Computational models are invaluable in capturing the complexities of real-world biological processes. Yet, the selection of appropriate algorithms for inference tasks, especially when dealing with real-world observational data, remains a challenging and underexplored area. This gap has spurred the development of various parameter estimation algorithms, particularly within the realm of Simulation-Based Inference (SBI), such as neural and statistical SBI methods. Limited research exists on how to make informed choices on SBI methods when faced with real-world data, which often results in some form of model misspecification. In this paper, we provide comprehensive guidelines for deciding between SBI approaches for complex biological models. We apply the guidelines to two agent-based models that describe cellular dynamics using real-world data. Our study unveils a critical insight: while neural SBI methods demand significantly fewer simulations for inference results, they tend to yield biased estimations, a trend persistent even with robust variants of these algorithms. On the other hand, the accuracy of statistical SBI methods enhances substantially as the number of simulations increases. This finding suggests that, given a sufficient computational budget, statistical SBI can surpass neural SBI in performance. Our results not only shed light on the efficacy of different SBI methodologies in real-world scenarios but also suggest potential avenues for enhancing neural SBI approaches. This study is poised to be a useful resource for computational biologists navigating the intricate landscape of SBI in biological modeling.

Machine learning and AI have been recently embraced by many companies. Machine Learning Operations, (MLOps), refers to the use of continuous software engineering processes, such as DevOps, in the deployment of machine learning models to production. Nevertheless, not all machine learning initiatives successfully transition to the production stage owing to the multitude of intricate factors involved. This article discusses the issues that exist in several components of the MLOps pipeline, namely the data manipulation pipeline, model building pipeline, and deployment pipeline. A systematic mapping study is performed to identify the challenges that arise in the MLOps system categorized by different focus areas. Using this data, realistic and applicable recommendations are offered for tools or solutions that can be used for their implementation. The main value of this work is it maps distinctive challenges in MLOps along with the recommended solutions outlined in our study. These guidelines are not specific to any particular tool and are applicable to both research and industrial settings.

Natural Language Processing (NLP) is a dynamic, interdisciplinary field that integrates intellectual traditions from computer science, linguistics, social science, and more. Despite its established presence, the definition of what constitutes NLP research remains debated. In this work, we quantitatively investigate what constitutes NLP by examining research papers. For this purpose, we propose a taxonomy and introduce NLPContributions, a dataset of nearly $2k$ research paper abstracts, expertly annotated to identify scientific contributions and classify their types according to this taxonomy. We also propose a novel task to automatically identify these elements, for which we train a strong baseline on our dataset. We present experimental results from this task and apply our model to $\sim$$29k$ NLP research papers to analyze their contributions, aiding in the understanding of the nature of NLP research. Our findings reveal a rising involvement of machine learning in NLP since the early nineties, alongside a declining focus on adding knowledge about language or people; again, in post-2020, there has been a resurgence of focus on language and people. We hope this work will spark discussions on our community norms and inspire efforts to consciously shape the future.

Neural backdoors represent insidious cybersecurity loopholes that render learning machinery vulnerable to unauthorised manipulations, potentially enabling the weaponisation of artificial intelligence with catastrophic consequences. A backdoor attack involves the clandestine infiltration of a trigger during the learning process, metaphorically analogous to hypnopaedia, where ideas are implanted into a subject's subconscious mind under the state of hypnosis or unconsciousness. When activated by a sensory stimulus, the trigger evokes conditioned reflex that directs a machine to mount a predetermined response. In this study, we propose a cybernetic framework for constant surveillance of backdoors threats, driven by the dynamic nature of untrustworthy data sources. We develop a self-aware unlearning mechanism to autonomously detach a machine's behaviour from the backdoor trigger. Through reverse engineering and statistical inference, we detect deceptive patterns and estimate the likelihood of backdoor infection. We employ model inversion to elicit artificial mental imagery, using stochastic processes to disrupt optimisation pathways and avoid convergent but potentially flawed patterns. This is followed by hypothesis analysis, which estimates the likelihood of each potentially malicious pattern being the true trigger and infers the probability of infection. The primary objective of this study is to maintain a stable state of equilibrium between knowledge fidelity and backdoor vulnerability.

This paper aims to answer one central question: to what extent can open-source generative text models be used in a workflow to approximate thematic analysis in social science research? To answer this question, we present the Generative AI-enabled Theme Organization and Structuring (GATOS) workflow, which uses open-source machine learning techniques, natural language processing tools, and generative text models to facilitate thematic analysis. To establish validity of the method, we present three case studies applying the GATOS workflow, leveraging these models and techniques to inductively create codebooks similar to traditional procedures using thematic analysis. Specifically, we investigate the extent to which a workflow comprising open-source models and tools can inductively produce codebooks that approach the known space of themes and sub-themes. To address the challenge of gleaning insights from these texts, we combine open-source generative text models, retrieval-augmented generation, and prompt engineering to identify codes and themes in large volumes of text, i.e., generate a qualitative codebook. The process mimics an inductive coding process that researchers might use in traditional thematic analysis by reading text one unit of analysis at a time, considering existing codes already in the codebook, and then deciding whether or not to generate a new code based on whether the extant codebook provides adequate thematic coverage. We demonstrate this workflow using three synthetic datasets from hypothetical organizational research settings: a study of teammate feedback in teamwork settings, a study of organizational cultures of ethical behavior, and a study of employee perspectives about returning to their offices after the pandemic. We show that the GATOS workflow is able to identify themes in the text that were used to generate the original synthetic datasets.

