arXiv subjects

Emilio Vital Brazil

Publications and source records attributed to Emilio Vital Brazil.

18 recordsLinked to original sources

arXiv2026

Understanding Structural Representation in Foundation Models for Polymers

From the relative scarcity of training data to the lack of standardized benchmarks, the creation of effective foundation models for polymers faces significant and multi-faceted challenges. At the core, many of these issues are tied directly to the structural representation of polymers. Here, we present a chemical language foundation model built on using a SMILES-based polymer graph representation (CPG) that incorporates polymer architectural features and connectivity that are often missing in other line notations. This foundation model exhibited excellent performance on 30 different polymer property benchmark datasets. Critical evaluation of the developed representation against other variations in control experiments reveals this approach to be a robust method of representing polymers in language-based foundation models. These experiments also reveal a strong invariance of structural representations to small perturbations, with many variations of structural representation exceeding or equaling state-of-the-art (SOTA) performance. Surprisingly, SMILES representations which are chemically or semantically invalid also provided near or SOTA performance in several instances--underscoring an unexamined blind spot in the development of chemistry language models. Examination of error sources and attention maps for the evaluated structural representations corroborate the findings of the control experiments, highlighting the ability of the model to interpolate SMILES sequence space in a manner that is loosely congruent to chemical and architectural space for polymers. Overall, this work highlights the surprising robustness of chemistry language models to structural representation perturbations and identifies the conditions under which CPG representation provides meaningful advantages.

cond-mat.soft↗

arXiv2025

Towards a Foundation Model for Partial Differential Equations Across Physics Domains

We present PDE-FM, a modular foundation model for physics-informed machine learning that unifies spatial, spectral, and temporal reasoning across heterogeneous partial differential equation (PDE) systems. PDE-FM combines spatial-spectral tokenization, physics-aware conditioning, and a Mamba-based state-space backbone with an operator-theoretic decoder, enabling scalable and data-efficient modeling of complex physical dynamics. In contrast to task-specific neural operators, PDE-FM is pretrained once on diverse PDE datasets and can be transferred to new physical regimes without architectural or data-specific modifications. Evaluated on twelve 2D and 3D datasets from The Well benchmark - spanning hydrodynamic, radiative, elastic, and astrophysical phenomena - PDE-FM achieves state-of-the-art accuracy in six domains, reducing mean VRMSE by 46% relative to prior operator-learning baselines. The model demonstrates robust cross-physics generalization, excelling in turbulent and radiative systems while maintaining strong performance in linear and steady-state regimes. These results suggest that large-scale pretraining across diverse physical processes can yield transferable representations of dynamics, marking a step toward unified, foundation-level surrogates for multi-physics simulation and scientific discovery.

cs.LG↗

arXiv2024

SELF-BART : A Transformer-based Molecular Representation Model using SELFIES

Large-scale molecular representation methods have revolutionized applications in material science, such as drug discovery, chemical modeling, and material design. With the rise of transformers, models now learn representations directly from molecular structures. In this study, we develop an encoder-decoder model based on BART that is capable of leaning molecular representations and generate new molecules. Trained on SELFIES, a robust molecular string representation, our model outperforms existing baselines in downstream tasks, demonstrating its potential in efficient and effective molecular data analysis and manipulation.

cs.CE↗

arXiv2024

A Large Encoder-Decoder Family of Foundation Models For Chemical Language

Large-scale pre-training methodologies for chemical language models represent a breakthrough in cheminformatics. These methods excel in tasks such as property prediction and molecule generation by learning contextualized representations of input tokens through self-supervised learning on large unlabeled corpora. Typically, this involves pre-training on unlabeled data followed by fine-tuning on specific tasks, reducing dependence on annotated datasets and broadening chemical language representation understanding. This paper introduces a large encoder-decoder chemical foundation models pre-trained on a curated dataset of 91 million SMILES samples sourced from PubChem, which is equivalent to 4 billion of molecular tokens. The proposed foundation model supports different complex tasks, including quantum property prediction, and offer flexibility with two main variants (289M and $8\times289M$). Our experiments across multiple benchmark datasets validate the capacity of the proposed model in providing state-of-the-art results for different tasks. We also provide a preliminary assessment of the compositionality of the embedding space as a prerequisite for the reasoning tasks. We demonstrate that the produced latent space is separable compared to the state-of-the-art with few-shot learning capabilities.

