Machine learning has promised to change the landscape of laboratory chemistry, with impressive results in molecular property prediction and reaction retro-synthesis. However, chemical datasets are often inaccessible to the machine learning community as they tend to require cleaning, thorough understanding of the chemistry, or are simply not available. In this paper, we introduce a novel dataset for yield prediction, providing the first-ever transient flow dataset for machine learning benchmarking, covering over 1200 process conditions. While previous datasets focus on discrete parameters, our experimental set-up allow us to sample a large number of continuous process conditions, generating new challenges for machine learning models. We focus on solvent selection, a task that is particularly difficult to model theoretically and therefore ripe for machine learning applications. We showcase benchmarking for regression algorithms, transfer-learning approaches, feature engineering, and active learning, with important applications towards solvent replacement and sustainable manufacturing.
We introduce FailureSensorIQ, a novel Multi-Choice Question-Answering (MCQA) benchmarking system designed to assess the ability of Large Language Models (LLMs) to reason and understand complex, domain-specific scenarios in Industry 4.0. Unlike traditional QA benchmarks, our system focuses on multiple aspects of reasoning through failure modes, sensor data, and the relationships between them across various industrial assets. Through this work, we envision a paradigm shift where modeling decisions are not only data-driven using statistical tools like correlation analysis and significance tests, but also domain-driven by specialized LLMs which can reason about the key contributors and useful patterns that can be captured with feature engineering. We evaluate the Industrial knowledge of over a dozen LLMs-including GPT-4, Llama, and Mistral-on FailureSensorIQ from different lens using Perturbation-Uncertainty-Complexity analysis, Expert Evaluation study, Asset-Specific Knowledge Gap analysis, ReAct agent using external knowledge-bases. Even though closed-source models with strong reasoning capabilities approach expert-level performance, the comprehensive benchmark reveals a significant drop in performance that is fragile to perturbations, distractions, and inherent knowledge gaps in the models. We also provide a real-world case study of how LLMs can drive the modeling decisions on 3 different failure prediction datasets related to various assets. We release: (a) expert-curated MCQA for various industrial assets, (b) FailureSensorIQ benchmark and Hugging Face leaderboard based on MCQA built from non-textual data found in ISO documents, and (c) LLMFeatureSelector, an LLM-based feature selection scikit-learn pipeline. The software is available at https://github.com/IBM/FailureSensorIQ.
The COVID-19 pandemic, caused by SARS-CoV-2, highlighted the critical need for accurate prediction of disease severity to optimize healthcare resource allocation and patient management. The spike protein, which facilitates viral entry into host cells, exhibits high mutation rates, particularly in the receptor-binding domain, influencing viral pathogenicity. Artificial intelligence approaches, such as deep learning, offer promising solutions for leveraging genomic and clinical data to predict disease outcomes. Objective: This study aimed to develop a hybrid CNN-LSTM deep learning model to predict COVID-19 severity using spike protein sequences and associated clinical metadata from South American patients. Methods: We retrieved 9,570 spike protein sequences from the GISAID database, of which 3,467 met inclusion criteria after standardization. The dataset included 2,313 severe and 1,154 mild cases. A feature engineering pipeline extracted features from sequences, while demographic and clinical variables were one-hot encoded. A hybrid CNN-LSTM architecture was trained, combining CNN layers for local pattern extraction and an LSTM layer for long-term dependency modeling. Results: The model achieved an F1 score of 82.92%, ROC-AUC of 0.9084, precision of 83.56%, and recall of 82.85%, demonstrating robust classification performance. Training stabilized at 85% accuracy with minimal overfitting. The most prevalent lineages (P.1, AY.99.2) and clades (GR, GK) aligned with regional epidemiological trends, suggesting potential associations between viral genetics and clinical outcomes. Conclusion: The CNN-LSTM hybrid model effectively predicted COVID-19 severity using spike protein sequences and clinical data, highlighting the utility of AI in genomic surveillance and precision public health. Despite limitations, this approach provides a framework for early severity prediction in future outbreaks.
