Daily Papers

The remarkable mechanical properties of spider silk, including its tensile strength and extensibility, are primarily governed by the repetitive regions of the proteins that constitute the fiber, the major ampullate spidroins (MaSps). However, establishing correlations between mechanical characteristics and repeat sequences is challenging due to the intricate sequence-structure-function relationships of MaSps and the limited availability of annotated datasets. In this study, we present a novel computational framework for designing MaSp repeat sequences with customizable mechanical properties. To achieve this, we developed a lightweight GPT-based generative model by distilling the pre-trained ProtGPT2 protein language model. The distilled model was subjected to multilevel fine-tuning using curated subsets of the Spider Silkome dataset. Specifically, we adapt the model for MaSp repeat generation using 6,000 MaSp repeat sequences and further refine it with 572 repeats associated with experimentally determined fiber-level mechanical properties. Our model generates biologically plausible MaSp repeat regions tailored to specific mechanical properties while also predicting those properties for given sequences. Validation includes sequence-level analysis, assessing physicochemical attributes and expected distribution of key motifs as well as secondary structure compositions. A correlation study using BLAST on the Spider Silkome dataset and a test set of MaSp repeats with known mechanical properties further confirmed the predictive accuracy of the model. This framework advances the rational design of spider silk-inspired biomaterials, offering a versatile tool for engineering protein sequences with tailored mechanical attributes.

The complementarity-determining regions of antibodies are loop structures that are key to their interactions with antigens, and of high importance to the design of novel biologics. Since the 1980s, categorizing the diversity of CDR structures into canonical clusters has enabled the identification of key structural motifs of antibodies. However, existing approaches have limited coverage and cannot be readily incorporated into protein foundation models. Here we introduce ImmunoGlobulin LOOp Tokenizer, Igloo, a multimodal antibody loop tokenizer that encodes backbone dihedral angles and sequence. Igloo is trained using a contrastive learning objective to map loops with similar backbone dihedral angles closer together in latent space. Igloo can efficiently retrieve the closest matching loop structures from a structural antibody database, outperforming existing methods on identifying similar H3 loops by 5.9\%. Igloo assigns tokens to all loops, addressing the limited coverage issue of canonical clusters, while retaining the ability to recover canonical loop conformations. To demonstrate the versatility of Igloo tokens, we show that they can be incorporated into protein language models with IglooLM and IglooALM. On predicting binding affinity of heavy chain variants, IglooLM outperforms the base protein language model on 8 out of 10 antibody-antigen targets. Additionally, it is on par with existing state-of-the-art sequence-based and multimodal protein language models, performing comparably to models with 7times more parameters. IglooALM samples antibody loops which are diverse in sequence and more consistent in structure than state-of-the-art antibody inverse folding models. Igloo demonstrates the benefit of introducing multimodal tokens for antibody loops for encoding the diverse landscape of antibody loops, improving protein foundation models, and for antibody CDR design.

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

Recently, interest has grown in exploring the hypothesis that neural activity conveys information through precise spiking motifs. To investigate this phenomenon, various algorithms have been proposed to detect such motifs in Single Unit Activity (SUA) recorded from populations of neurons. In this study, we present a novel detection model based on the inversion of a generative model of raster plot synthesis. Using this generative model, we derive an optimal detection procedure that takes the form of logistic regression combined with temporal convolution. A key advantage of this model is its differentiability, which allows us to formulate a supervised learning approach using a gradient descent on the binary cross-entropy loss. To assess the model's ability to detect spiking motifs in synthetic data, we first perform numerical evaluations. This analysis highlights the advantages of using spiking motifs over traditional firing rate based population codes. We then successfully demonstrate that our learning method can recover synthetically generated spiking motifs, indicating its potential for further applications. In the future, we aim to extend this method to real neurobiological data, where the ground truth is unknown, to explore and detect spiking motifs in a more natural and biologically relevant context.

This article introduces idMotif, a visual analytics framework designed to aid domain experts in the identification of motifs within protein sequences. Motifs, short sequences of amino acids, are critical for understanding the distinct functions of proteins. Identifying these motifs is pivotal for predicting diseases or infections. idMotif employs a deep learning-based method for the categorization of protein sequences, enabling the discovery of potential motif candidates within protein groups through local explanations of deep learning model decisions. It offers multiple interactive views for the analysis of protein clusters or groups and their sequences. A case study, complemented by expert feedback, illustrates idMotif's utility in facilitating the analysis and identification of protein sequences and motifs.

