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Dec 15

Transformers for molecular property prediction: Domain adaptation efficiently improves performance

Most of the current transformer-based chemical language models are pre-trained on millions to billions of molecules. However, the improvement from such scaling in dataset size is not confidently linked to improved molecular property prediction. The aim of this study is to investigate and overcome some of the limitations of transformer models in predicting molecular properties. Specifically, we examine the impact of pre-training dataset size and diversity on the performance of transformer models and investigate the use of domain adaptation as a technique for improving model performance. First, our findings indicate that increasing pretraining dataset size beyond 400K molecules from the GuacaMol dataset does not result in a significant improvement on four ADME endpoints, namely, solubility, permeability, microsomal stability, and plasma protein binding. Second, our results demonstrate that using domain adaptation by further training the transformer model on a small set of domain-relevant molecules, i.e., a few hundred to a few thousand, using multi-task regression of physicochemical properties was sufficient to significantly improve performance for three out of the four investigated ADME endpoints (P-value < 0.001). Finally, we observe that a model pre-trained on 400K molecules and domain adopted on a few hundred/thousand molecules performs similarly (P-value > 0.05) to more complicated transformer models like MolBERT(pre-trained on 1.3M molecules) and MolFormer (pre-trained on 100M molecules). A comparison to a random forest model trained on basic physicochemical properties showed similar performance to the examined transformer models. We believe that current transformer models can be improved through further systematic analysis of pre-training and downstream data, pre-training objectives, and scaling laws, ultimately leading to better and more helpful models.

  • 6 authors
·
Mar 5

Advance Real-time Detection of Traffic Incidents in Highways using Vehicle Trajectory Data

A significant number of traffic crashes are secondary crashes that occur because of an earlier incident on the road. Thus, early detection of traffic incidents is crucial for road users from safety perspectives with a potential to reduce the risk of secondary crashes. The wide availability of GPS devices now-a-days gives an opportunity of tracking and recording vehicle trajectories. The objective of this study is to use vehicle trajectory data for advance real-time detection of traffic incidents on highways using machine learning-based algorithms. The study uses three days of unevenly sequenced vehicle trajectory data and traffic incident data on I-10, one of the most crash-prone highways in Louisiana. Vehicle trajectories are converted to trajectories based on virtual detector locations to maintain spatial uniformity as well as to generate historical traffic data for machine learning algorithms. Trips matched with traffic incidents on the way are separated and along with other trips with similar spatial attributes are used to build a database for modeling. Multiple machine learning algorithms such as Logistic Regression, Random Forest, Extreme Gradient Boost, and Artificial Neural Network models are used to detect a trajectory that is likely to face an incident in the downstream road section. Results suggest that the Random Forest model achieves the best performance for predicting an incident with reasonable recall value and discrimination capability.

  • 2 authors
·
Aug 14, 2024

Using remotely sensed data for air pollution assessment

Air pollution constitutes a global problem of paramount importance that affects not only human health, but also the environment. The existence of spatial and temporal data regarding the concentrations of pollutants is crucial for performing air pollution studies and monitor emissions. However, although observation data presents great temporal coverage, the number of stations is very limited and they are usually built in more populated areas. The main objective of this work is to create models capable of inferring pollutant concentrations in locations where no observation data exists. A machine learning model, more specifically the random forest model, was developed for predicting concentrations in the Iberian Peninsula in 2019 for five selected pollutants: NO_2, O_3 SO_2, PM10, and PM2.5. Model features include satellite measurements, meteorological variables, land use classification, temporal variables (month, day of year), and spatial variables (latitude, longitude, altitude). The models were evaluated using various methods, including station 10-fold cross-validation, in which in each fold observations from 10\% of the stations are used as testing data and the rest as training data. The R^2, RMSE and mean bias were determined for each model. The NO_2 and O_3 models presented good values of R^2, 0.5524 and 0.7462, respectively. However, the SO_2, PM10, and PM2.5 models performed very poorly in this regard, with R^2 values of -0.0231, 0.3722, and 0.3303, respectively. All models slightly overestimated the ground concentrations, except the O_3 model. All models presented acceptable cross-validation RMSE, except the O_3 and PM10 models where the mean value was a little higher (12.5934 mu g/m^3 and 10.4737 mu g/m^3, respectively).

