Diffusion models have emerged as powerful tools for molecular generation, particularly in the context of 3D molecular structures. Inspired by non-equilibrium statistical physics, these models can generate 3D molecular structures with specific properties or requirements crucial to drug discovery. Diffusion models were particularly successful at learning 3D molecular geometries' complex probability distributions and their corresponding chemical and physical properties through forward and reverse diffusion processes. This review focuses on the technical implementation of diffusion models tailored for 3D molecular generation. It compares the performance, evaluation methods, and implementation details of various diffusion models used for molecular generation tasks. We cover strategies for atom and bond representation, architectures of reverse diffusion denoising networks, and challenges associated with generating stable 3D molecular structures. This review also explores the applications of diffusion models in $\textit{de novo}$ drug design and related areas of computational chemistry, such as structure-based drug design, including target-specific molecular generation, molecular docking, and molecular dynamics of protein-ligand complexes. We also cover conditional generation on physical properties, conformation generation, and fragment-based drug design. By summarizing the state-of-the-art diffusion models for 3D molecular generation, this review sheds light on their role in advancing drug discovery as well as their current limitations.

Traditional image clustering techniques only find a single grouping within visual data. In particular, they do not provide a possibility to explicitly define multiple types of clustering. This work explores the potential of large vision-language models to facilitate alternative image clustering. We propose Text-Guided Alternative Image Consensus Clustering (TGAICC), a novel approach that leverages user-specified interests via prompts to guide the discovery of diverse clusterings. To achieve this, it generates a clustering for each prompt, groups them using hierarchical clustering, and then aggregates them using consensus clustering. TGAICC outperforms image- and text-based baselines on four alternative image clustering benchmark datasets. Furthermore, using count-based word statistics, we are able to obtain text-based explanations of the alternative clusterings. In conclusion, our research illustrates how contemporary large vision-language models can transform explanatory data analysis, enabling the generation of insightful, customizable, and diverse image clusterings.

This survey presents an overview of methods for learning from video (LfV) in the context of reinforcement learning (RL) and robotics. We focus on methods capable of scaling to large internet video datasets and, in the process, extracting foundational knowledge about the world's dynamics and physical human behaviour. Such methods hold great promise for developing general-purpose robots. We open with an overview of fundamental concepts relevant to the LfV-for-robotics setting. This includes a discussion of the exciting benefits LfV methods can offer (e.g., improved generalization beyond the available robot data) and commentary on key LfV challenges (e.g., missing information in video and LfV distribution shifts). Our literature review begins with an analysis of video foundation model techniques that can extract knowledge from large, heterogeneous video datasets. Next, we review methods that specifically leverage video data for robot learning. Here, we categorise work according to which RL knowledge modality (KM) benefits from the use of video data. We additionally highlight techniques for mitigating LfV challenges, including reviewing action representations that address missing action labels in video. Finally, we examine LfV datasets and benchmarks, before concluding with a discussion of challenges and opportunities in LfV. Here, we advocate for scalable foundation model approaches that can leverage the full range of internet video data, and that target the learning of the most promising RL KMs: the policy and dynamics model. Overall, we hope this survey will serve as a comprehensive reference for the emerging field of LfV, catalysing further research in the area and facilitating progress towards the development of general-purpose robots.

As a leading cause of mortality among women globally, the precise and timely diagnosis of breast cancer remains imperative for optimizing patient outcomes. While traditional diagnostic methodologies [2] have historically relied heavily on uni-modal approaches, the evolving landscape of medical data analytics underscores the significance of integrating diverse data sources beyond conventional imaging modalities [3]. Figure 1 illustrates a generic model for breast cancer diagnosis within the Computer-Aided Detection (CAD) framework. As depicted in Figure 2, breast cancer detection can be performed using various data types, employing either unimodal or multimodal approaches. The process initiates with data pre-processing, followed by feature extraction. To enhance the learning of feature representations from image data, segmentation may be conducted prior to feature extraction. Subsequently, the detection model is applied to generate a diagnosis from the processed data. Based on this diagnosis, further analyses are performed, including sub-type classification, grade classification, recurrence and metastasis prediction, as well as the incorporation of crowdsourcing and human-in-the-loop methodologies. These steps culminate in a final decision that informs subsequent treatment and monitoring strategies.

In recent years, the landscape of e-learning has witnessed exceptional advancements, providing students with tools to improve their performance. In the pursuit of optimizing the e-learning experience, one emerging area of focus is the integration of recommender systems. By leveraging sophisticated algorithms, recommender systems aim to personalize the learning path by tailoring recommendations based on individual student performance, preferences, learning style and other factors.