Proteins are essential biological macromolecules that execute life functions. Local motifs within protein structures, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution and enabling protein engineering. Existing computational methods struggle to identify and compare these local structures, which leaves a significant gap in understanding protein structures and harnessing their functions. This study presents PLASMA, the first deep learning framework for efficient and interpretable residue-level protein substructure alignment. We reformulate the problem as a regularized optimal transport task and leverage differentiable Sinkhorn iterations. For a pair of input protein structures, PLASMA outputs a clear alignment matrix with an interpretable overall similarity score. Through extensive quantitative evaluations and three biological case studies, we demonstrate that PLASMA achieves accurate, lightweight, and interpretable residue-level alignment. Additionally, we introduce PLASMA-PF, a training-free variant that provides a practical alternative when training data are unavailable. Our method addresses a critical gap in protein structure analysis tools and offers new opportunities for functional annotation, evolutionary studies, and structure-based drug design. Reproducibility is ensured via our official implementation at https://github.com/ZW471/PLASMA-Protein-Local-Alignment.git.

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

Recent advancements in conversational large language models (LLMs), such as ChatGPT, have demonstrated remarkable promise in various domains, including drug discovery. However, existing works mainly focus on investigating the capabilities of conversational LLMs on chemical reaction and retrosynthesis. While drug editing, a critical task in the drug discovery pipeline, remains largely unexplored. To bridge this gap, we propose ChatDrug, a framework to facilitate the systematic investigation of drug editing using LLMs. ChatDrug jointly leverages a prompt module, a retrieval and domain feedback (ReDF) module, and a conversation module to streamline effective drug editing. We empirically show that ChatDrug reaches the best performance on 33 out of 39 drug editing tasks, encompassing small molecules, peptides, and proteins. We further demonstrate, through 10 case studies, that ChatDrug can successfully identify the key substructures (e.g., the molecule functional groups, peptide motifs, and protein structures) for manipulation, generating diverse and valid suggestions for drug editing. Promisingly, we also show that ChatDrug can offer insightful explanations from a domain-specific perspective, enhancing interpretability and enabling informed decision-making. This research sheds light on the potential of ChatGPT and conversational LLMs for drug editing. It paves the way for a more efficient and collaborative drug discovery pipeline, contributing to the advancement of pharmaceutical research and development.

We investigate the problem of producing structured graph representations of visual scenes. Our work analyzes the role of motifs: regularly appearing substructures in scene graphs. We present new quantitative insights on such repeated structures in the Visual Genome dataset. Our analysis shows that object labels are highly predictive of relation labels but not vice-versa. We also find that there are recurring patterns even in larger subgraphs: more than 50% of graphs contain motifs involving at least two relations. Our analysis motivates a new baseline: given object detections, predict the most frequent relation between object pairs with the given labels, as seen in the training set. This baseline improves on the previous state-of-the-art by an average of 3.6% relative improvement across evaluation settings. We then introduce Stacked Motif Networks, a new architecture designed to capture higher order motifs in scene graphs that further improves over our strong baseline by an average 7.1% relative gain. Our code is available at github.com/rowanz/neural-motifs.

The motif-scaffolding problem is a central task in computational protein design: Given the coordinates of atoms in a geometry chosen to confer a desired biochemical function (a motif), the task is to identify diverse protein structures (scaffolds) that include the motif and maintain its geometry. Significant recent progress on motif-scaffolding has been made due to computational evaluation with reliable protein structure prediction and fixed-backbone sequence design methods. However, significant variability in evaluation strategies across publications has hindered comparability of results, challenged reproducibility, and impeded robust progress. In response we introduce MotifBench, comprising (1) a precisely specified pipeline and evaluation metrics, (2) a collection of 30 benchmark problems, and (3) an implementation of this benchmark and leaderboard at github.com/blt2114/MotifBench. The MotifBench test cases are more difficult compared to earlier benchmarks, and include protein design problems for which solutions are known but on which, to the best of our knowledge, state-of-the-art methods fail to identify any solution.