  • 3 authors
·
Feb 4, 2024

Accelerating the Search for Superconductors Using Machine Learning

Prediction of critical temperature (T_c) of a superconductor remains a significant challenge in condensed matter physics. While the BCS theory explains superconductivity in conventional superconductors, there is no framework to predict T_c of unconventional, higher T_{c} superconductors. Quantum Structure Diagrams (QSD) were successful in establishing structure-property relationship for superconductors, quasicrystals, and ferroelectric materials starting from chemical composition. Building on the QSD ideas, we demonstrate that the principal component analysis of superconductivity data uncovers the clustering of various classes of superconductors. We use machine learning analysis and cleaned databases of superconductors to develop predictive models of T_c of a superconductor using its chemical composition. Earlier studies relied on datasets with inconsistencies, leading to suboptimal predictions. To address this, we introduce a data-cleaning workflow to enhance the statistical quality of superconducting databases by eliminating redundancies and resolving inconsistencies. With this improvised database, we apply a supervised machine learning framework and develop a Random Forest model to predict superconductivity and T_c as a function of descriptors motivated from Quantum Structure Diagrams. We demonstrate that this model generalizes effectively in reasonably accurate prediction of T_{c} of compounds outside the database. We further employ our model to systematically screen materials across materials databases as well as various chemically plausible combinations of elements and predict Tl_{5}Ba_{6}Ca_{6}Cu_{9}O_{29} to exhibit superconductivity with a T_{c} sim 105 K. Being based on the descriptors used in QSD's, our model bypasses structural information and predicts T_{c} merely from the chemical composition.

  • 2 authors
·
May 17

Understanding GEMM Performance and Energy on NVIDIA Ada Lovelace: A Machine Learning-Based Analytical Approach

Analytical framework for predicting General Matrix Multiplication (GEMM) performance on modern GPUs, focusing on runtime, power consumption, and energy efficiency. Our study employs two approaches: a custom-implemented tiled matrix multiplication kernel for fundamental analysis, and NVIDIA's CUTLASS library for comprehensive performance data collection across advanced configurations. Using the NVIDIA RTX 4070 as our experimental platform, we developed a Random Forest-based prediction model with multi-output regression capability. Through analysis of both naive tiled matrix multiplication with varying tile sizes (1 to 32) and 16,128 CUTLASS GEMM operations across diverse configurations, we identified critical performance patterns related to matrix dimensions, thread block configurations, and memory access patterns. Our framework achieved exceptional accuracy with an R^2 score of 0.98 for runtime prediction (mean error 15.57%) and 0.78 for power prediction (median error 5.42%). The system successfully predicts performance across matrix sizes, demonstrating robust scaling behavior. Our results show that optimal tile size selection can improve performance by up to 3.2x while reducing power consumption by 22% compared to baseline configurations. Analysis of shared memory utilization and SM occupancy reveals that tile sizes of 16x16 achieve the best balance between parallelism and resource usage. The implementation of our framework, including prediction models and analysis tools, is available as an open-source project at GPPerf [https://github.com/pavlyhalim/GPPerf].

  • 3 authors
·
Nov 25, 2024

FUSE : A Ridge and Random Forest-Based Metric for Evaluating MT in Indigenous Languages

This paper presents the winning submission of the RaaVa team to the AmericasNLP 2025 Shared Task 3 on Automatic Evaluation Metrics for Machine Translation (MT) into Indigenous Languages of America, where our system ranked first overall based on average Pearson correlation with the human annotations. We introduce Feature-Union Scorer (FUSE) for Evaluation, FUSE integrates Ridge regression and Gradient Boosting to model translation quality. In addition to FUSE, we explore five alternative approaches leveraging different combinations of linguistic similarity features and learning paradigms. FUSE Score highlights the effectiveness of combining lexical, phonetic, semantic, and fuzzy token similarity with learning-based modeling to improve MT evaluation for morphologically rich and low-resource languages. MT into Indigenous languages poses unique challenges due to polysynthesis, complex morphology, and non-standardized orthography. Conventional automatic metrics such as BLEU, TER, and ChrF often fail to capture deeper aspects like semantic adequacy and fluency. Our proposed framework, formerly referred to as FUSE, incorporates multilingual sentence embeddings and phonological encodings to better align with human evaluation. We train supervised models on human-annotated development sets and evaluate held-out test data. Results show that FUSE consistently achieves higher Pearson and Spearman correlations with human judgments, offering a robust and linguistically informed solution for MT evaluation in low-resource settings.