cs.LG↗

arXiv2023

Improving Molecular Properties Prediction Through Latent Space Fusion

Pre-trained Language Models have emerged as promising tools for predicting molecular properties, yet their development is in its early stages, necessitating further research to enhance their efficacy and address challenges such as generalization and sample efficiency. In this paper, we present a multi-view approach that combines latent spaces derived from state-of-the-art chemical models. Our approach relies on two pivotal elements: the embeddings derived from MHG-GNN, which represent molecular structures as graphs, and MoLFormer embeddings rooted in chemical language. The attention mechanism of MoLFormer is able to identify relations between two atoms even when their distance is far apart, while the GNN of MHG-GNN can more precisely capture relations among multiple atoms closely located. In this work, we demonstrate the superior performance of our proposed multi-view approach compared to existing state-of-the-art methods, including MoLFormer-XL, which was trained on 1.1 billion molecules, particularly in intricate tasks such as predicting clinical trial drug toxicity and inhibiting HIV replication. We assessed our approach using six benchmark datasets from MoleculeNet, where it outperformed competitors in five of them. Our study highlights the potential of latent space fusion and feature integration for advancing molecular property prediction. In this work, we use small versions of MHG-GNN and MoLFormer, which opens up an opportunity for further improvement when our approach uses a larger-scale dataset.

cs.LG↗

arXiv2023

Geo-Sketcher: Rapid 3D Geological Modeling using Geological and Topographic Map Sketches

The construction of 3D geological models is an essential task in oil/gas exploration, development and production. However, it is a cumbersome, time-consuming and error-prone task mainly because of the model's geometric and topological complexity. The models construction is usually separated into interpretation and 3D modeling, performed by different highly specialized individuals, which leads to inconsistencies and intensifies the challenges. In addition, the creation of models following geological rules is paramount for properly depicting static and dynamic properties of oil/gas reservoirs. In this work, we propose a sketch-based approach to expedite the creation of valid 3D geological models by mimicking how domain experts interpret geological structures, allowing creating models directly from interpretation sketches. Our sketch-based modeler (Geo-Sketcher) is based on sketches of standard 2D topographic and geological maps, comprised of lines, symbols and annotations. We developed a graph-based representation to enable (1) the automatic computation of the relative ages of rock series and layers, and (2) the embedding of specific geological rules directly in the sketching. We introduce the use of Hermite-Birkhoff Radial Basis Functions to interpolate the geological map constraints, and demonstrate the capabilities of our approach with a variety of results with different levels of complexity.

cs.GR↗

arXiv2023

Beyond Chemical Language: A Multimodal Approach to Enhance Molecular Property Prediction

We present a novel multimodal language model approach for predicting molecular properties by combining chemical language representation with physicochemical features. Our approach, MULTIMODAL-MOLFORMER, utilizes a causal multistage feature selection method that identifies physicochemical features based on their direct causal effect on a specific target property. These causal features are then integrated with the vector space generated by molecular embeddings from MOLFORMER. In particular, we employ Mordred descriptors as physicochemical features and identify the Markov blanket of the target property, which theoretically contains the most relevant features for accurate prediction. Our results demonstrate a superior performance of our proposed approach compared to existing state-of-the-art algorithms, including the chemical language-based MOLFORMER and graph neural networks, in predicting complex tasks such as biodegradability and PFAS toxicity estimation. Moreover, we demonstrate the effectiveness of our feature selection method in reducing the dimensionality of the Mordred feature space while maintaining or improving the model's performance. Our approach opens up promising avenues for future research in molecular property prediction by harnessing the synergistic potential of both chemical language and physicochemical features, leading to enhanced performance and advancements in the field.