In the realm of neuroscience, identifying distinctive patterns associated with neurological disorders via brain networks is crucial. Resting-state functional magnetic resonance imaging (fMRI) serves as a primary tool for mapping these networks by correlating blood-oxygen-level-dependent (BOLD) signals across different brain regions, defined as regions of interest (ROIs). Constructing these brain networks involves using atlases to parcellate the brain into ROIs based on various hypotheses of brain division. However, there is no standard atlas for brain network classification, leading to limitations in detecting abnormalities in disorders. Some recent methods have proposed utilizing multiple atlases, but they neglect consistency across atlases and lack ROI-level information exchange. To tackle these limitations, we propose an Atlas-Integrated Distillation and Fusion network (AIDFusion) to improve brain network classification using fMRI data. AIDFusion addresses the challenge of utilizing multiple atlases by employing a disentangle Transformer to filter out inconsistent atlas-specific information and distill distinguishable connections across atlases. It also incorporates subject- and population-level consistency constraints to enhance cross-atlas consistency. Additionally, AIDFusion employs an inter-atlas message-passing mechanism to fuse complementary information across brain regions. Experimental results on four datasets of different diseases demonstrate the effectiveness and efficiency of AIDFusion compared to state-of-the-art methods. A case study illustrates AIDFusion extract patterns that are both interpretable and consistent with established neuroscience findings.

Effective summarisation evaluation metrics enable researchers and practitioners to compare different summarisation systems efficiently. Estimating the effectiveness of an automatic evaluation metric, termed meta-evaluation, is a critically important research question. In this position paper, we review recent meta-evaluation practices for summarisation evaluation metrics and find that (1) evaluation metrics are primarily meta-evaluated on datasets consisting of examples from news summarisation datasets, and (2) there has been a noticeable shift in research focus towards evaluating the faithfulness of generated summaries. We argue that the time is ripe to build more diverse benchmarks that enable the development of more robust evaluation metrics and analyze the generalization ability of existing evaluation metrics. In addition, we call for research focusing on user-centric quality dimensions that consider the generated summary's communicative goal and the role of summarisation in the workflow.

To obtain better value estimation in reinforcement learning, we propose a novel algorithm based on the double actor-critic framework with temporal difference error-driven regularization, abbreviated as TDDR. TDDR employs double actors, with each actor paired with a critic, thereby fully leveraging the advantages of double critics. Additionally, TDDR introduces an innovative critic regularization architecture. Compared to classical deterministic policy gradient-based algorithms that lack a double actor-critic structure, TDDR provides superior estimation. Moreover, unlike existing algorithms with double actor-critic frameworks, TDDR does not introduce any additional hyperparameters, significantly simplifying the design and implementation process. Experiments demonstrate that TDDR exhibits strong competitiveness compared to benchmark algorithms in challenging continuous control tasks.

Relationships among teachers are known to influence their teaching-related perceptions. We study whether and how teachers' advising relationships (networks) are related to their perceptions of satisfaction, students, and influence over educational policies, recorded as their responses to a questionnaire (item responses). We propose a novel joint model of network and item responses (JNIRM) with correlated latent variables to understand these co-varying ties. This methodology allows the analyst to test and interpret the dependence between a network and item responses. Using JNIRM, we discover that teachers' advising relationships contribute to their perceptions of satisfaction and students more often than their perceptions of influence over educational policies. In addition, we observe that the complementarity principle applies in certain schools, where teachers tend to seek advice from those who are different from them. JNIRM shows superior parameter estimation and model fit over separately modeling the network and item responses with latent variable models.

We hear about artificial intelligence all the time nowadays--but what is it doing for astronomy? New research papers are published almost every week using AI for some new investigation in astronomy: classifying galaxies, identifying solar flares, exploring exoplanet atmospheres, and more. AI's biggest strength is that it can sort through mountains of data much faster than a human--a skill that's particularly timely as new telescopes are generating more and more data for astronomers to handle. "We can use [AI] to tackle problems we couldn't tackle before because they're too computationally expensive," said Daniela Huppenkothen, astronomer and data scientist at the Netherlands Institute for Space Research, in MIT Technology Review. One telescope in particular has many astronomers abuzz about AI: the Vera C. Rubin Observatory, scheduled to be completed in January 2025, just a few short months away.