  • 2 authors
·
Mar 28

MachineLearningLM: Continued Pretraining Language Models on Millions of Synthetic Tabular Prediction Tasks Scales In-Context ML

Large language models (LLMs) possess broad world knowledge and strong general-purpose reasoning ability, yet they struggle to learn from many in-context examples on standard machine learning (ML) tasks, that is, to leverage many-shot demonstrations purely via in-context learning (ICL) without gradient descent. We introduce MachineLearningLM, a portable continued-pretraining framework that equips a general-purpose LLM with robust in-context ML capability while preserving its general knowledge and reasoning for broader chat workflows. Our pretraining procedure synthesizes ML tasks from millions of structural causal models (SCMs), spanning shot counts up to 1,024. We begin with a random-forest teacher, distilling tree-based decision strategies into the LLM to strengthen robustness in numerical modeling. All tasks are serialized with a token-efficient prompt, enabling 3x to 6x more examples per context window and delivering up to 50x amortized throughput via batch inference. Despite a modest setup (Qwen-2.5-7B-Instruct with LoRA rank 8), MachineLearningLM outperforms strong LLM baselines (e.g., GPT-5-mini) by an average of about 15% on out-of-distribution tabular classification across finance, physics, biology, and healthcare domains. It exhibits a striking many-shot scaling law: accuracy increases monotonically as in-context demonstrations grow from 8 to 1,024. Without any task-specific training, it attains random-forest-level accuracy across hundreds of shots. General chat capabilities, including knowledge and reasoning, are preserved: it achieves 75.4% on MMLU.

  • 5 authors
·
Sep 8 8

Impact of a Batter in ODI Cricket Implementing Regression Models from Match Commentary

Cricket, "a Gentleman's Game", is a prominent sport rising worldwide. Due to the rising competitiveness of the sport, players and team management have become more professional with their approach. Prior studies predicted individual performance or chose the best team but did not highlight the batter's potential. On the other hand, our research aims to evaluate a player's impact while considering his control in various circumstances. This paper seeks to understand the conundrum behind this impactful performance by determining how much control a player has over the circumstances and generating the "Effective Runs",a new measure we propose. We first gathered the fundamental cricket data from open-source datasets; however, variables like pitch, weather, and control were not readily available for all matches. As a result, we compiled our corpus data by analyzing the commentary of the match summaries. This gave us an insight into the particular game's weather and pitch conditions. Furthermore, ball-by-ball inspection from the commentary led us to determine the control of the shots played by the batter. We collected data for the entire One Day International career, up to February 2022, of 3 prominent cricket players: Rohit G Sharma, David A Warner, and Kane S Williamson. Lastly, to prepare the dataset, we encoded, scaled, and split the dataset to train and test Machine Learning Algorithms. We used Multiple Linear Regression (MLR), Polynomial Regression, Support Vector Regression (SVR), Decision Tree Regression, and Random Forest Regression on each player's data individually to train them and predict the Impact the player will have on the game. Multiple Linear Regression and Random Forest give the best predictions accuracy of 90.16 percent and 87.12 percent, respectively.

  • 6 authors
·
Feb 22, 2023

Machine Learning Workflow to Explain Black-box Models for Early Alzheimer's Disease Classification Evaluated for Multiple Datasets

