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Remigiusz Kinas

Remigiusz Kinas contributes to research discovery and scholarly infrastructure.

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Artificial Intelligence Computation and Language Cell Behavior Genomics Multiagent Systems Quantitative Methods

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preprint2026arXiv

BioResearcher: Scenario-Guided Multi-Agent for Translational Medicine

Translational medicine turns underspecified development goals into evidence synthesis that must combine literature, trials, patents, and quantitative multi-omics analysis while preserving identifiers, uncertainty, and retrievable provenance. General-purpose foundation models and off-the-shelf tool-augmented or multi-agent systems are not built for this: they tend to produce single-shot answers or run open-endedly, and fall short on the auditable, scenario-specific workflows that heterogeneous biomedical sources demand. This paper introduces Ingenix BioResearcher, a scenario-guided multi-agent system that maps queries to versioned research playbooks, delegates to specialized subagents over 30+ tools and machine-learning endpoints, mixes structured database access with sandboxed code for genome-scale analyses, and applies claim-level multi-model reconciliation before editorial assembly. We evaluate BioResearcher across unit-level capabilities, open-ended biomedical reasoning, and end-to-end clinical discovery. It leads evaluated baselines on 109 single-step tests (83.49% pass rate; 0.892 average score), achieves strong biomedical benchmark performance (89.33% on BixBench-Verified-50 and the top 0.758 mean score on BaisBench Scientific Discovery), and leads on a 30-query clinical end-to-end benchmark with the highest positive hit rate (74.7% $\pm$ 3.3%) and negative clear rate (96.8% $\pm$ 0.2%). These results show broad, competitive performance across unit-level, open-ended, and end-to-end clinical evaluations.

preprint2026arXiv

OmicsLM: A Multimodal Large Language Model for Multi-Sample Omics Reasoning

Interpreting transcriptomic data is one of the most common analytical tasks in modern biology. Yet most current models either consume expression profiles without producing natural-language biological explanations, or reason in language without direct access to quantitative omics measurements. We introduce OmicsLM, a multimodal LLM that connects quantitative omics profiles with natural-language biological tasks. OmicsLM represents each transcriptomic profile as a compact continuous representation within the LLM context. This interface preserves quantitative expression signal while allowing natural-language instructions, explicit gene mentions, and multiple interleaved biological samples to be processed together in one model context. We train OmicsLM on more than 5.5 million instruction-following examples spanning over 70 task types, combining continuous transcriptomic inputs, experimental data rendered through diverse language templates, and free-text biological knowledge and question-answering data. This mixture covers cell type annotation, perturbation prediction, clinical prediction, pathway reasoning, and open-ended biological question answering. Existing benchmarks evaluate either profile-level prediction or text-only biological QA, leaving language-guided, multi-sample reasoning over real expression profiles unmeasured. To close this gap, we introduce GEO-OmicsQA, a benchmark for multi-sample biological question answering built from real Gene Expression Omnibus (GEO) studies. We demonstrate that OmicsLM can use expression profiles directly and perform comparably to specialized omics models on profile-level tasks, while outperforming both omics-specialized models and general LLMs on language-guided biological reasoning over expression data.

preprint2025arXiv

Bielik 11B v3: Multilingual Large Language Model for European Languages

We present Bielik 11B v3, a state-of-the-art language model highly optimized for the Polish language, while also maintaining strong capabilities in other European languages. This model extends the Mistral 7B v0.2 architecture, scaled to 11B parameters via depth up-scaling. Its development involved a comprehensive four-stage training pipeline: continuous pre-training, supervised fine-tuning (SFT), Direct Preference Optimization (DPO), and reinforcement learning. Comprehensive evaluations demonstrate that Bielik 11B v3 achieves exceptional performance. It significantly surpasses other specialized Polish language models and outperforms many larger models (with 2-6 times more parameters) on a wide range of tasks, from basic linguistic understanding to complex reasoning. The model's parameter efficiency, combined with extensive quantization options, allows for effective deployment across diverse hardware configurations. Bielik 11B v3 not only advances AI capabilities for the Polish language but also establishes a new benchmark for developing resource-efficient, high-performance models for less-represented languages.

preprint2025arXiv

Bielik 7B v0.1: A Polish Language Model -- Development, Insights, and Evaluation

We introduce Bielik 7B v0.1, a 7-billion-parameter generative text model for Polish language processing. Trained on curated Polish corpora, this model addresses key challenges in language model development through innovative techniques. These include Weighted Instruction Cross-Entropy Loss, which balances the learning of different instruction types, and Adaptive Learning Rate, which dynamically adjusts the learning rate based on training progress. To evaluate performance, we created the Open PL LLM Leaderboard and Polish MT-Bench, novel frameworks assessing various NLP tasks and conversational abilities. Bielik 7B v0.1 demonstrates significant improvements, achieving a 9 percentage point increase in average score compared to Mistral-7B-v0.1 on the RAG Reader task. It also excels in the Polish MT-Bench, particularly in Reasoning (6.15/10) and Role-playing (7.83/10) categories. This model represents a substantial advancement in Polish language AI, offering a powerful tool for diverse linguistic applications and setting new benchmarks in the field.

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