Prompt recovery in large language models (LLMs) is crucial for understanding how LLMs work and addressing concerns regarding privacy, copyright, etc. The trend towards inference-only APIs complicates this task by restricting access to essential outputs for recovery. To tackle this challenge, we extract prompt-related information from limited outputs and identify a strong(negative) correlation between output probability-based uncertainty and the success of prompt recovery. This finding led to the development of Deliberative PrOmpt RecoverY (DORY), our novel approach that leverages uncertainty to recover prompts accurately. DORY involves reconstructing drafts from outputs, refining these with hints, and filtering out noise based on uncertainty. Our evaluation across diverse LLMs and prompt benchmarks shows that DORY outperforms existing baselines, improving performance by approximately 10.82% and establishing a new state-of-the-art record in prompt recovery tasks. Significantly, DORY operates using a single LLM without any external resources or model, offering a cost-effective, user-friendly prompt recovery solution.

In the present article, we propose a paradigm shift on evolving Artificial Neural Networks (ANNs) towards a new bio-inspired design that is grounded on the structural properties, interactions, and dynamics of protein networks (PNs): the Artificial Protein Network (APN). This introduces several advantages previously unrealized by state-of-the-art approaches in NE: (1) We can draw inspiration from how nature, thanks to millions of years of evolution, efficiently encodes protein interactions in the DNA to translate our APN to silicon DNA. This helps bridge the gap between syntax and semantics observed in current NE approaches.

A timeline provides a total ordering of events and times, and is useful for a number of natural language understanding tasks. However, qualitative temporal graphs that can be derived directly from text -- such as TimeML annotations -- usually explicitly reveal only partial orderings of events and times. In this work, we apply prior work on solving point algebra problems to the task of extracting timelines from TimeML annotated texts, and develop an exact, end-to-end solution which we call TLEX (TimeLine EXtraction). TLEX transforms TimeML annotations into a collection of timelines arranged in a trunk-and-branch structure. Like what has been done in prior work, TLEX checks the consistency of the temporal graph and solves it; however, it adds two novel functionalities. First, it identifies specific relations involved in an inconsistency (which could then be manually corrected) and, second, TLEX performs a novel identification of sections of the timelines that have indeterminate order, information critical for downstream tasks such as aligning events from different timelines. We provide detailed descriptions and analysis of the algorithmic components in TLEX, and conduct experimental evaluations by applying TLEX to 385 TimeML annotated texts from four corpora. We show that 123 of the texts are inconsistent, 181 of them have more than one ``real world'' or main timeline, and there are 2,541 indeterminate sections across all four corpora. A sampling evaluation showed that TLEX is 98--100% accurate with 95% confidence along five dimensions: the ordering of time-points, the number of main timelines, the placement of time-points on main versus subordinate timelines, the connecting point of branch timelines, and the location of the indeterminate sections. We provide a reference implementation of TLEX, the extracted timelines for all texts, and the manual corrections of the inconsistent texts.

FDA Medical Device recalls are critical and time-sensitive events, requiring swift identification of impacted devices to inform the public of a recall event and ensure patient safety. The OpenFDA device recall dataset contains valuable information about ongoing device recall actions, but manually extracting relevant device information from the recall action summaries is a time-consuming task. Named Entity Recognition (NER) is a task in Natural Language Processing (NLP) that involves identifying and categorizing named entities in unstructured text. Existing NER models, including domain-specific models like BioBERT, struggle to correctly identify medical device trade names, part numbers and component terms within these summaries. To address this, we propose DeviceBERT, a medical device annotation, pre-processing and enrichment pipeline, which builds on BioBERT to identify and label medical device terminology in the device recall summaries with improved accuracy. Furthermore, we demonstrate that our approach can be applied effectively for performing entity recognition tasks where training data is limited or sparse.

The ability of Generative AI (GAI) technology to automatically check, synthesize and modify software engineering artifacts promises to revolutionize all aspects of software engineering. Using GAI for software engineering tasks is consequently one of the most rapidly expanding fields of software engineering research, with dozens of LLM-based code models having been published since 2021. However, the overwhelming majority of existing code models share a major weakness - they are exclusively trained on the syntactic facet of software, significantly lowering their trustworthiness in tasks dependent on software semantics. To address this problem, a new class of "Morescient" GAI is needed that is "aware" of (i.e., trained on) both the semantic and static facets of software. This, in turn, will require a new generation of software observation platforms capable of generating ultra-large quantities of execution observations in a structured and readily analyzable way. In this paper, we present a vision for how such "Morescient" GAI models can be engineered, evolved and disseminated according to the principles of open science.