Ribonucleic acids (RNAs) play a central role in cellular processes by interacting with proteins, small molecules, and other RNAs. Accurate prediction of these interactions is critical for understanding post-transcriptional regulation and advancing RNA-targeted therapeutics. However, existing computational methods are limited by their reliance on hand-crafted features, modality-specific architectures, and often require structural or physicochemical data, which are experimentally challenging to obtain and unavailable for many RNA molecules. These constraints hinder generalizability and fail to capture the complex, context-dependent semantics of RNA interactions. We present BioLLMNet, a unified sequence-only framework that leverages pretrained biological language models to encode rich, contextualized representations for both RNA molecules and their interacting partners, including proteins, small molecules, and other RNAs. Our key innovation is the introduction of a novel learnable gating mechanism, which dynamically computes feature-wise weights to adaptively integrate multimodal embeddings based on input context. This mechanism, proposed here for the first time in RNA interaction modeling, enables the model to emphasize the most informative features from each partner and achieves seamless fusion of heterogeneous modalities. As a result, BioLLMNet represents a unified framework and can flexibly and consistently model all three types of interaction (RNA-protein, RNA-small molecule, and RNA-RNA) within a shared architecture, eliminating the need for modality-specific designs. Comprehensive evaluations on benchmark data sets demonstrate that BioLLMNet achieves state-of-the-art performance across all three types of interaction. Our results underscore the power of language model-based representations combined with dynamic feature fusion for generalizable, modality-aware RNA interaction prediction.

BACKGROUND: While alignment has traditionally been the primary approach for establishing homology prior to phylogenetic inference, alignment-free methods offer a simplified alternative, particularly beneficial when handling genome-wide data involving long sequences and complex events such as rearrangements. Moreover, alignment-free methods become crucial for data types like genome skims, where assembly is impractical. However, despite these benefits, alignment-free techniques have not gained widespread acceptance since they lack the accuracy of alignment-based techniques, primarily due to their reliance on simplified models of pairwise distance calculation. RESULTS: Here, we present a likelihood based alignment-free technique for phylogenetic tree construction. We encode the presence or absence of k-mers in genome sequences in a binary matrix, and estimate phylogenetic trees using a maximum likelihood approach. A likelihood based alignment-free method for phylogeny estimation is implemented for the first time in a software named PEAFOWL, which is available at: https://github.com/hasin-abrar/Peafowl-repo . We analyze the performance of our method on seven real datasets and compare the results with the state of the art alignment-free methods. CONCLUSIONS: Results suggest that our method is competitive with existing alignment-free tools. This indicates that maximum likelihood based alignment-free methods may in the future be refined to outperform alignment-free methods relying on distance calculation as has been the case in the alignment-based setting.

MOTIVATION: Proteins are responsible for most biological functions, many of which require the interaction of more than one protein molecule. However, accurately predicting protein-protein interaction (PPI) sites (the interfacial residues of a protein that interact with other protein molecules) remains a challenge. The growing demand and cost associated with the reliable identification of PPI sites using conventional experimental methods call for computational tools for automated prediction and understanding of PPIs. RESULTS: We present Pair-EGRET, an edge-aggregated graph attention network that leverages the features extracted from pretrained transformer-like models to accurately predict PPI sites. Pair-EGRET works on a k-nearest neighbor graph, representing the 3D structure of a protein, and utilizes the cross-attention mechanism for accurate identification of interfacial residues of a pair of proteins. Through an extensive evaluation study using a diverse array of experimental data, evaluation metrics, and case studies on representative protein sequences, we demonstrate that Pair-EGRET can achieve remarkable performance in predicting PPI sites. Moreover, Pair-EGRET can provide interpretable insights from the learned cross-attention matrix. AVAILABILITY AND IMPLEMENTATION: Pair-EGRET is freely available in open source form at the GitHub Repository https://github.com/1705004/Pair-EGRET.

