arXiv subjects

Ole Winther

Publications and source records attributed to Ole Winther.

At least 37 records · Page 2Linked to original sources

arXiv2023

ThoughtSource: A central hub for large language model reasoning data

Large language models (LLMs) such as GPT-4 have recently demonstrated impressive results across a wide range of tasks. LLMs are still limited, however, in that they frequently fail at complex reasoning, their reasoning processes are opaque, they are prone to 'hallucinate' facts, and there are concerns about their underlying biases. Letting models verbalize reasoning steps as natural language, a technique known as chain-of-thought prompting, has recently been proposed as a way to address some of these issues. Here we present ThoughtSource, a meta-dataset and software library for chain-of-thought (CoT) reasoning. The goal of ThoughtSource is to improve future artificial intelligence systems by facilitating qualitative understanding of CoTs, enabling empirical evaluations, and providing training data. This first release of ThoughtSource integrates seven scientific/medical, three general-domain and five math word question answering datasets.

cs.CL↗

arXiv2023

Variational Open-Domain Question Answering

Retrieval-augmented models have proven to be effective in natural language processing tasks, yet there remains a lack of research on their optimization using variational inference. We introduce the Variational Open-Domain (VOD) framework for end-to-end training and evaluation of retrieval-augmented models, focusing on open-domain question answering and language modelling. The VOD objective, a self-normalized estimate of the Rényi variational bound, approximates the task marginal likelihood and is evaluated under samples drawn from an auxiliary sampling distribution (cached retriever and/or approximate posterior). It remains tractable, even for retriever distributions defined on large corpora. We demonstrate VOD's versatility by training reader-retriever BERT-sized models on multiple-choice medical exam questions. On the MedMCQA dataset, we outperform the domain-tuned Med-PaLM by +5.3% despite using 2.500$\times$ fewer parameters. Our retrieval-augmented BioLinkBERT model scored 62.9% on the MedMCQA and 55.0% on the MedQA-USMLE. Last, we show the effectiveness of our learned retriever component in the context of medical semantic search.

cs.CL↗

arXiv2023

Aligning Optimization Trajectories with Diffusion Models for Constrained Design Generation

Generative models have had a profound impact on vision and language, paving the way for a new era of multimodal generative applications. While these successes have inspired researchers to explore using generative models in science and engineering to accelerate the design process and reduce the reliance on iterative optimization, challenges remain. Specifically, engineering optimization methods based on physics still outperform generative models when dealing with constrained environments where data is scarce and precision is paramount. To address these challenges, we introduce Diffusion Optimization Models (DOM) and Trajectory Alignment (TA), a learning framework that demonstrates the efficacy of aligning the sampling trajectory of diffusion models with the optimization trajectory derived from traditional physics-based methods. This alignment ensures that the sampling process remains grounded in the underlying physical principles. Our method allows for generating feasible and high-performance designs in as few as two steps without the need for expensive preprocessing, external surrogate models, or additional labeled data. We apply our framework to structural topology optimization, a fundamental problem in mechanical design, evaluating its performance on in- and out-of-distribution configurations. Our results demonstrate that TA outperforms state-of-the-art deep generative models on in-distribution configurations and halves the inference computational cost. When coupled with a few steps of optimization, it also improves manufacturability for out-of-distribution conditions. By significantly improving performance and inference efficiency, DOM enables us to generate high-quality designs in just a few steps and guide them toward regions of high performance and manufacturability, paving the way for the widespread application of generative models in large-scale data-driven design.