In medical image analysis, feature engineering plays an important role in the design and performance of machine learning models. Persistent homology (PH), from the field of topological data analysis (TDA), demonstrates robustness and stability to data perturbations and addresses the limitation from traditional feature extraction approaches where a small change in input results in a large change in feature representation. Using PH, we store persistent topological and geometrical features in the form of the persistence barcode whereby large bars represent global topological features and small bars encapsulate geometrical information of the data. When multiple barcodes are computed from 2D or 3D medical images, two approaches can be used to construct the final topological feature vector in each dimension: aggregating persistence barcodes followed by featurization or concatenating topological feature vectors derived from each barcode. In this study, we conduct a comprehensive analysis across diverse medical imaging datasets to compare the effects of the two aforementioned approaches on the performance of classification models. The results of this analysis indicate that feature concatenation preserves detailed topological information from individual barcodes, yields better classification performance and is therefore a preferred approach when conducting similar experiments.
The ubiquity of social media platforms facilitates malicious linguistic steganography, posing significant security risks. Steganalysis is profoundly hindered by the challenge of identifying subtle cognitive inconsistencies arising from textual fragmentation and complex dialogue structures, and the difficulty in achieving robust aggregation of multi-dimensional weak signals, especially given extreme steganographic sparsity and sophisticated steganography. These core detection difficulties are compounded by significant data imbalance. This paper introduces GSDFuse, a novel method designed to systematically overcome these obstacles. GSDFuse employs a holistic approach, synergistically integrating hierarchical multi-modal feature engineering to capture diverse signals, strategic data augmentation to address sparsity, adaptive evidence fusion to intelligently aggregate weak signals, and discriminative embedding learning to enhance sensitivity to subtle inconsistencies. Experiments on social media datasets demonstrate GSDFuse's state-of-the-art (SOTA) performance in identifying sophisticated steganography within complex dialogue environments. The source code for GSDFuse is available at https://github.com/NebulaEmmaZh/GSDFuse.
Abstractive summarization of scientific papers has always been a research focus, yet existing methods face two main challenges. First, most summarization models rely on Encoder-Decoder architectures that treat papers as sequences of words, thus fail to fully capture the structured information inherent in scientific papers. Second, existing research often use keyword mapping or feature engineering to identify the structural information, but these methods struggle with the structural flexibility of scientific papers and lack robustness across different disciplines. To address these challenges, we propose a two-stage abstractive summarization framework that leverages automatic recognition of structural functions within scientific papers. In the first stage, we standardize chapter titles from numerous scientific papers and construct a large-scale dataset for structural function recognition. A classifier is then trained to automatically identify the key structural components (e.g., Background, Methods, Results, Discussion), which provides a foundation for generating more balanced summaries. In the second stage, we employ Longformer to capture rich contextual relationships across sections and generating context-aware summaries. Experiments conducted on two domain-specific scientific paper summarization datasets demonstrate that our method outperforms advanced baselines, and generates more comprehensive summaries. The code and dataset can be accessed at https://github.com/tongbao96/code-for-SFR-AS.
Wide & Deep, a simple yet effective learning architecture for recommendation systems developed by Google, has had a significant impact in both academia and industry due to its combination of the memorization ability of generalized linear models and the generalization ability of deep models. Graph convolutional networks (GCNs) remain dominant in node classification tasks; however, recent studies have highlighted issues such as heterophily and expressiveness, which focus on graph structure while seemingly neglecting the potential role of node features. In this paper, we propose a flexible framework GCNIII, which leverages the Wide & Deep architecture and incorporates three techniques: Intersect memory, Initial residual and Identity mapping. We provide comprehensive empirical evidence showing that GCNIII can more effectively balance the trade-off between over-fitting and over-generalization on various semi- and full- supervised tasks. Additionally, we explore the use of large language models (LLMs) for node feature engineering to enhance the performance of GCNIII in cross-domain node classification tasks. Our implementation is available at https://github.com/CYCUCAS/GCNIII.
Relational databases, organized into tables connected by primary-foreign key relationships, are a common format for organizing data. Making predictions on relational data often involves transforming them into a flat tabular format through table joins and feature engineering, which serve as input to tabular methods. However, designing features that fully capture complex relational patterns remains challenging. Graph Neural Networks (GNNs) offer a compelling alternative by inherently modeling these relationships, but their time overhead during inference limits their applicability for real-time scenarios. In this work, we aim to bridge this gap by leveraging existing feature engineering efforts to enhance the efficiency of GNNs in relational databases. Specifically, we use GNNs to capture complex relationships within relational databases, patterns that are difficult to featurize, while employing engineered features to encode temporal information, thereby avoiding the need to retain the entire historical graph and enabling the use of smaller, more efficient graphs. Our \textsc{LightRDL} approach not only improves efficiency, but also outperforms existing models. Experimental results on the RelBench benchmark demonstrate that our framework achieves up to $33\%$ performance improvement and a $526\times$ inference speedup compared to GNNs, making it highly suitable for real-time inference.