physics.chem-ph↗

arXiv2023

Retrospective End-User Walkthrough: A Method for Assessing How People Combine Multiple AI Models in Decision-Making Systems

Evaluating human-AI decision-making systems is an emerging challenge as new ways of combining multiple AI models towards a specific goal are proposed every day. As humans interact with AI in decision-making systems, multiple factors may be present in a task including trust, interpretability, and explainability, amongst others. In this context, this work proposes a retrospective method to support a more holistic understanding of how people interact with and connect multiple AI models and combine multiple outputs in human-AI decision-making systems. The method consists of employing a retrospective end-user walkthrough with the objective of providing support to HCI practitioners so that they may gain an understanding of the higher order cognitive processes in place and the role that AI model outputs play in human-AI decision-making. The method was qualitatively assessed with 29 participants (four participants in a pilot phase; 25 participants in the main user study) interacting with a human-AI decision-making system in the context of financial decision-making. The system combines visual analytics, three AI models for revenue prediction, AI-supported analogues analysis, and hypothesis testing using external news and natural language processing to provide multiple means for comparing companies. Beyond results on tasks and usability problems, outcomes presented suggest that the method is promising in highlighting why AI models are ignored, used, or trusted, and how future interactions are planned. We suggest that HCI practitioners researching human-AI interaction can benefit by adding this step to user studies in a debriefing stage as a retrospective Thinking-Aloud protocol would be applied, but with emphasis on revisiting tasks and understanding why participants ignored or connected predictions while performing a task.

cs.HC↗

arXiv2023

Knowledge-augmented Risk Assessment (KaRA): a hybrid-intelligence framework for supporting knowledge-intensive risk assessment of prospect candidates

Evaluating the potential of a prospective candidate is a common task in multiple decision-making processes in different industries. We refer to a prospect as something or someone that could potentially produce positive results in a given context, e.g., an area where an oil company could find oil, a compound that, when synthesized, results in a material with required properties, and so on. In many contexts, assessing the Probability of Success (PoS) of prospects heavily depends on experts' knowledge, often leading to biased and inconsistent assessments. We have developed the framework named KARA (Knowledge-augmented Risk Assessment) to address these issues. It combines multiple AI techniques that consider SMEs (Subject Matter Experts) feedback on top of a structured domain knowledge-base to support risk assessment processes of prospect candidates in knowledge-intensive contexts.

cs.AI↗

arXiv2023

Position Paper on Dataset Engineering to Accelerate Science

Data is a critical element in any discovery process. In the last decades, we observed exponential growth in the volume of available data and the technology to manipulate it. However, data is only practical when one can structure it for a well-defined task. For instance, we need a corpus of text broken into sentences to train a natural language machine-learning model. In this work, we will use the token \textit{dataset} to designate a structured set of data built to perform a well-defined task. Moreover, the dataset will be used in most cases as a blueprint of an entity that at any moment can be stored as a table. Specifically, in science, each area has unique forms to organize, gather and handle its datasets. We believe that datasets must be a first-class entity in any knowledge-intensive process, and all workflows should have exceptional attention to datasets' lifecycle, from their gathering to uses and evolution. We advocate that science and engineering discovery processes are extreme instances of the need for such organization on datasets, claiming for new approaches and tooling. Furthermore, these requirements are more evident when the discovery workflow uses artificial intelligence methods to empower the subject-matter expert. In this work, we discuss an approach to bringing datasets as a critical entity in the discovery process in science. We illustrate some concepts using material discovery as a use case. We chose this domain because it leverages many significant problems that can be generalized to other science fields.

