Bioinformatics

The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by fragmented distribution, inconsistent documentation, complex dependencies, and difficult-to-reproduce execution environments. As a result, reusing published tools and workflow adaptation to own date remains technically demanding and time-intensive, even for experienced users. Here, we present PoSyMed, an open and modular platform for the controlled integration, composition, and execution of bioinformatics tools and workflows. PoSyMed combines a backend-centered platform architecture with formal tool descriptions, controlled container-based build and execution processes, persistent workflow state, and a dialogue-based user interface. Large language models (LLM) are integrated not as autonomous decision-makers, but as human-computer interface with bounded semantic assistants that help identify tools, propose workflow steps, and support parameterization within a typed, validated, and human-supervised execution environment. PoSyMed is designed to improve reproducibility, traceability, and transparency in practical biomedical analysis within one platform. We describe the system architecture and evaluate its behavior across representative biological software scenarios with respect to workflow support, interaction design, and platform extensibility. PoSyMed is publicly available at https://apps.cosy.bio/posymed.

Large Language Models (LLMs) are increasingly adopted as conversational assistants in genomics, where they are mainly used to reason over biological knowledge, annotations, and analysis outputs through natural language interfaces. However, existing benchmarks either focus on specialized DNA models trained for sequence prediction or evaluate biological knowledge using text-only questions, leaving the behavior of general-purpose LLMs when directly exposed to raw genome sequences underexplored. We introduce GenomeQA, a benchmark designed to provide a controlled evaluation setting for general-purpose LLMs on sequence-based genome inference tasks. GenomeQA comprises 5,200 samples drawn from multiple biological databases, with sequence lengths ranging from 6 to 1,000 base pairs (bp), spanning six task families: Enhancer and Promoter Identification, Splice Site Identification, Taxonomic Classification, Histone Mark Prediction, Transcription Factor Binding Site Prediction, and TF Motif Prediction. Across six frontier LLMs, we find that models consistently outperform random baselines and can exploit local sequence signals such as GC content and short motifs, while performance degrades on tasks that require more indirect or multi-step inference over sequence patterns. GenomeQA establishes a diagnostic benchmark for studying and improving the use of general-purpose LLMs on raw genomic sequences.

The scale of biological datasets now routinely exceeds system memory, making data access rather than model computation the primary bottleneck in training machine-learning models. This bottleneck is particularly acute in biology, where widely used community data formats must support heterogeneous metadata, sparse and dense assays, and downstream analysis within established computational ecosystems. Here we present annbatch, a mini-batch loader native to anndata that enables out-of-core training directly on disk-backed datasets. Across single-cell transcriptomics, microscopy and whole-genome sequencing benchmarks, annbatch increases loading throughput by up to an order of magnitude and shortens training from days to hours, while remaining fully compatible with the scverse ecosystem. Annbatch establishes a practical data-loading infrastructure for scalable biological AI, allowing increasingly large and diverse datasets to be used without abandoning standard biological data formats. Github: https://github.com/scverse/annbatch

This paper proposes a new univariate filter feature selection (FFS) algorithm called KGroups. The majority of work in the literature focuses on investigating the relevance or redundancy estimations of feature selection (FS) methods. This has shown promising results and a real improvement of FFS methods' predictive performance. However, limited efforts have been made to investigate alternative FFS algorithms. This raises the following question: how much of the FFS methods' predictive performance depends on the selection algorithm rather than the relevance or the redundancy estimations? The majority of FFS methods fall into two categories: relevance maximisation (Max-Rel, also known as KBest) or simultaneous relevance maximisation and redundancy minimisation (mRMR). KBest is a univariate FFS algorithm that employs sorting (descending) for selection. mRMR is a multivariate FFS algorithm that employs an incremental search algorithm for selection. In this paper, we propose a new univariate mRMR called KGroups that employs clustering for selection. Extensive experiments on 14 high-dimensional biological benchmark datasets showed that KGroups achieves similar predictive performance compared to multivariate mRMR while being up to 821 times faster. KGroups is parameterisable, which leaves room for further predictive performance improvement through hyperparameter finetuning, unlike mRMR and KBest. KGroups outperforms KBest.