NeuralFoil is an open-source Python-based tool for rapid aerodynamics analysis of airfoils, similar in purpose to XFoil. Speedups ranging from 8x to 1,000x over XFoil are demonstrated, after controlling for equivalent accuracy. NeuralFoil computes both global and local quantities (lift, drag, velocity distribution, etc.) over a broad input space, including: an 18-dimensional space of airfoil shapes, possibly including control deflections; a 360 degree range of angles of attack; Reynolds numbers from $10^2$ to $10^{10}$; subsonic flows up to the transonic drag rise; and with varying turbulence parameters. Results match those of XFoil closely: the mean relative error of drag is 0.37% on simple cases, and remains as low as 2.0% on a test dataset with numerous post-stall and transitional cases. NeuralFoil facilitates gradient-based design optimization, due to its $C^\infty$-continuous solutions, automatic-differentiation-compatibility, and bounded computational cost without non-convergence issues. NeuralFoil is a hybrid of physics-informed machine learning techniques and analytical models. Here, physics information includes symmetries that are structurally embedded into the model architecture, feature engineering using domain knowledge, and guaranteed extrapolation to known limit cases. This work also introduces a new approach for surrogate model uncertainty quantification that enables robust design optimization. This work discusses the methodology and performance of NeuralFoil with several case studies, including a practical airfoil design optimization study including both aerodynamic and non-aerodynamic constraints. Here, NeuralFoil optimization is able to produce airfoils nearly identical in performance and shape to expert-designed airfoils within seconds; these computationally-optimized airfoils provide a useful starting point for further expert refinement.
Automated feature engineering plays a critical role in improving predictive model performance for tabular learning tasks. Traditional automated feature engineering methods are limited by their reliance on pre-defined transformations within fixed, manually designed search spaces, often neglecting domain knowledge. Recent advances using Large Language Models (LLMs) have enabled the integration of domain knowledge into the feature engineering process. However, existing LLM-based approaches use direct prompting or rely solely on validation scores for feature selection, failing to leverage insights from prior feature discovery experiments or establish meaningful reasoning between feature generation and data-driven performance. To address these challenges, we propose LLM-FE, a novel framework that combines evolutionary search with the domain knowledge and reasoning capabilities of LLMs to automatically discover effective features for tabular learning tasks. LLM-FE formulates feature engineering as a program search problem, where LLMs propose new feature transformation programs iteratively, and data-driven feedback guides the search process. Our results demonstrate that LLM-FE consistently outperforms state-of-the-art baselines, significantly enhancing the performance of tabular prediction models across diverse classification and regression benchmarks.
Texture recognition has recently been dominated by ImageNet-pre-trained deep Convolutional Neural Networks (CNNs), with specialized modifications and feature engineering required to achieve state-of-the-art (SOTA) performance. However, although Vision Transformers (ViTs) were introduced a few years ago, little is known about their texture recognition ability. Therefore, in this work, we introduce VORTEX (ViTs with Orderless and Randomized Token Encodings for Texture Recognition), a novel method that enables the effective use of ViTs for texture analysis. VORTEX extracts multi-depth token embeddings from pre-trained ViT backbones and employs a lightweight module to aggregate hierarchical features and perform orderless encoding, obtaining a better image representation for texture recognition tasks. This approach allows seamless integration with any ViT with the common transformer architecture. Moreover, no fine-tuning of the backbone is performed, since they are used only as frozen feature extractors, and the features are fed to a linear SVM. We evaluate VORTEX on nine diverse texture datasets, demonstrating its ability to achieve or surpass SOTA performance in a variety of texture analysis scenarios. By bridging the gap between texture recognition with CNNs and transformer-based architectures, VORTEX paves the way for adopting emerging transformer foundation models. Furthermore, VORTEX demonstrates robust computational efficiency when coupled with ViT backbones compared to CNNs with similar costs. The method implementation and experimental scripts are publicly available in our online repository.