cs.LG↗

arXiv2022

Toward Human-AI Co-creation to Accelerate Material Discovery

There is an increasing need in our society to achieve faster advances in Science to tackle urgent problems, such as climate changes, environmental hazards, sustainable energy systems, pandemics, among others. In certain domains like chemistry, scientific discovery carries the extra burden of assessing risks of the proposed novel solutions before moving to the experimental stage. Despite several recent advances in Machine Learning and AI to address some of these challenges, there is still a gap in technologies to support end-to-end discovery applications, integrating the myriad of available technologies into a coherent, orchestrated, yet flexible discovery process. Such applications need to handle complex knowledge management at scale, enabling knowledge consumption and production in a timely and efficient way for subject matter experts (SMEs). Furthermore, the discovery of novel functional materials strongly relies on the development of exploration strategies in the chemical space. For instance, generative models have gained attention within the scientific community due to their ability to generate enormous volumes of novel molecules across material domains. These models exhibit extreme creativity that often translates in low viability of the generated candidates. In this work, we propose a workbench framework that aims at enabling the human-AI co-creation to reduce the time until the first discovery and the opportunity costs involved. This framework relies on a knowledge base with domain and process knowledge, and user-interaction components to acquire knowledge and advise the SMEs. Currently,the framework supports four main activities: generative modeling, dataset triage, molecule adjudication, and risk assessment.

cs.LG↗

arXiv2021

Workflow Provenance in the Lifecycle of Scientific Machine Learning

Machine Learning (ML) has already fundamentally changed several businesses. More recently, it has also been profoundly impacting the computational science and engineering domains, like geoscience, climate science, and health science. In these domains, users need to perform comprehensive data analyses combining scientific data and ML models to provide for critical requirements, such as reproducibility, model explainability, and experiment data understanding. However, scientific ML is multidisciplinary, heterogeneous, and affected by the physical constraints of the domain, making such analyses even more challenging. In this work, we leverage workflow provenance techniques to build a holistic view to support the lifecycle of scientific ML. We contribute with (i) characterization of the lifecycle and taxonomy for data analyses; (ii) design principles to build this view, with a W3C PROV compliant data representation and a reference system architecture; and (iii) lessons learned after an evaluation in an Oil & Gas case using an HPC cluster with 393 nodes and 946 GPUs. The experiments show that the principles enable queries that integrate domain semantics with ML models while keeping low overhead (<1%), high scalability, and an order of magnitude of query acceleration under certain workloads against without our representation.

cs.DB↗

arXiv2019

Provenance Data in the Machine Learning Lifecycle in Computational Science and Engineering

Machine Learning (ML) has become essential in several industries. In Computational Science and Engineering (CSE), the complexity of the ML lifecycle comes from the large variety of data, scientists' expertise, tools, and workflows. If data are not tracked properly during the lifecycle, it becomes unfeasible to recreate a ML model from scratch or to explain to stakeholders how it was created. The main limitation of provenance tracking solutions is that they cannot cope with provenance capture and integration of domain and ML data processed in the multiple workflows in the lifecycle while keeping the provenance capture overhead low. To handle this problem, in this paper we contribute with a detailed characterization of provenance data in the ML lifecycle in CSE; a new provenance data representation, called PROV-ML, built on top of W3C PROV and ML Schema; and extensions to a system that tracks provenance from multiple workflows to address the characteristics of ML and CSE, and to allow for provenance queries with a standard vocabulary. We show a practical use in a real case in the Oil and Gas industry, along with its evaluation using 48 GPUs in parallel.

cs.DC↗

arXiv2019

Semantic Segmentation of Seismic Images

Almost all work to understand Earth's subsurface on a large scale relies on the interpretation of seismic surveys by experts who segment the survey (usually a cube) into layers; a process that is very time demanding. In this paper, we present a new deep neural network architecture specially designed to semantically segment seismic images with a minimal amount of training data. To achieve this, we make use of a transposed residual unit that replaces the traditional dilated convolution for the decode block. Also, instead of using a predefined shape for up-scaling, our network learns all the steps to upscale the features from the encoder. We train our neural network using the Penobscot 3D dataset; a real seismic dataset acquired offshore Nova Scotia, Canada. We compare our approach with two well-known deep neural network topologies: Fully Convolutional Network and U-Net. In our experiments, we show that our approach can achieve more than 99 percent of the mean intersection over union (mIOU) metric, outperforming the existing topologies. Moreover, our qualitative results show that the obtained model can produce masks very close to human interpretation with very little discontinuity.