Purpose: Hard-to-interpret Black-box Machine Learning (ML) were often used for early Alzheimer's Disease (AD) detection. Methods: To interpret eXtreme Gradient Boosting (XGBoost), Random Forest (RF), and Support Vector Machine (SVM) black-box models a workflow based on Shapley values was developed. All models were trained on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset and evaluated for an independent ADNI test set, as well as the external Australian Imaging and Lifestyle flagship study of Ageing (AIBL), and Open Access Series of Imaging Studies (OASIS) datasets. Shapley values were compared to intuitively interpretable Decision Trees (DTs), and Logistic Regression (LR), as well as natural and permutation feature importances. To avoid the reduction of the explanation validity caused by correlated features, forward selection and aspect consolidation were implemented. Results: Some black-box models outperformed DTs and LR. The forward-selected features correspond to brain areas previously associated with AD. Shapley values identified biologically plausible associations with moderate to strong correlations with feature importances. The most important RF features to predict AD conversion were the volume of the amygdalae, and a cognitive test score. Good cognitive test performances and large brain volumes decreased the AD risk. The models trained using cognitive test scores significantly outperformed brain volumetric models (p<0.05). Cognitive Normal (CN) vs. AD models were successfully transferred to external datasets. Conclusion: In comparison to previous work, improved performances for ADNI and AIBL were achieved for CN vs. Mild Cognitive Impairment (MCI) classification using brain volumes. The Shapley values and the feature importances showed moderate to strong correlations.

  • 2 authors
·
May 12, 2022

CardioForest: An Explainable Ensemble Learning Model for Automatic Wide QRS Complex Tachycardia Diagnosis from ECG

This study aims to develop and evaluate an ensemble machine learning-based framework for the automatic detection of Wide QRS Complex Tachycardia (WCT) from ECG signals, emphasizing diagnostic accuracy and interpretability using Explainable AI. The proposed system integrates ensemble learning techniques, i.e., an optimized Random Forest known as CardioForest, and models like XGBoost and LightGBM. The models were trained and tested on ECG data from the publicly available MIMIC-IV dataset. The testing was carried out with the assistance of accuracy, balanced accuracy, precision, recall, F1 score, ROC-AUC, and error rate (RMSE, MAE) measures. In addition, SHAP (SHapley Additive exPlanations) was used to ascertain model explainability and clinical relevance. The CardioForest model performed best on all metrics, achieving a test accuracy of 94.95%, a balanced accuracy of 88.31%, and high precision and recall metrics. SHAP analysis confirmed the model's ability to rank the most relevant ECG features, such as QRS duration, in accordance with clinical intuitions, thereby fostering trust and usability in clinical practice. The findings recognize CardioForest as an extremely dependable and interpretable WCT detection model. Being able to offer accurate predictions and transparency through explainability makes it a valuable tool to help cardiologists make timely and well-informed diagnoses, especially for high-stakes and emergency scenarios.

  • 7 authors
·
Sep 30

Large Language Models for Automated Data Science: Introducing CAAFE for Context-Aware Automated Feature Engineering

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 https://github.com/automl/CAAFE{code}, a simple https://colab.research.google.com/drive/1mCA8xOAJZ4MaB_alZvyARTMjhl6RZf0a{demo} and a https://pypi.org/project/caafe/{python package}.

  • 3 authors
·
May 5, 2023

OutRank: Speeding up AutoML-based Model Search for Large Sparse Data sets with Cardinality-aware Feature Ranking

The design of modern recommender systems relies on understanding which parts of the feature space are relevant for solving a given recommendation task. However, real-world data sets in this domain are often characterized by their large size, sparsity, and noise, making it challenging to identify meaningful signals. Feature ranking represents an efficient branch of algorithms that can help address these challenges by identifying the most informative features and facilitating the automated search for more compact and better-performing models (AutoML). We introduce OutRank, a system for versatile feature ranking and data quality-related anomaly detection. OutRank was built with categorical data in mind, utilizing a variant of mutual information that is normalized with regard to the noise produced by features of the same cardinality. We further extend the similarity measure by incorporating information on feature similarity and combined relevance. The proposed approach's feasibility is demonstrated by speeding up the state-of-the-art AutoML system on a synthetic data set with no performance loss. Furthermore, we considered a real-life click-through-rate prediction data set where it outperformed strong baselines such as random forest-based approaches. The proposed approach enables exploration of up to 300% larger feature spaces compared to AutoML-only approaches, enabling faster search for better models on off-the-shelf hardware.