MOTIVATION: With the recent breakthroughs in sequencing technology, phylogeny estimation at a larger scale has become a huge opportunity. For accurate estimation of large-scale phylogeny, substantial endeavor is being devoted in introducing new algorithms or upgrading current approaches. In this work, we endeavor to improve the Quartet Fiduccia and Mattheyses (QFM) algorithm to resolve phylogenetic trees of better quality with better running time. QFM was already being appreciated by researchers for its good tree quality, but fell short in larger phylogenomic studies due to its excessively slow running time. RESULTS: We have re-designed QFM so that it can amalgamate millions of quartets over thousands of taxa into a species tree with a great level of accuracy within a short amount of time. Named "QFM Fast and Improved (QFM-FI)", our version is 20 000× faster than the previous version and 400× faster than the widely used variant of QFM implemented in PAUP* on larger datasets. We have also provided a theoretical analysis of the running time and memory requirements of QFM-FI. We have conducted a comparative study of QFM-FI with other state-of-the-art phylogeny reconstruction methods, such as QFM, QMC, wQMC, wQFM, and ASTRAL, on simulated as well as real biological datasets. Our results show that QFM-FI improves on the running time and tree quality of QFM and produces trees that are comparable with state-of-the-art methods. AVAILABILITY AND IMPLEMENTATION: QFM-FI is open source and available at https://github.com/sharmin-mim/qfm_java.

MOTIVATION: Analyzing large-scale single-cell transcriptomic datasets generated using different technologies is challenging due to the presence of batch-specific systematic variations known as batch effects. Since biological and technological differences are often interspersed, detecting and accounting for batch effects in RNA-seq datasets are critical for effective data integration and interpretation. Low-dimensional embeddings, such as principal component analysis (PCA) are widely used in visual inspection and estimation of batch effects. Linear dimensionality reduction methods like PCA are effective in assessing the presence of batch effects, especially when batch effects exhibit linear patterns. However, batch effects are inherently complex and existing linear dimensionality reduction methods could be inadequate and imprecise in the presence of sophisticated nonlinear batch effects. RESULTS: We present Batch Effect Estimation using Nonlinear Embedding (BEENE), a deep nonlinear auto-encoder network which is specially tailored to generate an alternative lower dimensional embedding suitable for both linear and nonlinear batch effects. BEENE simultaneously learns the batch and biological variables from RNA-seq data, resulting in an embedding that is more robust and sensitive than PCA embedding in terms of detecting and quantifying batch effects. BEENE was assessed on a collection of carefully controlled simulated datasets as well as biological datasets, including two technical replicates of mouse embryogenesis cells, peripheral blood mononuclear cells from three largely different experiments and five studies of pancreatic islet cells. AVAILABILITY AND IMPLEMENTATION: BEENE is freely available as an open source project at https://github.com/ashiq24/BEENE.

Multiple sequence alignment has been the traditional and well established approach of sequence analysis and comparison, though it is time and memory consuming. As the scale of sequencing data is increasing day by day, the importance of faster yet accurate alignment-free methods is on the rise. Several alignment-free sequence analysis methods have been established in the literature in recent years, which extract numerical features from genomic data to analyze sequences and also to estimate phylogenetic relationship among genes and species. Minimal Absent Word (MAW) is an effective concept for representing characteristics of a sequence in an alignment-free manner. In this study, we present CD-MAWS, a distance measure based on cosine of the angle between composition vectors constructed using minimal absent words, for sequence analysis in a computationally inexpensive manner. We have benchmarked CD-MAWS using several AFProject datasets, such as Fish mtDNA, E.coli, Plants, Shigella and Yersinia datasets, and found it to perform quite well. Applied on several other biological datasets such as mammal mtDNA, bacterial genomes and viral genomes, CD-MAWS resolved phylogenetic relationships similar to or better than state-of-the-art alignment-free methods such as Mash, Skmer, Co-phylog and kSNP3.

MOTIVATION: Protein-protein interactions (PPIs) are central to most biological processes. However, reliable identification of PPI sites using conventional experimental methods is slow and expensive. Therefore, great efforts are being put into computational methods to identify PPI sites. RESULTS: We present Edge Aggregated GRaph Attention NETwork (EGRET), a highly accurate deep learning-based method for PPI site prediction, where we have used an edge aggregated graph attention network to effectively leverage the structural information. We, for the first time, have used transfer learning in PPI site prediction. Our proposed edge aggregated network, together with transfer learning, has achieved notable improvement over the best alternate methods. Furthermore, we systematically investigated EGRET's network behavior to provide insights about the causes of its decisions. AVAILABILITY: EGRET is freely available as an open source project at https://github.com/Sazan-Mahbub/EGRET. CONTACT: [email protected].