cs.LG↗

arXiv2023

Unifying Molecular and Textual Representations via Multi-task Language Modelling

The recent advances in neural language models have also been successfully applied to the field of chemistry, offering generative solutions for classical problems in molecular design and synthesis planning. These new methods have the potential to fuel a new era of data-driven automation in scientific discovery. However, specialized models are still typically required for each task, leading to the need for problem-specific fine-tuning and neglecting task interrelations. The main obstacle in this field is the lack of a unified representation between natural language and chemical representations, complicating and limiting human-machine interaction. Here, we propose the first multi-domain, multi-task language model that can solve a wide range of tasks in both the chemical and natural language domains. Our model can handle chemical and natural language concurrently, without requiring expensive pre-training on single domains or task-specific models. Interestingly, sharing weights across domains remarkably improves our model when benchmarked against state-of-the-art baselines on single-domain and cross-domain tasks. In particular, sharing information across domains and tasks gives rise to large improvements in cross-domain tasks, the magnitude of which increase with scale, as measured by more than a dozen of relevant metrics. Our work suggests that such models can robustly and efficiently accelerate discovery in physical sciences by superseding problem-specific fine-tuning and enhancing human-model interactions.

cs.LG↗

arXiv2023

Dermatological Diagnosis Explainability Benchmark for Convolutional Neural Networks

In recent years, large strides have been taken in developing machine learning methods for dermatological applications, supported in part by the success of deep learning (DL). To date, diagnosing diseases from images is one of the most explored applications of DL within dermatology. Convolutional neural networks (ConvNets) are the most common (DL) method in medical imaging due to their training efficiency and accuracy, although they are often described as black boxes because of their limited explainability. One popular way to obtain insight into a ConvNet's decision mechanism is gradient class activation maps (Grad-CAM). A quantitative evaluation of the Grad-CAM explainability has been recently made possible by the release of DermXDB, a skin disease diagnosis explainability dataset which enables explainability benchmarking of ConvNet architectures. In this paper, we perform a literature review to identify the most common ConvNet architectures used for this task, and compare their Grad-CAM explanations with the explanation maps provided by DermXDB. We identified 11 architectures: DenseNet121, EfficientNet-B0, InceptionV3, InceptionResNetV2, MobileNet, MobileNetV2, NASNetMobile, ResNet50, ResNet50V2, VGG16, and Xception. We pre-trained all architectures on an clinical skin disease dataset, and fine-tuned them on a DermXDB subset. Validation results on the DermXDB holdout subset show an explainability F1 score of between 0.35-0.46, with Xception displaying the highest explainability performance. NASNetMobile reports the highest characteristic-level explainability sensitivity, despite it's mediocre diagnosis performance. These results highlight the importance of choosing the right architecture for the desired application and target market, underline need for additional explainability datasets, and further confirm the need for explainability benchmarking that relies on quantitative analyses.

cs.CV↗

arXiv2023

Explainable Image Quality Assessments in Teledermatological Photography

Image quality is a crucial factor in the effectiveness and efficiency of teledermatological consultations. However, up to 50% of images sent by patients have quality issues, thus increasing the time to diagnosis and treatment. An automated, easily deployable, explainable method for assessing image quality is necessary to improve the current teledermatological consultation flow. We introduce ImageQX, a convolutional neural network for image quality assessment with a learning mechanism for identifying the most common poor image quality explanations: bad framing, bad lighting, blur, low resolution, and distance issues. ImageQX was trained on 26,635 photographs and validated on 9,874 photographs, each annotated with image quality labels and poor image quality explanations by up to 12 board-certified dermatologists. The photographic images were taken between 2017 and 2019 using a mobile skin disease tracking application accessible worldwide. Our method achieves expert-level performance for both image quality assessment and poor image quality explanation. For image quality assessment, ImageQX obtains a macro F1-score of 0.73 +- 0.01, which places it within standard deviation of the pairwise inter-rater F1-score of 0.77 +- 0.07. For poor image quality explanations, our method obtains F1-scores of between 0.37 +- 0.01 and 0.70 +- 0.01, similar to the inter-rater pairwise F1-score of between 0.24 +- 0.15 and 0.83 +- 0.06. Moreover, with a size of only 15 MB, ImageQX is easily deployable on mobile devices. With an image quality detection performance similar to that of dermatologists, incorporating ImageQX into the teledermatology flow can enable a better, faster flow for remote consultations.