  • 2 authors
·
Sep 4, 2023

FinAI-BERT: A Transformer-Based Model for Sentence-Level Detection of AI Disclosures in Financial Reports

The proliferation of artificial intelligence (AI) in financial services has prompted growing demand for tools that can systematically detect AI-related disclosures in corporate filings. While prior approaches often rely on keyword expansion or document-level classification, they fall short in granularity, interpretability, and robustness. This study introduces FinAI-BERT, a domain-adapted transformer-based language model designed to classify AI-related content at the sentence level within financial texts. The model was fine-tuned on a manually curated and balanced dataset of 1,586 sentences drawn from 669 annual reports of U.S. banks (2015 to 2023). FinAI-BERT achieved near-perfect classification performance (accuracy of 99.37 percent, F1 score of 0.993), outperforming traditional baselines such as Logistic Regression, Naive Bayes, Random Forest, and XGBoost. Interpretability was ensured through SHAP-based token attribution, while bias analysis and robustness checks confirmed the model's stability across sentence lengths, adversarial inputs, and temporal samples. Theoretically, the study advances financial NLP by operationalizing fine-grained, theme-specific classification using transformer architectures. Practically, it offers a scalable, transparent solution for analysts, regulators, and scholars seeking to monitor the diffusion and framing of AI across financial institutions.

  • 1 authors
·
Jun 29

Uncertainty quantification for improving radiomic-based models in radiation pneumonitis prediction

Background and Objective: Radiation pneumonitis (RP) is a side effect of thoracic radiation therapy. Recently, Machine learning (ML) models enhanced with radiomic and dosiomic features provide better predictions by incorporating spatial information beyond DVHs. However, to improve the clinical decision process, we propose to use uncertainty quantification (UQ) to improve the confidence in model prediction. This study evaluates the impact of post hoc UQ methods on the discriminative performance and calibration of ML models for RP prediction. Methods: This study evaluated four ML models: logistic regression (LR), support vector machines (SVM), extreme gradient boosting (XGB), and random forest (RF), using radiomic, dosiomic, and dosimetric features to predict RP. We applied UQ methods, including Patt scaling, isotonic regression, Venn-ABERS predictor, and Conformal Prediction, to quantify uncertainty. Model performance was assessed through Area Under the Receiver Operating Characteristic curve (AUROC), Area Under the Precision-Recall Curve (AUPRC), and Adaptive Calibration Error (ACE) using Leave-One-Out Cross-Validation (LOO-CV). Results: UQ methods enhanced predictive performance, particularly for high-certainty predictions, while also improving calibration. Radiomic and dosiomic features increased model accuracy but introduced calibration challenges, especially for non-linear models like XGB and RF. Performance gains from UQ methods were most noticeable at higher certainty thresholds. Conclusion: Integrating UQ into ML models with radiomic and dosiomic features improves both predictive accuracy and calibration, supporting more reliable clinical decision-making. The findings emphasize the value of UQ methods in enhancing applicability of predictive models for RP in healthcare settings.

  • 3 authors
·
Dec 27, 2024

LLM-based Multi-class Attack Analysis and Mitigation Framework in IoT/IIoT Networks

The Internet of Things has expanded rapidly, transforming communication and operations across industries but also increasing the attack surface and security breaches. Artificial Intelligence plays a key role in securing IoT, enabling attack detection, attack behavior analysis, and mitigation suggestion. Despite advancements, evaluations remain purely qualitative, and the lack of a standardized, objective benchmark for quantitatively measuring AI-based attack analysis and mitigation hinders consistent assessment of model effectiveness. In this work, we propose a hybrid framework combining Machine Learning (ML) for multi-class attack detection with Large Language Models (LLMs) for attack behavior analysis and mitigation suggestion. After benchmarking several ML and Deep Learning (DL) classifiers on the Edge-IIoTset and CICIoT2023 datasets, we applied structured role-play prompt engineering with Retrieval-Augmented Generation (RAG) to guide ChatGPT-o3 and DeepSeek-R1 in producing detailed, context-aware responses. We introduce novel evaluation metrics for quantitative assessment to guide us and an ensemble of judge LLMs, namely ChatGPT-4o, DeepSeek-V3, Mixtral 8x7B Instruct, Gemini 2.5 Flash, Meta Llama 4, TII Falcon H1 34B Instruct, xAI Grok 3, and Claude 4 Sonnet, to independently evaluate the responses. Results show that Random Forest has the best detection model, and ChatGPT-o3 outperformed DeepSeek-R1 in attack analysis and mitigation.

