Nikola Milosevic

Daniel Steinigen, Roman Teucher, Timm Heine Ruland et al.

Recent advancements in Large Language Models (LLMs) have showcased their proficiency in answering natural language queries. However, their effectiveness is hindered by limited domain-specific knowledge, raising concerns about the reliability of their responses. We introduce a hybrid system that augments LLMs with domain-specific knowledge graphs (KGs), thereby aiming to enhance factual correctness using a KG-based retrieval approach. We focus on a medical KG to demonstrate our methodology, which includes (1) pre-processing, (2) Cypher query generation, (3) Cypher query processing, (4) KG retrieval, and (5) LLM-enhanced response generation. We evaluate our system on a curated dataset of 69 samples, achieving a precision of 78\% in retrieving correct KG nodes. Our findings indicate that the hybrid system surpasses a standalone LLM in accuracy and completeness, as verified by an LLM-as-a-Judge evaluation method. This positions the system as a promising tool for applications that demand factual correctness and completeness, such as target identification -- a critical process in pinpointing biological entities for disease treatment or crop enhancement. Moreover, its intuitive search interface and ability to provide accurate responses within seconds make it well-suited for time-sensitive, precision-focused research contexts. We publish the source code together with the dataset and the prompt templates used.

Nikola Milosevic

As Large Language Models (LLMs) evolve into persistent scientific collaborators, context window saturation has emerged as a critical bottleneck. Scientific workflows involving iterative data analysis and hypothesis refinement rapidly saturate even extended contexts with dense technical content, while monolithic approaches suffer from quadratic cost scaling and cognitive degradation. We evaluate a Dual Process Memory Architecture that decouples immediate episodic needs (constant 10-message window) from long-term consolidated knowledge (growing at approximately 3 tokens/message). Unlike prior social agent memory systems, our domain-specific consolidation addresses contradictory parameter evolution, multi-hop reasoning across experimental phases, and precise technical fact retention. Through large-scale evaluation spanning 15,000 messages with cross-model validation across six LLMs from three families (OpenAI, Anthropic, Google), totaling 1,440 queries, we establish three key findings. First, while full-context models fail at 10,000 messages due to context overflow, our system maintains 70-85% accuracy with 1-2 second latency using 62% fewer tokens (45,434 vs 120,000+ limit). Second, cross-model validation reveals architecture-level trade-offs independent of specific LLMs: Dual Process excels at numeric/temporal queries (65-90% accuracy) while RAG excels at historical retrieval (60-85%), suggesting complementary deployment strategies. Third, we identify a "Sim-to-Real" gap where synthetic tests maintain constant memory but realistic workflows exhibit linear growth (about 3 tokens/message), with consolidation quality emerging as the primary scalability bottleneck. The architecture successfully manages profiles with 14,000+ scientific facts (125k tokens), demonstrating that domain-specific memory consolidation enables sustained operation beyond full-context limits.

Nikola Milosevic, Leonard Franz, Daniel Haeufle et al.

Constrained Markov decision processes (CMDPs) provide a principled model for handling constraints, such as safety and other auxiliary objectives, in reinforcement learning. The common approach of using additive-cost constraints and dual variables often hinders off-policy scalability. We propose a Control as Inference formulation based on stochastic decision horizons, where constraint violations attenuate reward contributions and shorten the effective planning horizon via state-action-dependent continuation. This yields survival-weighted objectives that remain replay-compatible for off-policy actor-critic learning. We propose two violation semantics, absorbing and virtual termination, that share the same survival-weighted return but result in distinct optimization structures that lead to SAC/MPO-style policy improvement. Experiments demonstrate improved sample efficiency and favorable return-violation trade-offs on standard benchmarks. Moreover, MPO with virtual termination (VT-MPO) scales effectively to our high-dimensional musculoskeletal Hyfydy setup.

Nikola Milosevic, Johannes Müller, Nico Scherf

Reinforcement Learning (RL) agents can solve diverse tasks but often exhibit unsafe behavior. Constrained Markov Decision Processes (CMDPs) address this by enforcing safety constraints, yet existing methods either sacrifice reward maximization or allow unsafe training. We introduce Constrained Trust Region Policy Optimization (C-TRPO), which reshapes the policy space geometry to ensure trust regions contain only safe policies, guaranteeing constraint satisfaction throughout training. We analyze its theoretical properties and connections to TRPO, Natural Policy Gradient (NPG), and Constrained Policy Optimization (CPO). Experiments show that C-TRPO reduces constraint violations while maintaining competitive returns.

Nikola Milosevic, Johannes Müller, Nico Scherf

In constrained Markov decision processes, enforcing constraints during training is often thought of as decreasing the final return. Recently, it was shown that constraints can be incorporated directly into the policy geometry, yielding an optimization trajectory close to the central path of a barrier method, which does not compromise final return. Building on this idea, we introduce Central Path Proximal Policy Optimization (C3PO), a simple modification of the PPO loss that produces policy iterates, that stay close to the central path of the constrained optimization problem. Compared to existing on-policy methods, C3PO delivers improved performance with tighter constraint enforcement, suggesting that central path-guided updates offer a promising direction for constrained policy optimization.