In this study, we implement a Wasserstein GAN with Gradient Penalty (WGAN-GP) to generate multi-channel resting-state EEG data and assess the quality of the synthesized signals through both visual and feature-based evaluations. Our results indicate that the model effectively captures the statistical and spectral characteristics of real EEG data, although challenges remain in replicating high-frequency oscillations in the frontal region. Additionally, we demonstrate that the Critic's learned representations can be reused for gender classification task, achieving an out-of-sample accuracy, significantly better than a shuffled-label baseline and a model trained directly on EEG data. These findings suggest that generative models can serve not only as EEG data generators but also as unsupervised feature extractors, reducing the need for manual feature engineering. This study highlights the potential of GAN-based unsupervised learning for EEG analysis, suggesting avenues for more data-efficient deep learning applications in neuroscience.
Electronic health records (EHRs) provide a comprehensive source of longitudinal patient data, encompassing structured modalities such as laboratory results, imaging data, and vital signs, and unstructured clinical notes. These datasets, after necessary preprocessing to clean and format the data for analysis, often remain in their raw EHR form, representing numerical or categorical values without further transformation into task-agnostic embeddings. While such raw EHR data enables predictive modeling, its reliance on manual feature engineering or downstream task-specific optimization limits its utility for general-purpose applications. Deep learning (DL) techniques, such as recurrent neural networks (RNNs) and Transformers, have facilitated predictive tasks like disease progression and diagnosis prediction. However, these methods often struggle to fully exploit the temporal and multimodal dependencies inherent in EHR data due to their reliance on pre-processed but untransformed raw EHR inputs. In this study, we introduce CAAT-EHR, a novel architecture designed to bridge this gap by generating robust, task-agnostic longitudinal embeddings from raw EHR data. CAAT-EHR leverages self- and cross-attention mechanisms in its encoder to integrate temporal and contextual relationships across multiple modalities, transforming the data into enriched embeddings that capture complex dependencies. An autoregressive decoder complements the encoder by predicting future time points data during pre-training, ensuring that the resulting embeddings maintain temporal consistency and alignment. CAAT-EHR eliminates the need for manual feature engineering and enables seamless transferability across diverse downstream tasks. Extensive evaluations on benchmark datasets, demonstrate the superiority of CAAT-EHR-generated embeddings over pre-processed raw EHR data and other baseline approaches.
Tree-based Genetic Programming (TGP) is a key evolutionary algorithm widely used in symbolic regression, feature engineering, and scientific modeling. Its high computational demands make GPU acceleration essential for scalable and high-performance evolutionary computation. However, GPU acceleration of TGP faces three key challenges: inefficient tree encoding, highly heterogeneous genetic operations, and limited parallelism in fitness evaluation. To address these challenges, we introduce EvoGP, a comprehensive GPU-accelerated TGP framework. First, we design a tensorized encoding scheme to represent tree with different structures as tensors with the same shape, optimizing memory access and enabling efficient parallel execution. Second, we propose a unified parallel framework for genetic operations by leveraging shared computational primitives and implementing dedicated CUDA kernels for scalable performance. Third, we present a fully parallel fitness evaluation strategy for symbolic regression, exploiting both population-level and data-level parallelism to maximize GPU utilization. Moreover, we implement a comprehensive library to provide rich algorithm operators and benchmark problems. EvoGP is extensively tested on various tasks, including symbolic regression, classification, and robotics control, demonstrating its versatility and effectiveness across diverse application scenarios. Experimental results show that EvoGP achieves up to a 140.89x speedup over the state-of-the-art GPU-based TGP implementation, while maintaining or exceeding the accuracy of baseline methods. EvoGP is open-source and accessible at: https://github.com/EMI-Group/evogp.
This paper presents a risk analysis of flowlines in the oil and gas sector using Geographic Information Systems (GIS) and machine learning (ML). Flowlines, vital conduits transporting oil, gas, and water from wellheads to surface facilities, often face under-assessment compared to transmission pipelines. This study addresses this gap using advanced tools to predict and mitigate failures, improving environmental safety and reducing human exposure. Extensive datasets from the Colorado Energy and Carbon Management Commission (ECMC) were processed through spatial matching, feature engineering, and geometric extraction to build robust predictive models. Various ML algorithms, including logistic regression, support vector machines, gradient boosting decision trees, and K-Means clustering, were used to assess and classify risks, with ensemble classifiers showing superior accuracy, especially when paired with Principal Component Analysis (PCA) for dimensionality reduction. Finally, a thorough data analysis highlighted spatial and operational factors influencing risks, identifying high-risk zones for focused monitoring. Overall, the study demonstrates the transformative potential of integrating GIS and ML in flowline risk management, proposing a data-driven approach that emphasizes the need for accurate data and refined models to improve safety in petroleum extraction.