  • 3 authors
·
Oct 30

Predicting Thermoelectric Power Factor of Bismuth Telluride During Laser Powder Bed Fusion Additive Manufacturing

An additive manufacturing (AM) process, like laser powder bed fusion, allows for the fabrication of objects by spreading and melting powder in layers until a freeform part shape is created. In order to improve the properties of the material involved in the AM process, it is important to predict the material characterization property as a function of the processing conditions. In thermoelectric materials, the power factor is a measure of how efficiently the material can convert heat to electricity. While earlier works have predicted the material characterization properties of different thermoelectric materials using various techniques, implementation of machine learning models to predict the power factor of bismuth telluride (Bi2Te3) during the AM process has not been explored. This is important as Bi2Te3 is a standard material for low temperature applications. Thus, we used data about manufacturing processing parameters involved and in-situ sensor monitoring data collected during AM of Bi2Te3, to train different machine learning models in order to predict its thermoelectric power factor. We implemented supervised machine learning techniques using 80% training and 20% test data and further used the permutation feature importance method to identify important processing parameters and in-situ sensor features which were best at predicting power factor of the material. Ensemble-based methods like random forest, AdaBoost classifier, and bagging classifier performed the best in predicting power factor with the highest accuracy of 90% achieved by the bagging classifier model. Additionally, we found the top 15 processing parameters and in-situ sensor features to characterize the material manufacturing property like power factor. These features could further be optimized to maximize power factor of the thermoelectric material and improve the quality of the products built using this material.

  • 6 authors
·
Mar 27, 2023

Online Recognition of Incomplete Gesture Data to Interface Collaborative Robots

Online recognition of gestures is critical for intuitive human-robot interaction (HRI) and further push collaborative robotics into the market, making robots accessible to more people. The problem is that it is difficult to achieve accurate gesture recognition in real unstructured environments, often using distorted and incomplete multisensory data. This paper introduces an HRI framework to classify large vocabularies of interwoven static gestures (SGs) and dynamic gestures (DGs) captured with wearable sensors. DG features are obtained by applying data dimensionality reduction to raw data from sensors (resampling with cubic interpolation and principal component analysis). Experimental tests were conducted using the UC2017 hand gesture dataset with samples from eight different subjects. The classification models show an accuracy of 95.6% for a library of 24 SGs with a random forest and 99.3% for 10 DGs using artificial neural networks. These results compare equally or favorably with different commonly used classifiers. Long short-term memory deep networks achieved similar performance in online frame-by-frame classification using raw incomplete data, performing better in terms of accuracy than static models with specially crafted features, but worse in training and inference time. The recognized gestures are used to teleoperate a robot in a collaborative process that consists in preparing a breakfast meal.

  • 3 authors
·
Apr 13, 2023

GlucoLens: Explainable Postprandial Blood Glucose Prediction from Diet and Physical Activity

Postprandial hyperglycemia, marked by the blood glucose level exceeding the normal range after meals, is a critical indicator of progression toward type 2 diabetes in prediabetic and healthy individuals. A key metric for understanding blood glucose dynamics after eating is the postprandial area under the curve (PAUC). Predicting PAUC in advance based on a person's diet and activity level and explaining what affects postprandial blood glucose could allow an individual to adjust their lifestyle accordingly to maintain normal glucose levels. In this paper, we propose GlucoLens, an explainable machine learning approach to predict PAUC and hyperglycemia from diet, activity, and recent glucose patterns. We conducted a five-week user study with 10 full-time working individuals to develop and evaluate the computational model. Our machine learning model takes multimodal data including fasting glucose, recent glucose, recent activity, and macronutrient amounts, and provides an interpretable prediction of the postprandial glucose pattern. Our extensive analyses of the collected data revealed that the trained model achieves a normalized root mean squared error (NRMSE) of 0.123. On average, GlucoLense with a Random Forest backbone provides a 16% better result than the baseline models. Additionally, GlucoLens predicts hyperglycemia with an accuracy of 74% and recommends different options to help avoid hyperglycemia through diverse counterfactual explanations. Code available: https://github.com/ab9mamun/GlucoLens.