eess.IV↗

arXiv2019

Netherlands Dataset: A New Public Dataset for Machine Learning in Seismic Interpretation

Machine learning and, more specifically, deep learning algorithms have seen remarkable growth in their popularity and usefulness in the last years. This is arguably due to three main factors: powerful computers, new techniques to train deeper networks and larger datasets. Although the first two are readily available in modern computers and ML libraries, the last one remains a challenge for many domains. It is a fact that big data is a reality in almost all fields nowadays, and geosciences are not an exception. However, to achieve the success of general-purpose applications such as ImageNet - for which there are +14 million labeled images for 1000 target classes - we not only need more data, we need more high-quality labeled data. When it comes to the Oil&Gas industry, confidentiality issues hamper even more the sharing of datasets. In this work, we present the Netherlands interpretation dataset, a contribution to the development of machine learning in seismic interpretation. The Netherlands F3 dataset acquisition was carried out in the North Sea, Netherlands offshore. The data is publicly available and contains pos-stack data, 8 horizons and well logs of 4 wells. For the purposes of our machine learning tasks, the original dataset was reinterpreted, generating 9 horizons separating different seismic facies intervals. The interpreted horizons were used to generate approximatelly 190,000 labeled images for inlines and crosslines. Finally, we present two deep learning applications in which the proposed dataset was employed and produced compelling results.

cs.LG↗

arXiv2019

Penobscot Dataset: Fostering Machine Learning Development for Seismic Interpretation

We have seen in the past years the flourishing of machine and deep learning algorithms in several applications such as image classification and segmentation, object detection and recognition, among many others. This was only possible, in part, because datasets like ImageNet -- with +14 million labeled images -- were created and made publicly available, providing researches with a common ground to compare their advances and extend the state-of-the-art. Although we have seen an increasing interest in machine learning in geosciences as well, we will only be able to achieve a significant impact in our community if we collaborate to build such a common basis. This is even more difficult when it comes to the Oil&Gas industry, in which confidentiality and commercial interests often hinder the sharing of datasets with others. In this letter, we present the Penobscot interpretation dataset, our contribution to the development of machine learning in geosciences, more specifically in seismic interpretation. The Penobscot 3D seismic dataset was acquired in the Scotian shelf, offshore Nova Scotia, Canada. The data is publicly available and comprises pre- and pos-stack data, 5 horizons and well logs of 2 wells. However, for the dataset to be of practical use for our tasks, we had to reinterpret the seismic, generating 7 horizons separating different seismic facies intervals. The interpreted horizons were used to generated +100,000 labeled images for inlines and crosslines. To demonstrate the utility of our dataset, results of two experiments are presented.

physics.geo-ph↗

arXiv2014

The Cost of Perfection for Matchings in Graphs

Perfect matchings and maximum weight matchings are two fundamental combinatorial structures. We consider the ratio between the maximum weight of a perfect matching and the maximum weight of a general matching. Motivated by the computer graphics application in triangle meshes, where we seek to convert a triangulation into a quadrangulation by merging pairs of adjacent triangles, we focus mainly on bridgeless cubic graphs. First, we characterize graphs that attain the extreme ratios. Second, we present a lower bound for all bridgeless cubic graphs. Third, we present upper bounds for subclasses of bridgeless cubic graphs, most of which are shown to be tight. Additionally, we present tight bounds for the class of regular bipartite graphs.

cs.DM↗

arXiv2014

DASS: Detail Aware Sketch-Based Surface Modeling

We present a sketch-based modeling system suitable for detail editing, based on a multilevel representation for surfaces. The main advantage of this representation allowing for the control of local (details) and global changes of the model. We used an adaptive mesh (4-8 mesh) and developed a label theory to construct a manifold structure, which is responsible for controlling local editing of the model. The overall shape and global modifications are defined by a variational implicit surface (Hermite RBF). Our system assembles the manifold structures to allow the user to add details without changing the overall shape, as well as edit the overall shape while repositioning details coherently.

cs.GR↗