Multiple sequence alignment (MSA) is a preliminary task for estimating phylogenies. It is used for homology inference among the sequences of a set of species. Generally, the MSA task is handled as a single-objective optimization process. The alignments computed under one criterion may be different from the alignments generated by other criteria, inferring discordant homologies and thus leading to different hypothesized evolutionary histories relating the sequences. The multiobjective (MO) formulation of MSA has recently been advocated by several researchers, to address this issue. An MO approach independently optimizes multiple (often conflicting) objective functions at the same time and outputs a set of competitive alignments. However, no conceptual or experimental rational from a real-world application perspective has been reported so far for any MO formulation of MSA. This article work investigates the impact of MO formulation in the context of an important scientific problem, namely, phylogeny estimation. Employing popular evolutionary MO algorithms, we show that: 1) trees inferred based on alignments produced by the existing MSA methods used in practice are substantially worse in quality than the trees inferred based on the alignment's output by an MO algorithm and 2) even high-quality alignments (according to popular measures available in the literature) may fail to achieve acceptable accuracy in generating phylogenetic trees. Thus, we essentially ask the following natural question: "can a phylogeny-aware (i.e., application-aware) metric guide in selecting appropriate MO formulations to ensure better phylogeny estimation?" Here, we report a carefully designed extensive experimental study that positively answers this question.

In this work we propose 3D-FFS, a novel approach to make sensor fusion based 3D object detection networks significantly faster using a class of computationally inexpensive heuristics. Existing sensor fusion based networks generate 3D region proposals by leveraging inferences from 2D object detectors. However, as images have no depth information, these networks rely on extracting semantic features of points from the entire scene to locate the object. By leveraging aggregated intrinsic properties (e.g. point density) of point cloud data, 3D-FFS can substantially constrain the 3D search space and thereby significantly reduce training time, inference time and memory consumption without sacrificing accuracy. To demonstrate the efficacy of 3D-FFS, we have integrated it with Frustum ConvNet (F-ConvNet), a prominent sensor fusion based 3D object detection model. We assess the performance of 3D-FFS on the KITTI dataset. Compared to F-ConvNet, we achieve improvements in training and inference times by up to 62.80% and 58.96%, respectively, while reducing the memory usage by up to 58.53%. Additionally, we achieve 0.36%, 0.59% and 2.19% improvements in accuracy for the Car, Pedestrian and Cyclist classes, respectively. 3D-FFS shows a lot of promise in domains with limited computing power, such as autonomous vehicles, drones and robotics where LiDAR-Camera based sensor fusion perception systems are widely used.

BACKGROUND: Genomic Islands (GIs) are clusters of genes that are mobilized through horizontal gene transfer. GIs play a pivotal role in bacterial evolution as a mechanism of diversification and adaptation to different niches. Therefore, identification and characterization of GIs in bacterial genomes is important for understanding bacterial evolution. However, quantifying GIs is inherently difficult, and the existing methods suffer from low prediction accuracy and precision-recall trade-off. Moreover, several of them are supervised in nature, and thus, their applications to newly sequenced genomes are riddled with their dependency on the functional annotation of existing genomes. RESULTS: We present SSG-LUGIA, a completely automated and unsupervised approach for identifying GIs and horizontally transferred genes. SSG-LUGIA is a novel method based on unsupervised anomaly detection technique, accompanied by further refinement using cues from signal processing literature. SSG-LUGIA leverages the atypical compositional biases of the alien genes to localize GIs in prokaryotic genomes. SSG-LUGIA was assessed on a large benchmark dataset `IslandPick' and on a set of 15 well-studied genomes in the literature and followed by a thorough analysis on the well-understood Salmonella typhi CT18 genome. Furthermore, the efficacy of SSG-LUGIA in identifying horizontally transferred genes was evaluated on two additional bacterial genomes, namely, those of Corynebacterium diphtheria NCTC13129 and Pseudomonas aeruginosa LESB58. SSG-LUGIA was examined on draft genomes and was demonstrated to be efficient as an ensemble method. CONCLUSIONS: Our results indicate that SSG-LUGIA achieved superior performance in comparison to frequently used existing methods. Importantly, it yielded a better trade-off between precision and recall than the existing methods. Its nondependency on the functional annotation of genomes makes it suitable for analyzing newly sequenced, yet uncharacterized genomes. Thus, our study is a significant advance in identification of GIs and horizontally transferred genes. SSG-LUGIA is available as an open source software at https://nibtehaz.github.io/SSG-LUGIA/.

