Reviewerly/exHarmony huggingface dataset:
Segmentation of 3D pore space from CT images using curvilinear skeleton: application to numerical simulation of microbial decomposition

Recent advances in 3D X-ray Computed Tomographic (CT) sensors have stimulated research efforts to unveil the extremely complex micro-scale processes that control the activity of soil microorganisms. Voxel-based description (up to hundreds millions voxels) of the pore space can be extracted, from grey level 3D CT scanner images, by means of simple image processing tools. Classical methods for numerical simulation of biological dynamics using mesh of voxels, such as Lattice Boltzmann Model (LBM), are too much time consuming. Thus, the use of more compact and reliable geometrical representations of pore space can drastically decrease the computational cost of the simulations. Several recent works propose basic analytic volume primitives (e.g. spheres, generalized cylinders, ellipsoids) to define a piece-wise approximation of pore space for numerical simulation of draining, diffusion and microbial decomposition. Such approaches work well but the drawback is that it generates approximation errors. In the present work, we study another alternative where pore space is described by means of geometrically relevant connected subsets of voxels (regions) computed from the curvilinear skeleton. Indeed, many works use the curvilinear skeleton (3D medial axis) for analyzing and partitioning 3D shapes within various domains (medicine, material sciences, petroleum engineering, etc.) but only a few ones in soil sciences. Within the context of soil sciences, most studies dealing with 3D medial axis focus on the determination of pore throats. Here, we segment pore space using curvilinear skeleton in order to achieve numerical simulation of microbial decomposition (including diffusion processes). We validate simulation outputs by comparison with other methods using different pore space geometrical representations (balls, voxels).
DeViL: Decoding Vision features into Language

Post-hoc explanation methods have often been criticised for abstracting away the decision-making process of deep neural networks. In this work, we would like to provide natural language descriptions for what different layers of a vision backbone have learned. Our DeViL method decodes vision features into language, not only highlighting the attribution locations but also generating textual descriptions of visual features at different layers of the network. We train a transformer network to translate individual image features of any vision layer into a prompt that a separate off-the-shelf language model decodes into natural language. By employing dropout both per-layer and per-spatial-location, our model can generalize training on image-text pairs to generate localized explanations. As it uses a pre-trained language model, our approach is fast to train, can be applied to any vision backbone, and produces textual descriptions at different layers of the vision network. Moreover, DeViL can create open-vocabulary attribution maps corresponding to words or phrases even outside the training scope of the vision model. We demonstrate that DeViL generates textual descriptions relevant to the image content on CC3M surpassing previous lightweight captioning models and attribution maps uncovering the learned concepts of the vision backbone. Finally, we show DeViL also outperforms the current state-of-the-art on the neuron-wise descriptions of the MILANNOTATIONS dataset. Code available at https://github.com/ExplainableML/DeViL
MultiWay-Adapater: Adapting large-scale multi-modal models for scalable image-text retrieval

As Multimodal Large Language Models (MLLMs) grow in size, adapting them to specialized tasks becomes increasingly challenging due to high computational and memory demands. Indeed, traditional fine-tuning methods are costly, due to the need for extensive, task-specific training. While efficient adaptation methods exist that aim to reduce these costs, in practice they suffer from shallow inter-modal alignment, which severely hurts model effectiveness. To tackle these computational challenges and improve inter-modal alignment, we introduce the MultiWay-Adapter (MWA), a novel framework featuring an 'Alignment Enhancer'. This enhancer deepens inter-modal alignment, enabling high transferability with minimal tuning effort. Our experiments show that unlike prior efficient tuning approaches, MWA maintains model effectiveness, while reducing training time by up-to 57%. MWA is also lightweight, increasing model size by only 2-3% (in terms of parameters) for state-of-the-art foundation models like BEiT-3 Large. These results demonstrate that MWA provides an efficient and effective adaptation method for MLLMs, significantly broadening their applicability.
No Data Augmentation? Alternative Regularizations for Effective Training on Small Datasets

Solving image classification tasks given small training datasets remains an open challenge for modern computer vision. Aggressive data augmentation and generative models are among the most straightforward approaches to overcoming the lack of data. However, the first fails to be agnostic to varying image domains, while the latter requires additional compute and careful design. In this work, we study alternative regularization strategies to push the limits of supervised learning on small image classification datasets. In particular, along with the model size and training schedule scaling, we employ a heuristic to select (semi) optimal learning rate and weight decay couples via the norm of model parameters. By training on only 1% of the original CIFAR-10 training set (i.e., 50 images per class) and testing on ciFAIR-10, a variant of the original CIFAR without duplicated images, we reach a test accuracy of 66.5%, on par with the best state-of-the-art methods.
On the Robustness of Post-hoc GNN Explainers to Label Noise