Biological AI models increasingly predict complex cellular responses, yet their learned representations remain disconnected from the molecular processes they aim to capture. We present CDT-III, which extends mechanism-oriented AI across the full central dogma: DNA, RNA, and protein. Its two-stage Virtual Cell Embedder architecture mirrors the spatial compartmentalization of the cell: VCE-N models transcription in the nucleus and VCE-C models translation in the cytosol. On five held-out genes, CDT-III achieves per-gene RNA r=0.843 and protein r=0.969. Adding protein prediction improves RNA performance (r=0.804 to 0.843), demonstrating that downstream tasks regularize upstream representations. Protein supervision sharpens DNA-level interpretability, increasing CTCF enrichment by 30%. Analysis of experimentally measured mRNA and protein responses reveals that the majority of genes with observable mRNA changes show opposite protein-level changes (66.7% at |log2FC|>0.01, rising to 87.5% at |log2FC|>0.02), exposing a fundamental limitation of RNA-only perturbation models. Despite this pervasive direction discordance, CDT-III correctly predicts both mRNA and protein responses. Applied to in silico CD52 knockdown approximating Alemtuzumab, the model predicts 29/29 protein changes correctly and rediscovers 5 of 7 known clinical side effects without clinical data. Gradient-based side effect profiling requires only unperturbed baseline data (r=0.939), enabling screening of all 2,361 genes without new experiments.

As bioinformatics software is increasingly applied across a broader range of scenarios and the rapid development of large language models (LLMs) further lowers the barriers to software use and development, the composition of the bioinformatics research community is undergoing substantial change. Consequently, a growing number of researchers require a deeper understanding of methodological details and software behavior. In this context, systematically analyzing the relationship between paper descriptions and code implementations is emerging as an important new challenge in the field. To address this challenge, we introduce paper-code consistency analysis as a new research perspective and construct BioCon, the first benchmark dataset for paper-code consistency analysis in bioinformatics. Furthermore, we develop a unified cross-modal analysis framework to systematically investigate this problem from three perspectives: sentence-level detection, cross-modal retrieval, and project-level assessment. Experimental results demonstrate that the proposed framework can effectively model the semantic relationships between scientific publications and software implementations. Further case studies reveal that paper-code inconsistency is not a single phenomenon but arises from multiple underlying causes, among which Author-Perceived Non-Essential Details represents the most prevalent category. These findings suggest that paper-code consistency analysis is not merely a technical problem but also raises broader discussions regarding knowledge dissemination, the boundaries of code disclosure, and community norms. We hope that this work will encourage the bioinformatics community to re-examine the relationship between scientific publications and software implementations while providing a foundation for future research in paper-code consistency analysis.

The Predictive Associative Memory (PAM) framework posits that useful relationships often connect items that co-occur in shared contexts rather than items that appear similar in embedding space. A contrastive MLP trained on co-occurrence annotations--Contrastive Association Learning (CAL)--has improved multi-hop passage retrieval and discovered narrative function at corpus scale in text. We test whether this principle transfers to molecular biology, where protein-protein interactions provide functional associations distinct from gene expression similarity. Four experiments across two biological domains map the operating envelope. On gene perturbation data (Replogle K562 CRISPRi, 2,285 genes), CAL trained on STRING protein interactions achieves cross-boundary AUC of 0.908 where expression similarity scores 0.518. A second gene dataset (DepMap, 17,725 genes) confirms the result after negative sampling correction, reaching cross-boundary AUC of 0.947. Two drug sensitivity experiments produce informative negatives that sharpen boundary conditions. Three cross-domain findings emerge: (1) inductive transfer succeeds in biology--a node-disjoint split with unseen genes yields AUC 0.826 (Delta +0.127)--where it fails in text (+/-0.10), suggesting physically grounded associations are more transferable than contingent co-occurrences; (2) CAL scores anti-correlate with interaction degree (Spearman r = -0.590), with gains concentrating on understudied genes with focused interaction profiles; (3) tighter association quality outperforms larger but noisier training sets, reversing the text pattern. Results are stable across training seeds (SD < 0.001) and cross-boundary threshold choices.

