Deep neural-network-based language models (LMs) are increasingly applied to large-scale protein sequence data to predict protein function. However, being largely black-box models and thus challenging to interpret, current protein LM approaches do not contribute to a fundamental understanding of sequence-function mappings, hindering rule-based biotherapeutic drug development. We argue that guidance drawn from linguistics, a field specialized in analytical rule extraction from natural language data, can aid with building more interpretable protein LMs that are more likely to learn relevant domain-specific rules. Differences between protein sequence data and linguistic sequence data require the integration of more domain-specific knowledge in protein LMs compared to natural language LMs. Here, we provide a linguistics-based roadmap for protein LM pipeline choices with regard to training data, tokenization, token embedding, sequence embedding, and model interpretation. Incorporating linguistic ideas into protein LMs enables the development of next-generation interpretable machine-learning models with the potential of uncovering the biological mechanisms underlying sequence-function relationships.

In this paper, we propose Multi-Modal Databases (MMDBs), which is a new class of database systems that can seamlessly query text and tables using SQL. To enable seamless querying of textual data using SQL in an MMDB, we propose to extend relational databases with so-called multi-modal operators (MMOps) which are based on the advances of recent large language models such as GPT-3. The main idea of MMOps is that they allow text collections to be treated as tables without the need to manually transform the data. As we show in our evaluation, our MMDB prototype can not only outperform state-of-the-art approaches such as text-to-table in terms of accuracy and performance but it also requires significantly less training data to fine-tune the model for an unseen text collection.

This review will introduce the latest advances in prompt engineering in the field of natural language processing (NLP) for the medical domain. First, we will provide a brief overview of the development of prompt engineering and emphasize its significant contributions to healthcare NLP applications such as question-answering systems, text summarization, and machine translation. With the continuous improvement of general large language models, the importance of prompt engineering in the healthcare domain is becoming increasingly prominent. The aim of this article is to provide useful resources and bridges for healthcare NLP researchers to better explore the application of prompt engineering in this field. We hope that this review can provide new ideas and inspire ample possibilities for research and application in medical NLP.

Yet, a significant portion is scattered and locked in data silos, leaving its potential untapped. Federated Machine Learning is a novel AI paradigm enabling the creation of AI models from decentralized, potentially siloed data. Hence, Federated Machine Learning could technically open data silos and therefore unlock economic potential. However, this requires collaboration between multiple parties owning data silos. Setting up collaborative business models is complex and often a reason for failure. Current literature lacks guidelines on which aspects must be considered to successfully realize collaborative AI projects. This research investigates the challenges of prevailing collaborative business models and distinct aspects of Federated Machine Learning. Through a systematic literature review, focus group, and expert interviews, we provide a systemized collection of socio-technical challenges and an extended Business Model Canvas for the initial viability assessment of collaborative AI projects.

Most real-world knowledge graphs, including Wikidata, DBpedia, and Yago are incomplete. Answering queries on such incomplete graphs is an important, but challenging problem. Recently, a number of approaches, including complex query decomposition (CQD), have been proposed to answer complex, multi-hop queries with conjunctions and disjunctions on such graphs. However, all state-of-the-art approaches only consider graphs consisting of entities and relations, neglecting literal values. In this paper, we propose LitCQD -- an approach to answer complex, multi-hop queries where both the query and the knowledge graph can contain numeric literal values: LitCQD can answer queries having numerical answers or having entity answers satisfying numerical constraints. For example, it allows to query (1)~persons living in New York having a certain age, and (2)~the average age of persons living in New York. We evaluate LitCQD on query types with and without literal values. To evaluate LitCQD, we generate complex, multi-hop queries and their expected answers on a version of the FB15k-237 dataset that was extended by literal values.