  • 7 authors
·
Mar 5

Predicting the duration of traffic incidents for Sydney greater metropolitan area using machine learning methods

This research presents a comprehensive approach to predicting the duration of traffic incidents and classifying them as short-term or long-term across the Sydney Metropolitan Area. Leveraging a dataset that encompasses detailed records of traffic incidents, road network characteristics, and socio-economic indicators, we train and evaluate a variety of advanced machine learning models including Gradient Boosted Decision Trees (GBDT), Random Forest, LightGBM, and XGBoost. The models are assessed using Root Mean Square Error (RMSE) for regression tasks and F1 score for classification tasks. Our experimental results demonstrate that XGBoost and LightGBM outperform conventional models with XGBoost achieving the lowest RMSE of 33.7 for predicting incident duration and highest classification F1 score of 0.62 for a 30-minute duration threshold. For classification, the 30-minute threshold balances performance with 70.84% short-term duration classification accuracy and 62.72% long-term duration classification accuracy. Feature importance analysis, employing both tree split counts and SHAP values, identifies the number of affected lanes, traffic volume, and types of primary and secondary vehicles as the most influential features. The proposed methodology not only achieves high predictive accuracy but also provides stakeholders with vital insights into factors contributing to incident durations. These insights enable more informed decision-making for traffic management and response strategies. The code is available by the link: https://github.com/Future-Mobility-Lab/SydneyIncidents

  • 4 authors
·
Jun 26, 2024

Comparison of biomedical relationship extraction methods and models for knowledge graph creation

Biomedical research is growing at such an exponential pace that scientists, researchers, and practitioners are no more able to cope with the amount of published literature in the domain. The knowledge presented in the literature needs to be systematized in such a way that claims and hypotheses can be easily found, accessed, and validated. Knowledge graphs can provide such a framework for semantic knowledge representation from literature. However, in order to build a knowledge graph, it is necessary to extract knowledge as relationships between biomedical entities and normalize both entities and relationship types. In this paper, we present and compare few rule-based and machine learning-based (Naive Bayes, Random Forests as examples of traditional machine learning methods and DistilBERT, PubMedBERT, T5 and SciFive-based models as examples of modern deep learning transformers) methods for scalable relationship extraction from biomedical literature, and for the integration into the knowledge graphs. We examine how resilient are these various methods to unbalanced and fairly small datasets. Our experiments show that transformer-based models handle well both small (due to pre-training on a large dataset) and unbalanced datasets. The best performing model was the PubMedBERT-based model fine-tuned on balanced data, with a reported F1-score of 0.92. DistilBERT-based model followed with F1-score of 0.89, performing faster and with lower resource requirements. BERT-based models performed better then T5-based generative models.

  • 2 authors
·
Jan 5, 2022

HyperTab: Hypernetwork Approach for Deep Learning on Small Tabular Datasets

Deep learning has achieved impressive performance in many domains, such as computer vision and natural language processing, but its advantage over classical shallow methods on tabular datasets remains questionable. It is especially challenging to surpass the performance of tree-like ensembles, such as XGBoost or Random Forests, on small-sized datasets (less than 1k samples). To tackle this challenge, we introduce HyperTab, a hypernetwork-based approach to solving small sample problems on tabular datasets. By combining the advantages of Random Forests and neural networks, HyperTab generates an ensemble of neural networks, where each target model is specialized to process a specific lower-dimensional view of the data. Since each view plays the role of data augmentation, we virtually increase the number of training samples while keeping the number of trainable parameters unchanged, which prevents model overfitting. We evaluated HyperTab on more than 40 tabular datasets of a varying number of samples and domains of origin, and compared its performance with shallow and deep learning models representing the current state-of-the-art. We show that HyperTab consistently outranks other methods on small data (with a statistically significant difference) and scores comparable to them on larger datasets. We make a python package with the code available to download at https://pypi.org/project/hypertab/

  • 3 authors
·
Apr 7, 2023

Matbench Discovery -- An evaluation framework for machine learning crystal stability prediction

