Protein *sequence* design has seen significant advances through discrete diffusion and autoregressive approaches, yet the potential of continuous diffusion remains underexplored. Here, we present *DiMA*, a latent diffusion framework that operates on protein language model representations. Through systematic exploration of architectural choices and diffusion components, we develop a robust methodology that generalizes across multiple protein encoders ranging from 8M to 3B parameters. We demonstrate that our framework achieves consistently high performance across sequence-only (ESM-2, ESMc), dual-decodable (CHEAP), and multimodal (SaProt) representations using the same architecture and training approach. We conduct extensive evaluation of existing methods alongside *DiMA* using multiple metrics across two protein modalities, covering quality, diversity, novelty, and distribution matching of generated proteins. *DiMA* consistently produces novel, high-quality and diverse protein sequences and achieves strong results compared to baselines such as autoregressive, discrete diffusion and flow matching language models. The model demonstrates versatile functionality, supporting conditional generation tasks including protein family-generation, motif scaffolding and infilling, and fold-specific sequence design, despite being trained solely on sequence data. This work provides a universal continuous diffusion framework for protein sequence generation, offering both architectural insights and practical applicability across various protein design scenarios. Code is released at [GitHub](https://github.com/MeshchaninovViacheslav/DiMA).

This paper introduces a novel information retrieval (IR) task of Conversational Entity Retrieval from a Knowledge Graph (CER-KG), which extends non-conversational entity retrieval from a knowledge graph (KG) to the conversational scenario. The user queries in CER-KG dialog turns may rely on the results of the preceding turns, which are KG entities. Similar to the conversational document IR, CER-KG can be viewed as a sequence of interrelated ranking tasks. To enable future research on CER-KG, we created QBLink-KG, a publicly available benchmark that was adapted from QBLink, a benchmark for text-based conversational reading comprehension of Wikipedia. As an initial approach to CER-KG, we experimented with Transformer- and LSTM-based query encoders in combination with the Neural Architecture for Conversational Entity Retrieval (NACER), our proposed feature-based neural architecture for entity ranking in CER-KG. NACER computes the ranking score of a candidate KG entity by taking into account diverse lexical and semantic matching signals between various KG components in its neighborhood, such as entities, categories, and literals, as well as entities in the results of the preceding turns in dialog history. The reported experimental results reveal the key challenges of CER-KG along with the possible directions for new approaches to this task.

MOTIVATION: Accurate prediction of change in protein stability due to point mutations is an attractive goal that remains unachieved. Despite the high interest in this area, little consideration has been given to the transformer architecture, which is dominant in many fields of machine learning. RESULTS: In this work, we introduce PROSTATA, a predictive model built in a knowledge-transfer fashion on a new curated dataset. PROSTATA demonstrates advantage over existing solutions based on neural networks. We show that the large improvement margin is due to both the architecture of the model and the quality of the new training dataset. This work opens up opportunities to develop new lightweight and accurate models for protein stability assessment. AVAILABILITY AND IMPLEMENTATION: PROSTATA is available at https://github.com/AIRI-Institute/PROSTATA and https://prostata.airi.net.

The problem of ad-hoc structured document retrieval arises in many information access scenarios, from Web to product search. Yet neither deep neural networks, which have been successfully applied to ad-hoc information retrieval and Web search, nor the attention mechanism, which has been shown to significantly improve the performance of deep neural networks on natural language processing tasks, have been explored in the context of this problem. In this paper, we propose a deep neural architecture for ad-hoc structured document retrieval, which utilizes attention mechanism to determine important phrases in keyword queries as well as the relative importance of matching those phrases in different fields of structured documents. Experimental evaluation on publicly available collections for Web document, product and entity retrieval from knowledge graphs indicates superior retrieval accuracy of the proposed neural architecture relative to both state-of-the-art neural architectures for ad-hoc document retrieval and probabilistic models for ad-hoc structured document retrieval.

The DBpedia-entity collection has been used as a standard test collection for entity search in recent years. We develop and release a new version of this test collection, DBpedia-Entity v2, which uses a more recent DBpedia dump and a unified candidate result pool from the same set of retrieval models. Relevance judgments are also collected in a uniform way, using the same group of crowdsourcing workers, following the same assessment guidelines. The result is an up-to-date and consistent test collection.To facilitate further research, we also provide details about the pre-processing and indexing steps, and include baseline results from both classical and recently developed entity search methods.

Accurate projection of terms in free-text queries onto structured entity representations is one of the fundamental problems in entity retrieval from knowledge graphs. In this paper, we demonstrate that existing retrieval models for ad-hoc structured and unstructured document retrieval fall short of addressing this problem, due to their rigid assumptions. According to these assumptions, either all query concepts of the same type (unigrams and bigrams) are projected onto the fields of entity representations with identical weights or such projection is determined based only on one simple statistic, which makes it sensitive to data sparsity. To address this issue, we propose the Parametrized Fielded Sequential Dependence Model (PFSDM) and the Parametrized Fielded Full Dependence Model (PFFDM), two novel models for entity retrieval from knowledge graphs, which infer the user's intent behind each individual query concept by dynamically estimating its projection onto the fields of structured entity representations based on a small number of statistical and linguistic features. Experimental results obtained on several publicly available benchmarks indicate that PFSDM and PFFDM consistently outperform state-of-the-art retrieval models for the task of entity retrieval from knowledge graph.

Previously proposed approaches to ad-hoc entity retrieval in the Web of Data (ERWD) used multi-fielded representation of entities and relied on standard unigram bag-of-words retrieval models. Although retrieval models incorporating term dependencies have been shown to be significantly more effective than the unigram bag-of-words ones for ad hoc document retrieval, it is not known whether accounting for term dependencies can improve retrieval from the Web of Data. In this work, we propose a novel retrieval model that incorporates term dependencies into structured document retrieval and apply it to the task of ERWD. In the proposed model, the document field weights and the relative importance of unigrams and bigrams are optimized with respect to the target retrieval metric using a learning-to-rank method. Experiments on a publicly available benchmark indicate significant improvement of the accuracy of retrieval results by the proposed model over state-of-the-art retrieval models for ERWD.