cs.CV↗

arXiv2022

Image Super-Resolution With Deep Variational Autoencoders

Image super-resolution (SR) techniques are used to generate a high-resolution image from a low-resolution image. Until now, deep generative models such as autoregressive models and Generative Adversarial Networks (GANs) have proven to be effective at modelling high-resolution images. VAE-based models have often been criticised for their feeble generative performance, but with new advancements such as VDVAE, there is now strong evidence that deep VAEs have the potential to outperform current state-of-the-art models for high-resolution image generation. In this paper, we introduce VDVAE-SR, a new model that aims to exploit the most recent deep VAE methodologies to improve upon the results of similar models. VDVAE-SR tackles image super-resolution using transfer learning on pretrained VDVAEs. The presented model is competitive with other state-of-the-art models, having comparable results on image quality metrics.

cs.CV↗

arXiv2022

DermX: an end-to-end framework for explainable automated dermatological diagnosis

Dermatological diagnosis automation is essential in addressing the high prevalence of skin diseases and critical shortage of dermatologists. Despite approaching expert-level diagnosis performance, convolutional neural network (ConvNet) adoption in clinical practice is impeded by their limited explainability, and by subjective, expensive explainability validations. We introduce DermX and DermX+, an end-to-end framework for explainable automated dermatological diagnosis. DermX is a clinically-inspired explainable dermatological diagnosis ConvNet, trained using DermXDB, a 554 image dataset annotated by eight dermatologists with diagnoses, supporting explanations, and explanation attention maps. DermX+ extends DermX with guided attention training for explanation attention maps. Both methods achieve near-expert diagnosis performance, with DermX, DermX+, and dermatologist F1 scores of 0.79, 0.79, and 0.87, respectively. We assess the explanation performance in terms of identification and localization by comparing model-selected with dermatologist-selected explanations, and gradient-weighted class-activation maps with dermatologist explanation maps, respectively. DermX obtained an identification F1 score of 0.77, while DermX+ obtained 0.79. The localization F1 score is 0.39 for DermX and 0.35 for DermX+. These results show that explainability does not necessarily come at the expense of predictive power, as our high-performance models provide expert-inspired explanations for their diagnoses without lowering their diagnosis performance.

eess.IV↗

arXiv2022

NeuralNEB -- Neural Networks can find Reaction Paths Fast

Quantum mechanical methods like Density Functional Theory (DFT) are used with great success alongside efficient search algorithms for studying kinetics of reactive systems. However, DFT is prohibitively expensive for large scale exploration. Machine Learning (ML) models have turned out to be excellent emulators of small molecule DFT calculations and could possibly replace DFT in such tasks. For kinetics, success relies primarily on the models capability to accurately predict the Potential Energy Surface (PES) around transition-states and Minimal Energy Paths (MEPs). Previously this has not been possible due to scarcity of relevant data in the literature. In this paper we train state of the art equivariant Graph Neural Network (GNN)-based models on around 10.000 elementary reactions from the Transition1x dataset. We apply the models as potentials for the Nudged Elastic Band (NEB) algorithm and achieve a Mean Average Error (MAE) of 0.13+/-0.03 eV on barrier energies on unseen reactions. We compare the results against equivalent models trained on QM9 and ANI1x. We also compare with and outperform Density Functional based Tight Binding (DFTB) on both accuracy and computational resource. The implication is that ML models, given relevant data, are now at a level where they can be applied for downstream tasks in quantum chemistry transcending prediction of simple molecular features.

physics.comp-ph↗

arXiv2022

Transition1x -- a Dataset for Building Generalizable Reactive Machine Learning Potentials