Matbench Discovery simulates the deployment of machine learning (ML) energy models in a high-throughput search for stable inorganic crystals. We address the disconnect between (i) thermodynamic stability and formation energy and (ii) in-domain vs out-of-distribution performance. Alongside this paper, we publish a Python package to aid with future model submissions and a growing online leaderboard with further insights into trade-offs between various performance metrics. To answer the question which ML methodology performs best at materials discovery, our initial release explores a variety of models including random forests, graph neural networks (GNN), one-shot predictors, iterative Bayesian optimizers and universal interatomic potentials (UIP). Ranked best-to-worst by their test set F1 score on thermodynamic stability prediction, we find CHGNet > M3GNet > MACE > ALIGNN > MEGNet > CGCNN > CGCNN+P > Wrenformer > BOWSR > Voronoi tessellation fingerprints with random forest. The top 3 models are UIPs, the winning methodology for ML-guided materials discovery, achieving F1 scores of ~0.6 for crystal stability classification and discovery acceleration factors (DAF) of up to 5x on the first 10k most stable predictions compared to dummy selection from our test set. We also highlight a sharp disconnect between commonly used global regression metrics and more task-relevant classification metrics. Accurate regressors are susceptible to unexpectedly high false-positive rates if those accurate predictions lie close to the decision boundary at 0 eV/atom above the convex hull where most materials are. Our results highlight the need to focus on classification metrics that actually correlate with improved stability hit rate.

  • 6 authors
·
Aug 28, 2023

ATM Cash demand forecasting in an Indian Bank with chaos and deep learning

This paper proposes to model chaos in the ATM cash withdrawal time series of a big Indian bank and forecast the withdrawals using deep learning methods. It also considers the importance of day-of-the-week and includes it as a dummy exogenous variable. We first modelled the chaos present in the withdrawal time series by reconstructing the state space of each series using the lag, and embedding dimension found using an auto-correlation function and Cao's method. This process converts the uni-variate time series into multi variate time series. The "day-of-the-week" is converted into seven features with the help of one-hot encoding. Then these seven features are augmented to the multivariate time series. For forecasting the future cash withdrawals, using algorithms namely ARIMA, random forest (RF), support vector regressor (SVR), multi-layer perceptron (MLP), group method of data handling (GMDH), general regression neural network (GRNN), long short term memory neural network and 1-dimensional convolutional neural network. We considered a daily cash withdrawals data set from an Indian commercial bank. After modelling chaos and adding exogenous features to the data set, we observed improvements in the forecasting for all models. Even though the random forest (RF) yielded better Symmetric Mean Absolute Percentage Error (SMAPE) value, deep learning algorithms, namely LSTM and 1D CNN, showed similar performance compared to RF, based on t-test.

  • 2 authors
·
Aug 24, 2020

POINT$^{2}$: A Polymer Informatics Training and Testing Database

The advancement of polymer informatics has been significantly propelled by the integration of machine learning (ML) techniques, enabling the rapid prediction of polymer properties and expediting the discovery of high-performance polymeric materials. However, the field lacks a standardized workflow that encompasses prediction accuracy, uncertainty quantification, ML interpretability, and polymer synthesizability. In this study, we introduce POINT^{2} (POlymer INformatics Training and Testing), a comprehensive benchmark database and protocol designed to address these critical challenges. Leveraging the existing labeled datasets and the unlabeled PI1M dataset, a collection of approximately one million virtual polymers generated via a recurrent neural network trained on the realistic polymers, we develop an ensemble of ML models, including Quantile Random Forests, Multilayer Perceptrons with dropout, Graph Neural Networks, and pretrained large language models. These models are coupled with diverse polymer representations such as Morgan, MACCS, RDKit, Topological, Atom Pair fingerprints, and graph-based descriptors to achieve property predictions, uncertainty estimations, model interpretability, and template-based polymerization synthesizability across a spectrum of properties, including gas permeability, thermal conductivity, glass transition temperature, melting temperature, fractional free volume, and density. The POINT^{2} database can serve as a valuable resource for the polymer informatics community for polymer discovery and optimization.

  • 5 authors
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Mar 30