Nikola Milosevic, Nico Scherf

Reward maximization, safe exploration, and intrinsic motivation are often studied as separate objectives in reinforcement learning (RL). We present a unified geometric framework, that views these goals as instances of a single optimization problem on the space of achievable long-term behavior in an environment. Within this framework, classical methods such as policy mirror descent, natural policy gradient, and trust-region algorithms naturally generalize to nonlinear utilities and convex constraints. We illustrate how this perspective captures robustness, safety, exploration, and diversity objectives, and outline open challenges at the interface of geometry and deep RL.

Nikola Milosevic, Gesine Müller, Jan Huisken et al.

In this work, we introduce the concept of Active Representation Learning, a novel class of problems that intertwines exploration and representation learning within partially observable environments. We extend ideas from Active Simultaneous Localization and Mapping (active SLAM), and translate them to scientific discovery problems, exemplified by adaptive microscopy. We explore the need for a framework that derives exploration skills from representations that are in some sense actionable, aiming to enhance the efficiency and effectiveness of data collection and model building in the natural sciences.

Nikola Milosevic, Wolfgang Thielemann

Biomedical research is growing at such an exponential pace that scientists, researchers, and practitioners are no more able to cope with the amount of published literature in the domain. The knowledge presented in the literature needs to be systematized in such a way that claims and hypotheses can be easily found, accessed, and validated. Knowledge graphs can provide such a framework for semantic knowledge representation from literature. However, in order to build a knowledge graph, it is necessary to extract knowledge as relationships between biomedical entities and normalize both entities and relationship types. In this paper, we present and compare few rule-based and machine learning-based (Naive Bayes, Random Forests as examples of traditional machine learning methods and DistilBERT, PubMedBERT, T5 and SciFive-based models as examples of modern deep learning transformers) methods for scalable relationship extraction from biomedical literature, and for the integration into the knowledge graphs. We examine how resilient are these various methods to unbalanced and fairly small datasets. Our experiments show that transformer-based models handle well both small (due to pre-training on a large dataset) and unbalanced datasets. The best performing model was the PubMedBERT-based model fine-tuned on balanced data, with a reported F1-score of 0.92. DistilBERT-based model followed with F1-score of 0.89, performing faster and with lower resource requirements. BERT-based models performed better then T5-based generative models.

Nikola Milosevic, Gangamma Kalappa, Hesam Dadafarin et al.

Medical health records and clinical summaries contain a vast amount of important information in textual form that can help advancing research on treatments, drugs and public health. However, the majority of these information is not shared because they contain private information about patients, their families, or medical staff treating them. Regulations such as HIPPA in the US, PHIPPA in Canada and GDPR regulate the protection, processing and distribution of this information. In case this information is de-identified and personal information are replaced or redacted, they could be distributed to the research community. In this paper, we present MASK, a software package that is designed to perform the de-identification task. The software is able to perform named entity recognition using some of the state-of-the-art techniques and then mask or redact recognized entities. The user is able to select named entity recognition algorithm (currently implemented are two versions of CRF-based techniques and BiLSTM-based neural network with pre-trained GLoVe and ELMo embedding) and masking algorithm (e.g. shift dates, replace names/locations, totally redact entity).

Nikola Milosevic, Junfan Huang

In the past decade, the cyber-crime related to mobile devices has increased. Mobile devices, especially the ones running on Android operating system are particularly interesting to malware creators, as the users often keep the biggest amount of personal information on their mobile devices, such as their contacts, social media profiles, emails, and bank accounts. Both dynamic and static malware analysis is necessary to prevent and detect malware, as both techniques have their benefits and shortcomings. In this paper, we propose a deep learning technique that relies on LSTM and encoder-decoder neural network architectures for dynamic malware analysis based on CPU, memory and battery usage. The proposed system is able to detect and notify users about anomalies in system that is likely consequence of malware behaviour. The method was implemented as a part of OWASP Seraphimdroids anti-malware mechanism and notifies users about anomalies on their devices. The method proved to perform with an F1-score of 79.2%.

Maksim Belousov, Nikola Milosevic, Ghada Alfattni et al.