Centralized training with decentralized execution (CTDE) is a widely-used learning paradigm that has achieved significant success in complex tasks. However, partial observability issues and the absence of effectively shared signals between agents often limit its effectiveness in fostering cooperation. While communication can address this challenge, it simultaneously reduces the algorithm's practicality. Drawing inspiration from human team cooperative learning, we propose a novel paradigm that facilitates a gradual shift from explicit communication to tacit cooperation. In the initial training stage, we promote cooperation by sharing relevant information among agents and concurrently reconstructing this information using each agent's local trajectory. We then combine the explicitly communicated information with the reconstructed information to obtain mixed information. Throughout the training process, we progressively reduce the proportion of explicitly communicated information, facilitating a seamless transition to fully decentralized execution without communication. Experimental results in various scenarios demonstrate that the performance of our method without communication can approaches or even surpasses that of QMIX and communication-based methods.

This tutorial survey provides an overview of recent non-asymptotic advances in statistical learning theory as relevant to control and system identification. While there has been substantial progress across all areas of control, the theory is most well-developed when it comes to linear system identification and learning for the linear quadratic regulator, which are the focus of this manuscript. From a theoretical perspective, much of the labor underlying these advances has been in adapting tools from modern high-dimensional statistics and learning theory. While highly relevant to control theorists interested in integrating tools from machine learning, the foundational material has not always been easily accessible. To remedy this, we provide a self-contained presentation of the relevant material, outlining all the key ideas and the technical machinery that underpin recent results. We also present a number of open problems and future directions.

Knowledge graphs (KG) have become an important data organization paradigm. The available textual query languages for information retrieval from KGs, as SPARQL for RDF-structured data, do not provide means for involving non-technical experts in the data access process. Visual query formalisms, alongside form-based and natural language-based ones, offer means for easing user involvement in the data querying process. ViziQuer is a visual query notation and tool offering visual diagrammatic means for describing rich data queries, involving optional and negation constructs, as well as aggregation and subqueries. In this paper we review the visual ViziQuer notation from the end-user point of view and describe the conceptual and technical solutions (including abstract syntax model, followed by a generation model for textual queries) that allow mapping of the visual diagrammatic query notation into the textual SPARQL language, thus enabling the execution of rich visual queries over the actual knowledge graphs. The described solutions demonstrate the viability of the model-based approach in translating complex visual notation into a complex textual one; they serve as semantics by implementation description of the ViziQuer language and provide building blocks for further services in the ViziQuer tool context.

We present a novel application of category theory for deep learning. We show how category theory can be used to understand and work with the linear layer functions of group equivariant neural networks whose layers are some tensor power space of $\mathbb{R}^{n}$ for the groups $S_n$, $O(n)$, $Sp(n)$, and $SO(n)$. By using category theoretic constructions, we build a richer structure that is not seen in the original formulation of these neural networks, leading to new insights. In particular, we outline the development of an algorithm for quickly computing the result of a vector that is passed through an equivariant, linear layer for each group in question. The success of our approach suggests that category theory could be beneficial for other areas of deep learning.

This paper presents a comprehensive and practical guide for practitioners and end-users working with Large Language Models (LLMs) in their downstream natural language processing (NLP) tasks. We provide discussions and insights into the usage of LLMs from the perspectives of models, data, and downstream tasks. Firstly, we offer an introduction and brief summary of current GPT- and BERT-style LLMs. Then, we discuss the influence of pre-training data, training data, and test data. Most importantly, we provide a detailed discussion about the use and non-use cases of large language models for various natural language processing tasks, such as knowledge-intensive tasks, traditional natural language understanding tasks, natural language generation tasks, emergent abilities, and considerations for specific tasks.We present various use cases and non-use cases to illustrate the practical applications and limitations of LLMs in real-world scenarios. We also try to understand the importance of data and the specific challenges associated with each NLP task. Furthermore, we explore the impact of spurious biases on LLMs and delve into other essential considerations, such as efficiency, cost, and latency, to ensure a comprehensive understanding of deploying LLMs in practice. This comprehensive guide aims to provide researchers and practitioners with valuable insights and best practices for working with LLMs, thereby enabling the successful implementation of these models in a wide range of NLP tasks. A curated list of practical guide resources of LLMs, regularly updated, can be found at \url{https://github.com/Mooler0410/LLMsPracticalGuide}.