Unlike the predictable scaling laws in natural language processing and computer vision, protein language models (PLMs) scale poorly: for many tasks, models within the same family plateau or even decrease in performance, with mid-sized models often outperforming the largest in the family. We introduce Reverse Distillation, a principled framework that decomposes large PLM representations into orthogonal subspaces guided by smaller models of the same family. The resulting embeddings have a nested, Matryoshka-style structure: the first k dimensions of a larger model's embedding are exactly the representation from the smaller model. This ensures that larger reverse-distilled models consistently outperform smaller ones. A motivating intuition is that smaller models, constrained by capacity, preferentially encode broadly-shared protein features. Reverse distillation isolates these shared features and orthogonally extracts additional contributions from larger models, preventing interference between the two. On ProteinGym benchmarks, reverse-distilled ESM-2 variants outperform their respective baselines at the same embedding dimensionality, with the reverse-distilled 15 billion parameter model achieving the strongest performance. Our framework is generalizable to any model family where scaling challenges persist. Code and trained models are available at https://github.com/rohitsinghlab/plm_reverse_distillation.

Modern Protein Language Models (PLMs) apply transformer-based model architectures from natural language processing to biological sequences, predicting a variety of protein functions and properties. However, protein language has key differences from natural language, such as a rich functional space despite a vocabulary of only 20 amino acids. These differences motivate research into how transformer-based architectures operate differently in the protein domain and how we can better leverage PLMs to solve protein-related tasks. In this work, we begin by directly comparing how the distribution of information stored across layers of attention heads differs between the protein and natural language domain. Furthermore, we adapt a simple early-exit technique-originally used in the natural language domain to improve efficiency at the cost of performance-to achieve both increased accuracy and substantial efficiency gains in protein non-structural property prediction by allowing the model to automatically select protein representations from the intermediate layers of the PLMs for the specific task and protein at hand. We achieve performance gains ranging from 0.4 to 7.01 percentage points while simultaneously improving efficiency by over 10 percent across models and non-structural prediction tasks. Our work opens up an area of research directly comparing how language models change behavior when moved into the protein domain and advances language modeling in biological domains.

Motivation: Pre-trained protein language models (PLMs) such as ESM-2 have become the default representation for biological sequence tasks, but they are computationally heavy and require GPUs both for embedding and for fine-tuning. Whether they are actually necessary for sequence classification, as opposed to structure prediction, is rarely tested against strong, principled, lightweight alternatives. This question has direct practical stakes for large-scale genomic surveillance, where embedding millions of sequences on commodity hardware is a recurring bottleneck.\ Results: We introduce Murmur2Vec, an alignment-free, training-free embedding that aggregates $k$-mer counts into a small hash table via the deterministic MurmurHash function, and we cast it as a randomized sketch of the classical $k$-mer spectrum kernel. We provide a complete theoretical treatment: closed-form bias/variance of the inner product, an unbiased signed variant with a Johnson--Lindenstrauss-type concentration bound, an excess-risk bound for downstream linear classifiers that makes the bias--variance trade-off in the hash-table size explicit, and an implicit-regularization mechanism by which collisions damage frequent non-discriminative $k$-mers more than rare lineage-defining ones. Across four classification tasks, SARS-CoV-2 spike lineage (22 classes), HIV-1 Env subtype (8 classes), and two protein-family benchmarks (8 and 6 classes), Murmur2Vec matches a LoRA-fine-tuned 650M-parameter ESM-2 model on the two tasks for which LoRA fine-tuning was run to convergence (SARS-CoV-2 and HIV-1) and ties frozen ESM-2 on the two protein-family tasks, and it outperforms the fine-tuned model on the hardest task (SARS-CoV-2 lineage: $0.854$ vs.\ $0.807$ accuracy; macro-F1 $0.684$ vs.\ $0.401$).

Modeling protein sequences as a language has made language models a powerful tool in computational biology, yet the language itself remains poorly understood. A key step toward understanding it is identifying its constituent units. In natural languages, morphemes can occur in multiple forms; similarly, in proteins, mutations can give rise to variations of a unit that persist through evolution, forming families of related units. We introduce PUMA (Protein Units via Mutation-Aware Merging), an algorithm that learns protein units from sequence and explores their mutational variants using substitution matrices, forming a genealogy of unit families. Our results show that mutations remaining within a PUMA family are more often benign than the substitution matrix alone predicts, and that PUMA genealogy improves molecular function representations compared to treating units independently. A case study of a unit family demonstrates relatedness beyond homology. PUMA achieves competitive performance on downstream tasks when used as a protein language model tokenizer. Moreover, collapsing units into families results in a smaller embedding table and faster training. Together, these results support PUMA as a biologically grounded protein vocabulary that organizes protein units into plausible families of mutational variants. The source code is available at https://github.com/boun-tabi-lifelu/PUMA.