Motivation: Enhancers are important cis-regulatory elements that regulate a wide range of biological functions and enhance the transcription of target genes. Although many feature extraction methods have been proposed to improve the performance of enhancer identification, they cannot learn position-related multiscale contextual information from raw DNA sequences. Results: In this article, we propose a novel enhancer identification method (iEnhancer-ELM) based on BERT-like enhancer language models. iEnhancer-ELM tokenizes DNA sequences with multi-scale k-mers and extracts contextual information of different scale k-mers related with their positions via an multi-head attention mechanism. We first evaluate the performance of different scale k-mers, then ensemble them to improve the performance of enhancer identification. The experimental results on two popular benchmark datasets show that our model outperforms stateof-the-art methods. We further illustrate the interpretability of iEnhancer-ELM. For a case study, we discover 30 enhancer motifs via a 3-mer-based model, where 12 of motifs are verified by STREME and JASPAR, demonstrating our model has a potential ability to unveil the biological mechanism of enhancer. Availability and implementation: The models and associated code are available at https://github.com/chen-bioinfo/iEnhancer-ELM Contact: junjiechen@hit.edu.cn Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Image processing concepts can visualize the different anatomy structure of the human body. Recent advancements in the field of deep learning have made it possible to detect the growth of cancerous tissue just by a patient's brain Magnetic Resonance Imaging (MRI) scans. These methods require very high accuracy and meager false negative rates to be of any practical use. This paper presents a Convolutional Neural Network (CNN) based transfer learning approach to classify the brain MRI scans into two classes using three pre-trained models. The performances of these models are compared with each other. Experimental results show that the Resnet-50 model achieves the highest accuracy and least false negative rates as 95% and zero respectively. It is followed by VGG-16 and Inception-V3 model with an accuracy of 90% and 55% respectively.

Sequential tests and their implied confidence sequences, which are valid at arbitrary stopping times, promise flexible statistical inference and on-the-fly decision making. However, strong guarantees are limited to parametric sequential tests that under-cover in practice or concentration-bound-based sequences that over-cover and have suboptimal rejection times. In this work, we consider \cite{robbins1970boundary}'s delayed-start normal-mixture sequential probability ratio tests, and we provide the first asymptotic type-I-error and expected-rejection-time guarantees under general non-parametric data generating processes, where the asymptotics are indexed by the test's burn-in time. The type-I-error results primarily leverage a martingale strong invariance principle and establish that these tests (and their implied confidence sequences) have type-I error rates approaching a desired $\alpha$-level. The expected-rejection-time results primarily leverage an identity inspired by It\^o's lemma and imply that, in certain asymptotic regimes, the expected rejection time approaches the minimum possible among $\alpha$-level tests. We show how to apply our results to sequential inference on parameters defined by estimating equations, such as average treatment effects. Together, our results establish these (ostensibly parametric) tests as general-purpose, non-parametric, and near-optimal. We illustrate this via numerical experiments.

Plant breeders and agricultural researchers can increase crop productivity by identifying desirable features, disease resistance, and nutritional content by analysing the Dry Bean dataset. This study analyses and compares different Support Vector Machine (SVM) classification algorithms, namely linear, polynomial, and radial basis function (RBF), along with other popular classification algorithms. The analysis is performed on the Dry Bean Dataset, with PCA (Principal Component Analysis) conducted as a preprocessing step for dimensionality reduction. The primary evaluation metric used is accuracy, and the RBF SVM kernel algorithm achieves the highest Accuracy of 93.34%, Precision of 92.61%, Recall of 92.35% and F1 Score as 91.40%. Along with adept visualization and empirical analysis, this study offers valuable guidance by emphasizing the importance of considering different SVM algorithms for complex and non-linear structured datasets.

Potatoes are the third-largest food crop globally, but their production frequently encounters difficulties because of aggressive pest infestations. The aim of this study is to investigate the various types and characteristics of these pests and propose an efficient PotatoPestNet AI-based automatic potato pest identification system. To accomplish this, we curated a reliable dataset consisting of eight types of potato pests. We leveraged the power of transfer learning by employing five customized, pre-trained transfer learning models: CMobileNetV2, CNASLargeNet, CXception, CDenseNet201, and CInceptionV3, in proposing a robust PotatoPestNet model to accurately classify potato pests. To improve the models' performance, we applied various augmentation techniques, incorporated a global average pooling layer, and implemented proper regularization methods. To further enhance the performance of the models, we utilized random search (RS) optimization for hyperparameter tuning. This optimization technique played a significant role in fine-tuning the models and achieving improved performance. We evaluated the models both visually and quantitatively, utilizing different evaluation metrics. The robustness of the models in handling imbalanced datasets was assessed using the Receiver Operating Characteristic (ROC) curve. Among the models, the Customized Tuned Inception V3 (CTInceptionV3) model, optimized through random search, demonstrated outstanding performance. It achieved the highest accuracy (91%), precision (91%), recall (91%), and F1-score (91%), showcasing its superior ability to accurately identify and classify potato pests.