Proposed as a solution to the inherent black-box limitations of graph neural networks (GNNs), post-hoc GNN explainers aim to provide precise and insightful explanations of the behaviours exhibited by trained GNNs. Despite their recent notable advancements in academic and industrial contexts, the robustness of post-hoc GNN explainers remains unexplored when confronted with label noise. To bridge this gap, we conduct a systematic empirical investigation to evaluate the efficacy of diverse post-hoc GNN explainers under varying degrees of label noise. Our results reveal several key insights: Firstly, post-hoc GNN explainers are susceptible to label perturbations. Secondly, even minor levels of label noise, inconsequential to GNN performance, harm the quality of generated explanations substantially. Lastly, we engage in a discourse regarding the progressive recovery of explanation effectiveness with escalating noise levels.
ControlMat: A Controlled Generative Approach to Material Capture

Material reconstruction from a photograph is a key component of 3D content creation democratization. We propose to formulate this ill-posed problem as a controlled synthesis one, leveraging the recent progress in generative deep networks. We present ControlMat, a method which, given a single photograph with uncontrolled illumination as input, conditions a diffusion model to generate plausible, tileable, high-resolution physically-based digital materials. We carefully analyze the behavior of diffusion models for multi-channel outputs, adapt the sampling process to fuse multi-scale information and introduce rolled diffusion to enable both tileability and patched diffusion for high-resolution outputs. Our generative approach further permits exploration of a variety of materials which could correspond to the input image, mitigating the unknown lighting conditions. We show that our approach outperforms recent inference and latent-space-optimization methods, and carefully validate our diffusion process design choices. Supplemental materials and additional details are available at: https://gvecchio.com/controlmat/.
NLLB-CLIP -- train performant multilingual image retrieval model on a budget

Today, the exponential rise of large models developed by academic and industrial institutions with the help of massive computing resources raises the question of whether someone without access to such resources can make a valuable scientific contribution. To explore this, we tried to solve the challenging task of multilingual image retrieval having a limited budget of $1,000. As a result, we present NLLB-CLIP - CLIP model with a text encoder from the NLLB model. To train the model, we used an automatically created dataset of 106,246 good-quality images with captions in 201 languages derived from the LAION COCO dataset. We trained multiple models using image and text encoders of various sizes and kept different parts of the model frozen during the training. We thoroughly analyzed the trained models using existing evaluation datasets and newly created XTD200 and Flickr30k-200 datasets. We show that NLLB-CLIP is comparable in quality to state-of-the-art models and significantly outperforms them on low-resource languages.
Towards Universal Image Embeddings: A Large-Scale Dataset and Challenge for Generic Image Representations

Fine-grained and instance-level recognition methods are commonly trained and evaluated on specific domains, in a model per domain scenario. Such an approach, however, is impractical in real large-scale applications. In this work, we address the problem of universal image embedding, where a single universal model is trained and used in multiple domains. First, we leverage existing domain-specific datasets to carefully construct a new large-scale public benchmark for the evaluation of universal image embeddings, with 241k query images, 1.4M index images and 2.8M training images across 8 different domains and 349k classes. We define suitable metrics, training and evaluation protocols to foster future research in this area. Second, we provide a comprehensive experimental evaluation on the new dataset, demonstrating that existing approaches and simplistic extensions lead to worse performance than an assembly of models trained for each domain separately. Finally, we conducted a public research competition on this topic, leveraging industrial datasets, which attracted the participation of more than 1k teams worldwide. This exercise generated many interesting research ideas and findings which we present in detail. Project webpage: https://cmp.felk.cvut.cz/univ_emb/
The impact of electronic health records (EHR) data continuity on prediction model fairness and racial-ethnic disparities

Electronic health records (EHR) data have considerable variability in data completeness across sites and patients. Lack of "EHR data-continuity" or "EHR data-discontinuity", defined as "having medical information recorded outside the reach of an EHR system" can lead to a substantial amount of information bias. The objective of this study was to comprehensively evaluate (1) how EHR data-discontinuity introduces data bias, (2) case finding algorithms affect downstream prediction models, and (3) how algorithmic fairness is associated with racial-ethnic disparities. We leveraged our EHRs linked with Medicaid and Medicare claims data in the OneFlorida+ network and used a validated measure (i.e., Mean Proportions of Encounters Captured [MPEC]) to estimate patients' EHR data continuity. We developed a machine learning model for predicting type 2 diabetes (T2D) diagnosis as the use case for this work. We found that using cohorts selected by different levels of EHR data-continuity affects utilities in disease prediction tasks. The prediction models trained on high continuity data will have a worse fit on low continuity data. We also found variations in racial and ethnic disparities in model performances and model fairness in models developed using different degrees of data continuity. Our results suggest that careful evaluation of data continuity is critical to improving the validity of real-world evidence generated by EHR data and health equity.
TensorBank:Tensor Lakehouse for Foundation Model Training