Machine Learning (ML) models have, in contrast to their usefulness in molecular dynamics studies, had limited success as surrogate potentials for reaction barrier search. It is due to the scarcity of training data in relevant transition state regions of chemical space. Currently, available datasets for training ML models on small molecular systems almost exclusively contain configurations at or near equilibrium. In this work, we present the dataset Transition1x containing 9.6 million Density Functional Theory (DFT) calculations of forces and energies of molecular configurations on and around reaction pathways at the wB97x/6-31G(d) level of theory. The data was generated by running Nudged Elastic Band (NEB) calculations with DFT on 10k reactions while saving intermediate calculations. We train state-of-the-art equivariant graph message-passing neural network models on Transition1x and cross-validate on the popular ANI1x and QM9 datasets. We show that ML models cannot learn features in transition-state regions solely by training on hitherto popular benchmark datasets. Transition1x is a new challenging benchmark that will provide an important step towards developing next-generation ML force fields that also work far away from equilibrium configurations and reactive systems.

physics.chem-ph↗

arXiv2022

Inductive Biases for Object-Centric Representations in the Presence of Complex Textures

Understanding which inductive biases could be helpful for the unsupervised learning of object-centric representations of natural scenes is challenging. In this paper, we systematically investigate the performance of two models on datasets where neural style transfer was used to obtain objects with complex textures while still retaining ground-truth annotations. We find that by using a single module to reconstruct both the shape and visual appearance of each object, the model learns more useful representations and achieves better object separation. In addition, we observe that adjusting the latent space size is insufficient to improve segmentation performance. Finally, the downstream usefulness of the representations is significantly more strongly correlated with segmentation quality than with reconstruction accuracy.

cs.CV↗

arXiv2022

SCHA-VAE: Hierarchical Context Aggregation for Few-Shot Generation

A few-shot generative model should be able to generate data from a novel distribution by only observing a limited set of examples. In few-shot learning the model is trained on data from many sets from distributions sharing some underlying properties such as sets of characters from different alphabets or objects from different categories. We extend current latent variable models for sets to a fully hierarchical approach with an attention-based point to set-level aggregation and call our method SCHA-VAE for Set-Context-Hierarchical-Aggregation Variational Autoencoder. We explore likelihood-based model comparison, iterative data sampling, and adaptation-free out-of-distribution generalization. Our results show that the hierarchical formulation better captures the intrinsic variability within the sets in the small data regime. This work generalizes deep latent variable approaches to few-shot learning, taking a step toward large-scale few-shot generation with a formulation that readily works with current state-of-the-art deep generative models.

cs.LG↗

arXiv2022

Reconstructing the exit wave in high-resolution transmission electron microscopy using machine learning

Reconstruction of the exit wave function is an important route to interpreting high-resolution transmission electron microscopy (HRTEM) images. Here we demonstrate that convolutional neural networks can be used to reconstruct the exit wave from a short focal series of HRTEM images, with a fidelity comparable to conventional exit wave reconstruction. We use a fully convolutional neural network based on the U-Net architecture, and demonstrate that we can train it on simulated exit waves and simulated HRTEM images of graphene-supported molybdenum disulphide (an industrial desulfurization catalyst). We then apply the trained network to analyse experimentally obtained images from similar samples, and obtain exit waves that clearly show the atomically resolved structure of both the MoS$_2$ nanoparticles and the graphene support. We also show that it is possible to successfully train the neural networks to reconstruct exit waves for 3400 different two-dimensional materials taken from the Computational 2D Materials Database of known and proposed two-dimensional materials.

cond-mat.mtrl-sci↗

arXiv2022

Generalization and Robustness Implications in Object-Centric Learning

The idea behind object-centric representation learning is that natural scenes can better be modeled as compositions of objects and their relations as opposed to distributed representations. This inductive bias can be injected into neural networks to potentially improve systematic generalization and performance of downstream tasks in scenes with multiple objects. In this paper, we train state-of-the-art unsupervised models on five common multi-object datasets and evaluate segmentation metrics and downstream object property prediction. In addition, we study generalization and robustness by investigating the settings where either a single object is out of distribution -- e.g., having an unseen color, texture, or shape -- or global properties of the scene are altered -- e.g., by occlusions, cropping, or increasing the number of objects. From our experimental study, we find object-centric representations to be useful for downstream tasks and generally robust to most distribution shifts affecting objects. However, when the distribution shift affects the input in a less structured manner, robustness in terms of segmentation and downstream task performance may vary significantly across models and distribution shifts.

