For matched clusters, we augment the \rdmpr,catalog by the SPT detection significance. For unmatched objects we use the SPT detection threshold as an upper limit on the SZe signature. Using a Bayesian population model applied to the collected multi-wavelength data, we explore various physically motivated models to describe the relationship between observed richness and halo mass. Our analysis reveals the limitations of a simple lognormal scatter model in describing the data. We rule out significant contamination by unvirialized objects at the high-richness end of the sample. While dedicated simulations offer a well-fitting calibration of projection effects, our findings suggest the presence of redshift-dependent trends that these simulations may not have captured. Our findings highlight that modeling the selection function of optically detected clusters remains a complicated challenge, requiring a combination of simulation and data-driven approaches.