Storing and streaming high dimensional data for foundation model training became a critical requirement with the rise of foundation models beyond natural language. In this paper we introduce TensorBank, a petabyte scale tensor lakehouse capable of streaming tensors from Cloud Object Store (COS) to GPU memory at wire speed based on complex relational queries. We use Hierarchical Statistical Indices (HSI) for query acceleration. Our architecture allows to directly address tensors on block level using HTTP range reads. Once in GPU memory, data can be transformed using PyTorch transforms. We provide a generic PyTorch dataset type with a corresponding dataset factory translating relational queries and requested transformations as an instance. By making use of the HSI, irrelevant blocks can be skipped without reading them as those indices contain statistics on their content at different hierarchical resolution levels. This is an opinionated architecture powered by open standards and making heavy use of open-source technology. Although, hardened for production use using geospatial-temporal data, this architecture generalizes to other use case like computer vision, computational neuroscience, biological sequence analysis and more.
Focal Surface Projection: Extending Projector Depth-of-Field Using a Phase-Only Spatial Light Modulator

We present a focal surface projection to solve the narrow depth-of-field problem in projection mapping applications. We apply a phase-only spatial light modulator to realize nonuniform focusing distances, whereby the projected contents appear focused on a surface with considerable depth variations. The feasibility of the proposed technique was validated through a physical experiment.
VFFINDER: A Graph-based Approach for Automated Silent Vulnerability-Fix Identification

The increasing reliance of software projects on third-party libraries has raised concerns about the security of these libraries due to hidden vulnerabilities. Managing these vulnerabilities is challenging due to the time gap between fixes and public disclosures. Moreover, a significant portion of open-source projects silently fix vulnerabilities without disclosure, impacting vulnerability management. Existing tools like OWASP heavily rely on public disclosures, hindering their effectiveness in detecting unknown vulnerabilities. To tackle this problem, automated identification of vulnerability-fixing commits has emerged. However, identifying silent vulnerability fixes remains challenging. This paper presents VFFINDER, a novel graph-based approach for automated silent vulnerability fix identification. VFFINDER captures structural changes using Abstract Syntax Trees (ASTs) and represents them in annotated ASTs. VFFINDER distinguishes vulnerability-fixing commits from non-fixing ones using attention-based graph neural network models to extract structural features. We conducted experiments to evaluate VFFINDER on a dataset of 36K+ fixing and non-fixing commits in 507 real-world C/C++ projects. Our results show that VFFINDER significantly improves the state-of-the-art methods by 39-83% in Precision, 19-148% in Recall, and 30-109% in F1. Especially, VFFINDER speeds up the silent fix identification process by up to 47% with the same review effort of 5% compared to the existing approaches.
Model-based Offline Policy Optimization with Adversarial Network

Model-based offline reinforcement learning (RL), which builds a supervised transition model with logging dataset to avoid costly interactions with the online environment, has been a promising approach for offline policy optimization. As the discrepancy between the logging data and online environment may result in a distributional shift problem, many prior works have studied how to build robust transition models conservatively and estimate the model uncertainty accurately. However, the over-conservatism can limit the exploration of the agent, and the uncertainty estimates may be unreliable. In this work, we propose a novel Model-based Offline policy optimization framework with Adversarial Network (MOAN). The key idea is to use adversarial learning to build a transition model with better generalization, where an adversary is introduced to distinguish between in-distribution and out-of-distribution samples. Moreover, the adversary can naturally provide a quantification of the model's uncertainty with theoretical guarantees. Extensive experiments showed that our approach outperforms existing state-of-the-art baselines on widely studied offline RL benchmarks. It can also generate diverse in-distribution samples, and quantify the uncertainty more accurately.
S3C: Semi-Supervised VQA Natural Language Explanation via Self-Critical Learning

VQA Natural Language Explanation (VQA-NLE) task aims to explain the decision-making process of VQA models in natural language. Unlike traditional attention or gradient analysis, free-text rationales can be easier to understand and gain users' trust. Existing methods mostly use post-hoc or self-rationalization models to obtain a plausible explanation. However, these frameworks are bottlenecked by the following challenges: 1) the reasoning process cannot be faithfully responded to and suffer from the problem of logical inconsistency. 2) Human-annotated explanations are expensive and time-consuming to collect. In this paper, we propose a new Semi-Supervised VQA-NLE via Self-Critical Learning (S3C), which evaluates the candidate explanations by answering rewards to improve the logical consistency between answers and rationales. With a semi-supervised learning framework, the S3C can benefit from a tremendous amount of samples without human-annotated explanations. A large number of automatic measures and human evaluations all show the effectiveness of our method. Meanwhile, the framework achieves a new state-of-the-art performance on the two VQA-NLE datasets.
Leveraging BERT Language Models for Multi-Lingual ESG Issue Identification