cs.LG↗

arXiv2022

Few-Shot Diffusion Models

Denoising diffusion probabilistic models (DDPM) are powerful hierarchical latent variable models with remarkable sample generation quality and training stability. These properties can be attributed to parameter sharing in the generative hierarchy, as well as a parameter-free diffusion-based inference procedure. In this paper, we present Few-Shot Diffusion Models (FSDM), a framework for few-shot generation leveraging conditional DDPMs. FSDMs are trained to adapt the generative process conditioned on a small set of images from a given class by aggregating image patch information using a set-based Vision Transformer (ViT). At test time, the model is able to generate samples from previously unseen classes conditioned on as few as 5 samples from that class. We empirically show that FSDM can perform few-shot generation and transfer to new datasets. We benchmark variants of our method on complex vision datasets for few-shot learning and compare to unconditional and conditional DDPM baselines. Additionally, we show how conditioning the model on patch-based input set information improves training convergence.

cs.CV↗

arXiv2022

The Role of Pretrained Representations for the OOD Generalization of Reinforcement Learning Agents

Building sample-efficient agents that generalize out-of-distribution (OOD) in real-world settings remains a fundamental unsolved problem on the path towards achieving higher-level cognition. One particularly promising approach is to begin with low-dimensional, pretrained representations of our world, which should facilitate efficient downstream learning and generalization. By training 240 representations and over 10,000 reinforcement learning (RL) policies on a simulated robotic setup, we evaluate to what extent different properties of pretrained VAE-based representations affect the OOD generalization of downstream agents. We observe that many agents are surprisingly robust to realistic distribution shifts, including the challenging sim-to-real case. In addition, we find that the generalization performance of a simple downstream proxy task reliably predicts the generalization performance of our RL agents under a wide range of OOD settings. Such proxy tasks can thus be used to select pretrained representations that will lead to agents that generalize.

cs.LG↗

arXiv2021

Calibrated Uncertainty for Molecular Property Prediction using Ensembles of Message Passing Neural Networks

Data-driven methods based on machine learning have the potential to accelerate computational analysis of atomic structures. In this context, reliable uncertainty estimates are important for assessing confidence in predictions and enabling decision making. However, machine learning models can produce badly calibrated uncertainty estimates and it is therefore crucial to detect and handle uncertainty carefully. In this work we extend a message passing neural network designed specifically for predicting properties of molecules and materials with a calibrated probabilistic predictive distribution. The method presented in this paper differs from previous work by considering both aleatoric and epistemic uncertainty in a unified framework, and by recalibrating the predictive distribution on unseen data. Through computer experiments, we show that our approach results in accurate models for predicting molecular formation energies with well calibrated uncertainty in and out of the training data distribution on two public molecular benchmark datasets, QM9 and PC9. The proposed method provides a general framework for training and evaluating neural network ensemble models that are able to produce accurate predictions of properties of molecules with well calibrated uncertainty estimates.

cs.LG↗

arXiv2021

Attend, Copy, Parse -- End-to-end information extraction from documents

Document information extraction tasks performed by humans create data consisting of a PDF or document image input, and extracted string outputs. This end-to-end data is naturally consumed and produced when performing the task because it is valuable in and of itself. It is naturally available, at no additional cost. Unfortunately, state-of-the-art word classification methods for information extraction cannot use this data, instead requiring word-level labels which are expensive to create and consequently not available for many real life tasks. In this paper we propose the Attend, Copy, Parse architecture, a deep neural network model that can be trained directly on end-to-end data, bypassing the need for word-level labels. We evaluate the proposed architecture on a large diverse set of invoices, and outperform a state-of-the-art production system based on word classification. We believe our proposed architecture can be used on many real life information extraction tasks where word classification cannot be used due to a lack of the required word-level labels.

cs.CL↗