MOTIVATION: Species tree estimation from genes sampled from throughout the whole genome is complicated due to the gene tree-species tree discordance. Incomplete lineage sorting (ILS) is one of the most frequent causes for this discordance, where alleles can coexist in populations for periods that may span several speciation events. Quartet-based summary methods for estimating species trees from a collection of gene trees are becoming popular due to their high accuracy and statistical guarantee under ILS. Generating quartets with appropriate weights, where weights correspond to the relative importance of quartets, and subsequently amalgamating the weighted quartets to infer a single coherent species tree can allow for a statistically consistent way of estimating species trees. However, handling weighted quartets is challenging. RESULTS: We propose wQFM, a highly accurate method for species tree estimation from multi-locus data, by extending the quartet FM (QFM) algorithm to a weighted setting. wQFM was assessed on a collection of simulated and real biological datasets, including the avian phylogenomic dataset, which is one of the largest phylogenomic datasets to date. We compared wQFM with wQMC, which is the best alternate method for weighted quartet amalgamation, and with ASTRAL, which is one of the most accurate and widely used coalescent-based species tree estimation methods. Our results suggest that wQFM matches or improves upon the accuracy of wQMC and ASTRAL. AVAILABILITY AND IMPLEMENTATION: Datasets studied in this article and wQFM (in open-source form) are available at https://github.com/Mahim1997/wQFM-2020. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Species tree estimation from multi-locus data is complicated as biological processes can result in different loci having different evolutionary histories. Incomplete lineage sorting (ILS), modeled by the multi-species coalescent (MSC), is considered to be a dominant cause for gene tree incongruence. Various optimization criteria (e.g., quartet score, pseudo-likelihood, etc.) are statistically consistent under the MSC model, meaning that they return the true species tree with high probability given sufficiently large numbers of accurate gene trees. However, the number of genes is limited and estimating highly accurate gene trees is difficult. Therefore, even popular methods, optimizing a particular criterion, may fail to reconstruct highly accurate trees under practical model conditions with limited numbers of genes and in the presence of gene tree estimation error. In this study, we advocate multi-objective optimization to tackle this challenge. Particularly, we present a multi-objective metaheuristic (i.e., SNOGA), a modified version of the popular NSGAII, which combines various optimization criteria to find a suitable search space containing highly accurate species trees.

MOTIVATION: Protein structures provide basic insight into how they can interact with other proteins, their functions and biological roles in an organism. Experimental methods (e.g. X-ray crystallography and nuclear magnetic resonance spectroscopy) for predicting the secondary structure (SS) of proteins are very expensive and time consuming. Therefore, developing efficient computational approaches for predicting the SS of protein is of utmost importance. Advances in developing highly accurate SS prediction methods have mostly been focused on 3-class (Q3) structure prediction. However, 8-class (Q8) resolution of SS contains more useful information and is much more challenging than the Q3 prediction. RESULTS: We present SAINT, a highly accurate method for Q8 structure prediction, which incorporates self-attention mechanism (a concept from natural language processing) with the Deep Inception-Inside-Inception network in order to effectively capture both the short- and long-range interactions among the amino acid residues. SAINT offers a more interpretable framework than the typical black-box deep neural network methods. Through an extensive evaluation study, we report the performance of SAINT in comparison with the existing best methods on a collection of benchmark datasets, namely, TEST2016, TEST2018, CASP12 and CASP13. Our results suggest that self-attention mechanism improves the prediction accuracy and outperforms the existing best alternate methods. SAINT is the first of its kind and offers the best known Q8 accuracy. Thus, we believe SAINT represents a major step toward the accurate and reliable prediction of SSs of proteins. AVAILABILITY AND IMPLEMENTATION: SAINT is freely available as an open-source project at https://github.com/SAINTProtein/SAINT.