Environmental, Social, and Governance (ESG) has been used as a metric to measure the negative impacts and enhance positive outcomes of companies in areas such as the environment, society, and governance. Recently, investors have increasingly recognized the significance of ESG criteria in their investment choices, leading businesses to integrate ESG principles into their operations and strategies. The Multi-Lingual ESG Issue Identification (ML-ESG) shared task encompasses the classification of news documents into 35 distinct ESG issue labels. In this study, we explored multiple strategies harnessing BERT language models to achieve accurate classification of news documents across these labels. Our analysis revealed that the RoBERTa classifier emerged as one of the most successful approaches, securing the second-place position for the English test dataset, and sharing the fifth-place position for the French test dataset. Furthermore, our SVM-based binary model tailored for the Chinese language exhibited exceptional performance, earning the second-place rank on the test dataset.
On the Complexity of Differentially Private Best-Arm Identification with Fixed Confidence

Best Arm Identification (BAI) problems are progressively used for data-sensitive applications, such as designing adaptive clinical trials, tuning hyper-parameters, and conducting user studies to name a few. Motivated by the data privacy concerns invoked by these applications, we study the problem of BAI with fixed confidence under $\epsilon$-global Differential Privacy (DP). First, to quantify the cost of privacy, we derive a lower bound on the sample complexity of any $\delta$-correct BAI algorithm satisfying $\epsilon$-global DP. Our lower bound suggests the existence of two privacy regimes depending on the privacy budget $\epsilon$. In the high-privacy regime (small $\epsilon$), the hardness depends on a coupled effect of privacy and a novel information-theoretic quantity, called the Total Variation Characteristic Time. In the low-privacy regime (large $\epsilon$), the sample complexity lower bound reduces to the classical non-private lower bound. Second, we propose AdaP-TT, an $\epsilon$-global DP variant of the Top Two algorithm. AdaP-TT runs in arm-dependent adaptive episodes and adds Laplace noise to ensure a good privacy-utility trade-off. We derive an asymptotic upper bound on the sample complexity of AdaP-TT that matches with the lower bound up to multiplicative constants in the high-privacy regime. Finally, we provide an experimental analysis of AdaP-TT that validates our theoretical results.
Sample Size in Natural Language Processing within Healthcare Research

Sample size calculation is an essential step in most data-based disciplines. Large enough samples ensure representativeness of the population and determine the precision of estimates. This is true for most quantitative studies, including those that employ machine learning methods, such as natural language processing, where free-text is used to generate predictions and classify instances of text. Within the healthcare domain, the lack of sufficient corpora of previously collected data can be a limiting factor when determining sample sizes for new studies. This paper tries to address the issue by making recommendations on sample sizes for text classification tasks in the healthcare domain. Models trained on the MIMIC-III database of critical care records from Beth Israel Deaconess Medical Center were used to classify documents as having or not having Unspecified Essential Hypertension, the most common diagnosis code in the database. Simulations were performed using various classifiers on different sample sizes and class proportions. This was repeated for a comparatively less common diagnosis code within the database of diabetes mellitus without mention of complication. Smaller sample sizes resulted in better results when using a K-nearest neighbours classifier, whereas larger sample sizes provided better results with support vector machines and BERT models. Overall, a sample size larger than 1000 was sufficient to provide decent performance metrics. The simulations conducted within this study provide guidelines that can be used as recommendations for selecting appropriate sample sizes and class proportions, and for predicting expected performance, when building classifiers for textual healthcare data. The methodology used here can be modified for sample size estimates calculations with other datasets.
Distributionally Robust Model-based Reinforcement Learning with Large State Spaces

Three major challenges in reinforcement learning are the complex dynamical systems with large state spaces, the costly data acquisition processes, and the deviation of real-world dynamics from the training environment deployment. To overcome these issues, we study distributionally robust Markov decision processes with continuous state spaces under the widely used Kullback-Leibler, chi-square, and total variation uncertainty sets. We propose a model-based approach that utilizes Gaussian Processes and the maximum variance reduction algorithm to efficiently learn multi-output nominal transition dynamics, leveraging access to a generative model (i.e., simulator). We further demonstrate the statistical sample complexity of the proposed method for different uncertainty sets. These complexity bounds are independent of the number of states and extend beyond linear dynamics, ensuring the effectiveness of our approach in identifying near-optimal distributionally-robust policies. The proposed method can be further combined with other model-free distributionally robust reinforcement learning methods to obtain a near-optimal robust policy. Experimental results demonstrate the robustness of our algorithm to distributional shifts and its superior performance in terms of the number of samples needed.