In this study, we explore the use of a transformer-based language model as an encoder to predict the band gaps of semiconductor materials directly from their text descriptions. Quantum chemistry simulations, including Density Functional Theory (DFT), are computationally intensive and time-consuming, which limits their practicality for high-throughput material screening, particularly for complex systems. Shallow machine learning (ML) models, while effective, often require extensive data preprocessing to convert non-numerical material properties into numerical inputs. In contrast, our approach leverages textual data directly, bypassing the need for complex feature engineering. We generate material descriptions in two formats: formatted strings combining features and natural language text generated using the ChatGPT API. We demonstrate that the RoBERTa model, pre-trained on natural language processing tasks, performs effectively as an encoder for prediction tasks. With minimal fine-tuning, it achieves a mean absolute error (MAE) of approximately 0.33 eV, performing better than shallow machine learning models such as Support Vector Regression, Random Forest, and XGBoost. Even when only the linear regression head is trained while keeping the RoBERTa encoder layers frozen, the accuracy remains nearly identical to that of the fully trained model. This demonstrates that the pre-trained RoBERTa encoder is highly adaptable for processing domain-specific text related to material properties, such as the band gap, significantly reducing the need for extensive retraining. This study highlights the potential of transformer-based language models to serve as efficient and versatile encoders for semiconductor materials property prediction tasks.
Foundation models have become popular in forecasting due to their ability to make accurate predictions, even with minimal fine-tuning on specific datasets. In this paper, we demonstrate how the newly released regression variant of TabPFN, a general tabular foundation model, can be applied to time series forecasting. We propose a straightforward approach, TabPFN-TS, which pairs TabPFN with simple feature engineering to achieve strong forecasting performance. Despite its simplicity and with only 11M parameters, TabPFN-TS outperforms Chronos-Mini, a model of similar size, and matches or even slightly outperforms Chronos-Large, which has 65-fold more parameters. A key strength of our method lies in its reliance solely on artificial data during pre-training, avoiding the need for large training datasets and eliminating the risk of benchmark contamination.
As the field of automated machine learning (AutoML) advances, it becomes increasingly important to incorporate domain knowledge into these systems. We present an approach for doing so by harnessing the power of large language models (LLMs). Specifically, we introduce Context-Aware Automated Feature Engineering (CAAFE), a feature engineering method for tabular datasets that utilizes an LLM to iteratively generate additional semantically meaningful features for tabular datasets based on the description of the dataset. The method produces both Python code for creating new features and explanations for the utility of the generated features. Despite being methodologically simple, CAAFE improves performance on 11 out of 14 datasets -- boosting mean ROC AUC performance from 0.798 to 0.822 across all dataset - similar to the improvement achieved by using a random forest instead of logistic regression on our datasets. Furthermore, CAAFE is interpretable by providing a textual explanation for each generated feature. CAAFE paves the way for more extensive semi-automation in data science tasks and emphasizes the significance of context-aware solutions that can extend the scope of AutoML systems to semantic AutoML. We release our $\href{https://github.com/automl/CAAFE}{code}$, a simple $\href{https://colab.research.google.com/drive/1mCA8xOAJZ4MaB_alZvyARTMjhl6RZf0a}{demo}$ and a $\href{https://pypi.org/project/caafe/}{python\ package}$.
In this study, we focus on automated approaches to detect depression from clinical interviews using multi-modal machine learning (ML). Our approach differentiates from other successful ML methods such as context-aware analysis through feature engineering and end-to-end deep neural networks for depression detection utilizing the Distress Analysis Interview Corpus. We propose a novel method that incorporates: (1) pre-trained Transformer combined with data augmentation based on topic modelling for textual data; and (2) deep 1D convolutional neural network (CNN) for acoustic feature modeling. The simulation results demonstrate the effectiveness of the proposed method for training multi-modal deep learning models. Our deep 1D CNN and Transformer models achieved state-of-the-art performance for audio and text modalities respectively. Combining them in a multi-modal framework also outperforms state-of-the-art for the combined setting. Code available at https://github.com/genandlam/multi-modal-depression-detection
This paper introduces GLARE an Arabic Apps Reviews dataset collected from Saudi Google PlayStore. It consists of 76M reviews, 69M of which are Arabic reviews of 9,980 Android Applications. We present the data collection methodology, along with a detailed Exploratory Data Analysis (EDA) and Feature Engineering on the gathered reviews. We also highlight possible use cases and benefits of the dataset.