Multiple sequence alignment (MSA) is a basic step in many analyses in bioinformatics, including predicting the structure and function of proteins, orthology prediction and estimating phylogenies. The objective of MSA is to infer the homology among the sequences of chosen species. Commonly, the MSAs are inferred by optimizing a single objective function. The alignments estimated under one criterion may be different to the alignments generated by other criteria, inferring discordant homologies and thus leading to different evolutionary histories relating the sequences. In the recent past, researchers have advocated for the multi-objective formulation of MSA, to address this issue, where multiple conflicting objective functions are being optimized simultaneously to generate a set of alignments. However, no theoretical or empirical justification with respect to a real-life application has been shown for a particular multi-objective formulation. In this study, we investigate the impact of multi-objective formulation in the context of phylogenetic tree estimation. In essence, we ask the question whether a phylogeny-aware metric can guide us in choosing appropriate multi-objective formulations. Employing evolutionary optimization, we demonstrate that trees estimated on the alignments generated by multi-objective formulation are substantially better than the trees estimated by the state-of-the-art MSA tools, including PASTA, T-Coffee, MAFFT etc.

Species tree estimation from gene trees can be complicated by gene duplication and loss, and "gene tree parsimony" (GTP) is one approach for estimating species trees from multiple gene trees. In its standard formulation, the objective is to find a species tree that minimizes the total number of gene duplications and losses with respect to the input set of gene trees. Although much is known about GTP, little is known about how to treat inputs containing some incomplete gene trees (i.e., gene trees lacking one or more of the species). We present new theory for GTP considering whether the incompleteness is due to gene birth and death (i.e., true biological loss) or taxon sampling, and present dynamic programming algorithms that can be used for an exact but exponential time solution for small numbers of taxa, or as a heuristic for larger numbers of taxa. We also prove that the "standard" calculations for duplications and losses exactly solve GTP when incompleteness results from taxon sampling, although they can be incorrect when incompleteness results from true biological loss. The software for the DP algorithm is freely available as open source code at https://github.com/shamsbayzid/DynaDup.

MOTIVATION: Species trees provide insight into basic biology, including the mechanisms of evolution and how it modifies biomolecular function and structure, biodiversity and co-evolution between genes and species. Yet, gene trees often differ from species trees, creating challenges to species tree estimation. One of the most frequent causes for conflicting topologies between gene trees and species trees is incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent. While many methods have been developed to estimate species trees from multiple genes, some which have statistical guarantees under the multi-species coalescent model, existing methods are too computationally intensive for use with genome-scale analyses or have been shown to have poor accuracy under some realistic conditions. RESULTS: We present ASTRAL, a fast method for estimating species trees from multiple genes. ASTRAL is statistically consistent, can run on datasets with thousands of genes and has outstanding accuracy-improving on MP-EST and the population tree from BUCKy, two statistically consistent leading coalescent-based methods. ASTRAL is often more accurate than concatenation using maximum likelihood, except when ILS levels are low or there are too few gene trees. AVAILABILITY AND IMPLEMENTATION: ASTRAL is available in open source form at https://github.com/smirarab/ASTRAL/. Datasets studied in this article are available at http://www.cs.utexas.edu/users/phylo/datasets/astral. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: Species tree estimation in the presence of incomplete lineage sorting (ILS) is a major challenge for phylogenomic analysis. Although many methods have been developed for this problem, little is understood about the relative performance of these methods when estimated gene trees are poorly estimated, owing to inadequate phylogenetic signal. RESULTS: We explored the performance of some methods for estimating species trees from multiple markers on simulated datasets in which gene trees differed from the species tree owing to ILS. We included *BEAST, concatenated analysis and several 'summary methods': BUCKy, MP-EST, minimize deep coalescence, matrix representation with parsimony and the greedy consensus. We found that *BEAST and concatenation gave excellent results, often with substantially improved accuracy over the other methods. We observed that *BEAST's accuracy is largely due to its ability to co-estimate the gene trees and species tree. However, *BEAST is computationally intensive, making it challenging to run on datasets with 100 or more genes or with more than 20 taxa. We propose a new approach to species tree estimation in which the genes are partitioned into sets, and the species tree is estimated from the resultant 'supergenes'. We show that this technique improves the scalability of *BEAST without affecting its accuracy and improves the accuracy of the summary methods. Thus, naive binning can improve phylogenomic analysis in the presence of ILS. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.