Learning with multiple modalities is crucial for automated brain tumor segmentation from magnetic resonance imaging data. Explicitly optimizing the common information shared among all modalities (e.g., by maximizing the total correlation) has been shown to achieve better feature representations and thus enhance the segmentation performance. However, existing approaches are oblivious to partial common information shared by subsets of the modalities. In this paper, we show that identifying such partial common information can significantly boost the discriminative power of image segmentation models. In particular, we introduce a novel concept of partial common information mask (PCI-mask) to provide a fine-grained characterization of what partial common information is shared by which subsets of the modalities. By solving a masked correlation maximization and simultaneously learning an optimal PCI-mask, we identify the latent microstructure of partial common information and leverage it in a self-attention module to selectively weight different feature representations in multi-modal data. We implement our proposed framework on the standard U-Net. Our experimental results on the Multi-modal Brain Tumor Segmentation Challenge (BraTS) datasets outperform those of state-of-the-art segmentation baselines, with validation Dice similarity coefficients of 0.920, 0.897, 0.837 for the whole tumor, tumor core, and enhancing tumor on BraTS-2020.

Obesity is a critical healthcare issue affecting the United States. The least risky treatments available for obesity are behavioral interventions meant to promote diet and exercise. Often these interventions contain a mobile component that allows interventionists to collect participants level data and provide participants with incentives and goals to promote long term behavioral change. Recently, there has been interest in using direct financial incentives to promote behavior change. However, adherence is challenging in these interventions, as each participant will react differently to different incentive structure and amounts, leading researchers to consider personalized interventions. The key challenge for personalization, is that the clinicians do not know a priori how best to administer incentives to participants, and given finite intervention budgets how to disburse costly resources efficiently. In this paper, we consider this challenge of designing personalized weight loss interventions that use direct financial incentives to motivate weight loss while remaining within a budget. We create a machine learning approach that is able to predict how individuals may react to different incentive schedules within the context of a behavioral intervention. We use this predictive model in an adaptive framework that over the course of the intervention computes what incentives to disburse to participants and remain within the study budget. We provide both theoretical guarantees for our modeling and optimization approaches as well as demonstrate their performance in a simulated weight loss study. Our results highlight the cost efficiency and effectiveness of our personalized intervention design for weight loss.

Nanobodies (Nb) are monomeric heavy-chain fragments derived from heavy-chain only antibodies naturally found in Camelids and Sharks. Their considerably small size ( 3-4 nm; 13 kDa) and favorable biophysical properties make them attractive targets for recombinant production. Furthermore, their unique ability to bind selectively to specific antigens, such as toxins, chemicals, bacteria, and viruses, makes them powerful tools in cell biology, structural biology, medical diagnostics, and future therapeutic agents in treating cancer and other serious illnesses. However, a critical challenge in nanobodies production is the unavailability of nanobodies for a majority of antigens. Although some computational methods have been proposed to screen potential nanobodies for given target antigens, their practical application is highly restricted due to their reliance on 3D structures. Moreover, predicting nanobodyantigen interactions (binding) is a time-consuming and labor-intensive task. This study aims to develop a machine-learning method to predict Nanobody-Antigen binding solely based on the sequence data. We curated a comprehensive dataset of Nanobody-Antigen binding and nonbinding data and devised an embedding method based on gapped k-mers to predict binding based only on sequences of nanobody and antigen. Our approach achieves up to 90% accuracy in binding prediction and is significantly more efficient compared to the widely-used computational docking technique.

Our research investigates the potential of Large-scale Language Models (LLMs), specifically OpenAI's GPT, in credit risk assessment--a binary classification task. Our findings suggest that LLMs, when directed by judiciously designed prompts and supplemented with domainspecific knowledge, can parallel the performance of traditional Machine Learning (ML) models. Intriguingly, they achieve this with significantly less data--40 times less, utilizing merely 20 data points compared to the ML's 800. LLMs particularly excel in minimizing false positives and enhancing fairness, both being vital aspects of risk analysis. While our results did not surpass those of classical ML models, they underscore the potential of LLMs in analogous tasks, laying a groundwork for future explorations into harnessing the capabilities of LLMs in diverse ML tasks.

Discriminatory language and biases are often present in hate speech during conversations, which usually lead to negative impacts on targeted groups such as those based on race, gender, and religion. To tackle this issue, we propose an approach that involves a two-step process: first, detecting hate speech using a classifier, and then utilizing a debiasing component that generates less biased or unbiased alternatives through prompts. We evaluated our approach on a benchmark dataset and observed reduction in negativity due to hate speech comments. The proposed method contributes to the ongoing efforts to reduce biases in online discourse and promote a more inclusive and fair environment for communication.