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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., Comment: NeurIPS AI4Mat 2024

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., Comment: 14 pages, 3 figures, 14 tables

Objective: To report imaging protocol and scheduling variance in routine care of glioblastoma patients in order to demonstrate challenges of integrating deep-learning models in glioblastoma care pathways. Additionally, to understand the most common imaging studies and image contrasts to inform the development of potentially robust deep-learning models. Methods: MR imaging data were analysed from a random sample of five patients from the prospective cohort across five participating sites of the ZGBM consortium. Reported clinical and treatment data alongside DICOM header information were analysed to understand treatment pathway imaging schedules. Results: All sites perform all structural imaging at every stage in the pathway except for the presurgical study, where in some sites only contrast-enhanced T1-weighted imaging is performed. Diffusion MRI is the most common non-structural imaging type, performed at every site. Conclusion: The imaging protocol and scheduling varies across the UK, making it challenging to develop machine-learning models that could perform robustly at other centres. Structural imaging is performed most consistently across all centres. Advances in knowledge: Successful translation of deep-learning models will likely be based on structural post-treatment imaging unless there is significant effort made to standardise non-structural or peri-operative imaging protocols and schedules.

Incorporating Generative AI (GenAI) and Large Language Models (LLMs) in education can enhance teaching efficiency and enrich student learning. Current LLM usage involves conversational user interfaces (CUIs) for tasks like generating materials or providing feedback. However, this presents challenges including the need for educator expertise in AI and CUIs, ethical concerns with high-stakes decisions, and privacy risks. CUIs also struggle with complex tasks. To address these, we propose transitioning from CUIs to user-friendly applications leveraging LLMs via API calls. We present a framework for ethically incorporating GenAI into educational tools and demonstrate its application in our tool, Feedback Copilot, which provides personalized feedback on student assignments. Our evaluation shows the effectiveness of this approach, with implications for GenAI researchers, educators, and technologists. This work charts a course for the future of GenAI in education., Comment: submission to C&E AI

This document describes a two-day meeting held for the Principal Investigators (PIs) of NSF CyberTraining grants. The report covers invited talks, panels, and six breakout sessions. The meeting involved over 80 PIs and NSF program managers (PMs). The lessons recorded in detail in the report are a wealth of information that could help current and future PIs, as well as NSF PMs, understand the future directions suggested by the PI community. The meeting was held simultaneously with that of the PIs of the NSF Cyberinfrastructure for Sustained Scientific Innovation (CSSI) program. This co-location led to two joint sessions: one with NSF speakers and the other on broader impact. Further, the joint poster and refreshment sessions benefited from the interactions between CSSI and CyberTraining PIs., Comment: 38 pages, 3 main sections and 2 Appendix sections, 2 figures, 19 tables; updated version: author corrections

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., Comment: 8 Pages, 4 Figures - Submited to the AI4Science Workshop - Neurips 2023

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., Comment: 21 pages, 30 Figures

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., Comment: 14 pages, 6 Figures, 5 tables. Submited to NEURIPS 2023, Under review

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.

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., Comment: Published at 2nd Annual AAAI Workshop on AI to Accelerate Science and Engineering (AI2ASE) https://ai-2-ase.github.io/papers/16%5cSubmission%5cAAAI_Dataset_Engineering-8.pdf

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., Comment: Published at 2nd Annual AAAI Workshop on AI to Accelerate Science and Engineering (AI2ASE) https://ai-2-ase.github.io/papers/17%5cSubmission%5cKaRA_AI2ASE_Workshop-3.pdf. arXiv admin note: text overlap with arXiv:2211.04257

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., Comment: 9 pages, 5 figures, NeurIPS 2022 WS: AI4Science

Modern neural networks use building blocks such as convolutions that are equivariant to arbitrary 2D translations. However, these vanilla blocks are not equivariant to arbitrary 3D translations in the projective manifold. Even then, all monocular 3D detectors use vanilla blocks to obtain the 3D coordinates, a task for which the vanilla blocks are not designed for. This paper takes the first step towards convolutions equivariant to arbitrary 3D translations in the projective manifold. Since the depth is the hardest to estimate for monocular detection, this paper proposes Depth EquiVarIAnt NeTwork (DEVIANT) built with existing scale equivariant steerable blocks. As a result, DEVIANT is equivariant to the depth translations in the projective manifold whereas vanilla networks are not. The additional depth equivariance forces the DEVIANT to learn consistent depth estimates, and therefore, DEVIANT achieves state-of-the-art monocular 3D detection results on KITTI and Waymo datasets in the image-only category and performs competitively to methods using extra information. Moreover, DEVIANT works better than vanilla networks in cross-dataset evaluation. Code and models at https://github.com/abhi1kumar/DEVIANT, Comment: ECCV 2022

Recognizing scenes and objects in 3D from a single image is a longstanding goal of computer vision with applications in robotics and AR/VR. For 2D recognition, large datasets and scalable solutions have led to unprecedented advances. In 3D, existing benchmarks are small in size and approaches specialize in few object categories and specific domains, e.g. urban driving scenes. Motivated by the success of 2D recognition, we revisit the task of 3D object detection by introducing a large benchmark, called Omni3D. Omni3D re-purposes and combines existing datasets resulting in 234k images annotated with more than 3 million instances and 98 categories. 3D detection at such scale is challenging due to variations in camera intrinsics and the rich diversity of scene and object types. We propose a model, called Cube R-CNN, designed to generalize across camera and scene types with a unified approach. We show that Cube R-CNN outperforms prior works on the larger Omni3D and existing benchmarks. Finally, we prove that Omni3D is a powerful dataset for 3D object recognition and show that it improves single-dataset performance and can accelerate learning on new smaller datasets via pre-training., Comment: CVPR 2023, Project website: https://omni3d.garrickbrazil.com/