Monitoring the administration of drugs and adverse drug reactions are key parts of pharmacovigilance. In this paper, we explore the extraction of drug mentions and drug-related information (reason for taking a drug, route, frequency, dosage, strength, form, duration, and adverse events) from hospital discharge summaries through deep learning that relies on various representations for clinical named entity recognition. This work was officially part of the 2018 n2c2 shared task, and we use the data supplied as part of the task. We developed two deep learning architecture based on recurrent neural networks and pre-trained language models. We also explore the effect of augmenting word representations with semantic features for clinical named entity recognition. Our feature-augmented BiLSTM-CRF model performed with F1-score of 92.67% and ranked 4th for entity extraction sub-task among submitted systems to n2c2 challenge. The recurrent neural networks that use the pre-trained domain-specific word embeddings and a CRF layer for label optimization perform drug, adverse event and related entities extraction with micro-averaged F1-score of over 91%. The augmentation of word vectors with semantic features extracted using available clinical NLP toolkits can further improve the performance. Word embeddings that are pre-trained on a large unannotated corpus of relevant documents and further fine-tuned to the task perform rather well. However, the augmentation of word embeddings with semantic features can help improve the performance (primarily by boosting precision) of drug-related named entity recognition from electronic health records.

Maksim Belousov, Nikola Milosevic, William Dixon et al.

Adverse drug reactions (ADRs) are unwanted or harmful effects experienced after the administration of a certain drug or a combination of drugs, presenting a challenge for drug development and drug administration. In this paper, we present a set of taggers for extracting adverse drug reactions and related entities, including factors, severity, negations, drug class and animal. The systems used a mix of rule-based, machine learning (CRF) and deep learning (BLSTM with word2vec embeddings) methodologies in order to annotate the data. The systems were submitted to adverse drug reaction shared task, organised during Text Analytics Conference in 2017 by National Institute for Standards and Technology, archiving F1-scores of 76.00 and 75.61 respectively.

Nikola Milosevic, Dimitar Marinov, Abdullah Gok et al.

In the past decade, social innovation projects have gained the attention of policy makers, as they address important social issues in an innovative manner. A database of social innovation is an important source of information that can expand collaboration between social innovators, drive policy and serve as an important resource for research. Such a database needs to have projects described and summarized. In this paper, we propose and compare several methods (e.g. SVM-based, recurrent neural network based, ensambled) for describing projects based on the text that is available on project websites. We also address and propose a new metric for automated evaluation of summaries based on topic modelling.

Nikola Milosevic, Cassie Gregson, Robert Hernandez et al.

The scientific literature is growing exponentially, and professionals are no more able to cope with the current amount of publications. Text mining provided in the past methods to retrieve and extract information from text; however, most of these approaches ignored tables and figures. The research done in mining table data still does not have an integrated approach for mining that would consider all complexities and challenges of a table. Our research is examining the methods for extracting numerical (number of patients, age, gender distribution) and textual (adverse reactions) information from tables in the clinical literature. We present a requirement analysis template and an integral methodology for information extraction from tables in clinical domain that contains 7 steps: (1) table detection, (2) functional processing, (3) structural processing, (4) semantic tagging, (5) pragmatic processing, (6) cell selection and (7) syntactic processing and extraction. Our approach performed with the F-measure ranged between 82 and 92%, depending on the variable, task and its complexity.

Nikola Milosevic, Goran Nenadic

Simile is a figure of speech that compares two things through the use of connection words, but where comparison is not intended to be taken literally. They are often used in everyday communication, but they are also a part of linguistic cultural heritage. In this paper we present a methodology for semi-automated collection of similes from the World Wide Web using text mining and machine learning techniques. We expanded an existing corpus by collecting 442 similes from the internet and adding them to the existing corpus collected by Vuk Stefanovic Karadzic that contained 333 similes. We, also, introduce crowdsourcing to the collection of figures of speech, which helped us to build corpus containing 787 unique similes.

Nikola Milosevic, Goran Nenadic

Similes are natural language expressions used to compare unlikely things, where the comparison is not taken literally. They are often used in everyday communication and are an important part of cultural heritage. Having an up-to-date corpus of similes is challenging, as they are constantly coined and/or adapted to the contemporary times. In this paper we present a methodology for semi-automated collection of similes from the world wide web using text mining techniques. We expanded an existing corpus of traditional similes (containing 333 similes) by collecting 446 additional expressions. We, also, explore how crowdsourcing can be used to extract and curate new similes.

Nikola Milosevic

Long term investment is one of the major investment strategies. However, calculating intrinsic value of some company and evaluating shares for long term investment is not easy, since analyst have to care about a large number of financial indicators and evaluate them in a right manner. So far, little help in predicting the direction of the company value over the longer period of time has been provided from the machines. In this paper we present a machine learning aided approach to evaluate the equity's future price over the long time. Our method is able to correctly predict whether some company's value will be 10% higher or not over the period of one year in 76.5% of cases.

Nikola Milosevic

People are producing more written material then anytime in the history. The increase is so high that professionals from the various fields are no more able to cope with this amount of publications. Text mining tools can offer tools to help them and one of the tools that can aid information retrieval and information extraction is semantic text annotation. In this report we present Marvin, a text annotator written in Java, which can be used as a command line tool and as a Java library. Marvin is able to annotate text using multiple sources, including WordNet, MetaMap, DBPedia and thesauri represented as SKOS.