Remigiusz Kinas

Krzysztof Ociepa, Łukasz Flis, Remigiusz Kinas et al.

The development of the Bielik v3 PL series, encompassing both the 7B and 11B parameter variants, represents a significant milestone in the field of language-specific large language model (LLM) optimization. While general-purpose models often demonstrate impressive multilingual capabilities, they frequently suffer from a fundamental architectural inefficiency: the use of universal tokenizers. These tokenizers, typically designed to cover a broad spectrum of languages, often fail to capture the morphological nuances of specific languages like Polish, leading to higher fertility ratios, increased inference costs, and restricted effective context windows. This report details the transition from the universal Mistral-based tokenization to a dedicated Polish-optimized vocabulary for the Bielik v3 models, exploring the FOCUS-based embedding initialization, the multi-stage pretraining curriculum, and the subsequent post-training alignment involving Supervised Fine-Tuning, Direct Preference Optimization, and Reinforcement Learning through Group Relative Policy Optimization with verifiable rewards.

Maciej Sypetkowski, Joanna Krawczyk, Łukasz Smoliński et al.

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.

Remigiusz Kinas, Joanna Krawczyk, Rafał Powalski et al.

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.

Adam Trybus, Bartosz Bartnicki, Remigiusz Kinas

This paper presents a research program dedicated to evaluating and advancing the reasoning capabilities of Bielik, a Polish large language model. The study describes a number of stages of work: initial benchmarking and creation of evaluation methodology, analyzing of comparative results with other LLMs and outlining of future prospects that take into account the limitations of the analyses conducted so far and aims to keep Bielik in the race give the ever-changing -- and competitive -- AI landscape.

Remigiusz Kinas, Paweł Kiszczak, Sergio P. Perez et al.

This report details the creation of Bielik-Minitron-7B, a compressed 7.35B parameter version of the Bielik-11B-v3.0 model, specifically optimized for European languages. By leveraging a two-stage compression methodology inspired by the NVIDIA Minitron approach, we combined structured hybrid pruning and knowledge distillation to reduce the model's parameter count by 33.4%, from 11.04B to 7.35B. We utilized the NVIDIA Model Optimizer for structural pruning and the NVIDIA NeMo Framework for logit-based distillation for quality recovery. Following distillation, the model underwent a rigorous alignment pipeline consisting of Supervised Fine-Tuning (SFT), Direct Preference Optimization (DPO-P), and Reinforcement Learning (GRPO). Our final model successfully recovered approximately 90% of the baseline model's performance while providing up to 50% inference speedup. This approach demonstrates an efficient pathway to create language models for less-represented languages, preserving the original model quality while reducing inference deployment costs.

Krzysztof Ociepa, Łukasz Flis, Remigiusz Kinas et al.

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.

Krzysztof Ociepa, Łukasz Flis, Krzysztof Wróbel et al.

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.

Krzysztof Ociepa, Łukasz Flis, Remigiusz Kinas et al.

We introduce Bielik v3, a series of parameter-efficient generative text models (1.5B and 4.5B) optimized for Polish language processing. These models demonstrate that smaller, well-optimized architectures can achieve performance comparable to much larger counterparts while requiring substantially fewer computational resources. Our approach incorporates several key innovations: a custom Polish tokenizer (APT4) that significantly improves token efficiency, Weighted Instruction Cross-Entropy Loss to balance learning across instruction types, and Adaptive Learning Rate that dynamically adjusts based on training progress. Trained on a meticulously curated corpus of 292 billion tokens spanning 303 million documents, these models excel across multiple benchmarks, including the Open PL LLM Leaderboard, Complex Polish Text Understanding Benchmark, Polish EQ-Bench, and Polish Medical Leaderboard. The 4.5B parameter model achieves results competitive with models 2-3 times its size, while the 1.5B model delivers strong performance despite its extremely compact profile. These advances establish new benchmarks for parameter-efficient language modeling in less-represented languages, making high-quality Polish language AI more accessible for resource-constrained applications.

Krzysztof Ociepa, Łukasz Flis, Krzysztof Wróbel et al.

We present Bielik 11B v2, a state-of-the-art language model optimized for Polish text processing. Built on the Mistral 7B v0.2 architecture and scaled to 11B parameters using depth up-scaling, this model demonstrates exceptional performance across Polish language benchmarks while maintaining strong cross-lingual capabilities. We introduce two key technical innovations: Weighted Instruction Cross-Entropy Loss, which optimizes learning across diverse instruction types by assigning quality-based weights to training examples, and Adaptive Learning Rate, which dynamically adjusts based on context length. Comprehensive evaluation across multiple benchmarks demonstrates that Bielik 11B v2 outperforms many larger models, including those with 2-6 times more parameters, and significantly surpasses other specialized Polish language models on tasks ranging from linguistic understanding to complex reasoning. The model's parameter efficiency and extensive quantization options enable deployment across various hardware configurations, advancing Polish language AI capabilities and establishing new benchmarks for resource-efficient language modeling in less-represented languages.