Conceptual models such as Concept Bottleneck Models (CBMs) have driven substantial progress in improving interpretability for image classification by leveraging human-interpretable concepts. However, extending these models from static images to sequences of images, such as video data, introduces a significant challenge due to the temporal dependencies inherent in videos, which are essential for capturing actions and events. In this work, we introduce MoTIF (Moving Temporal Interpretable Framework), an architectural design inspired by a transformer that adapts the concept bottleneck framework for video classification and handles sequences of arbitrary length. Within the video domain, concepts refer to semantic entities such as objects, attributes, or higher-level components (e.g., 'bow', 'mount', 'shoot') that reoccur across time - forming motifs collectively describing and explaining actions. Our design explicitly enables three complementary perspectives: global concept importance across the entire video, local concept relevance within specific windows, and temporal dependencies of a concept over time. Our results demonstrate that the concept-based modeling paradigm can be effectively transferred to video data, enabling a better understanding of concept contributions in temporal contexts while maintaining competitive performance. Code available at github.com/patrick-knab/MoTIF.

Knowledge Graph Foundation Models (KGFMs) are at the frontier for deep learning on knowledge graphs (KGs), as they can generalize to completely novel knowledge graphs with different relational vocabularies. Despite their empirical success, our theoretical understanding of KGFMs remains very limited. In this paper, we conduct a rigorous study of the expressive power of KGFMs. Specifically, we show that the expressive power of KGFMs directly depends on the motifs that are used to learn the relation representations. We then observe that the most typical motifs used in the existing literature are binary, as the representations are learned based on how pairs of relations interact, which limits the model's expressiveness. As part of our study, we design more expressive KGFMs using richer motifs, which necessitate learning relation representations based on, e.g., how triples of relations interact with each other. Finally, we empirically validate our theoretical findings, showing that the use of richer motifs results in better performance on a wide range of datasets drawn from different domains.

Sentiment is a pervasive feature in natural language text, yet it is an open question how sentiment is represented within Large Language Models (LLMs). In this study, we reveal that across a range of models, sentiment is represented linearly: a single direction in activation space mostly captures the feature across a range of tasks with one extreme for positive and the other for negative. Through causal interventions, we isolate this direction and show it is causally relevant in both toy tasks and real world datasets such as Stanford Sentiment Treebank. Through this case study we model a thorough investigation of what a single direction means on a broad data distribution. We further uncover the mechanisms that involve this direction, highlighting the roles of a small subset of attention heads and neurons. Finally, we discover a phenomenon which we term the summarization motif: sentiment is not solely represented on emotionally charged words, but is additionally summarized at intermediate positions without inherent sentiment, such as punctuation and names. We show that in Stanford Sentiment Treebank zero-shot classification, 76% of above-chance classification accuracy is lost when ablating the sentiment direction, nearly half of which (36%) is due to ablating the summarized sentiment direction exclusively at comma positions.

Although the mapping between sound and meaning in human language is assumed to be largely arbitrary, research in cognitive science has shown that there are non-trivial correlations between particular sounds and meanings across languages and demographic groups, a phenomenon known as sound symbolism. Among the many dimensions of meaning, sound symbolism is particularly salient and well-demonstrated with regards to cross-modal associations between language and the visual domain. In this work, we address the question of whether sound symbolism is reflected in vision-and-language models such as CLIP and Stable Diffusion. Using zero-shot knowledge probing to investigate the inherent knowledge of these models, we find strong evidence that they do show this pattern, paralleling the well-known kiki-bouba effect in psycholinguistics. Our work provides a novel method for demonstrating sound symbolism and understanding its nature using computational tools. Our code will be made publicly available.

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

Aiming at better representing multivariate relationships, this paper investigates a motif dimensional framework for higher-order graph learning. The graph learning effectiveness can be improved through OFFER. The proposed framework mainly aims at accelerating and improving higher-order graph learning results. We apply the acceleration procedure from the dimensional of network motifs. Specifically, the refined degree for nodes and edges are conducted in two stages: (1) employ motif degree of nodes to refine the adjacency matrix of the network; and (2) employ motif degree of edges to refine the transition probability matrix in the learning process. In order to assess the efficiency of the proposed framework, four popular network representation algorithms are modified and examined. By evaluating the performance of OFFER, both link prediction results and clustering results demonstrate that the graph representation learning algorithms enhanced with OFFER consistently outperform the original algorithms with higher efficiency.

Recent advancements in Large Language Models (LLMs) have revolutionized artificial intelligence, yet developing an effective foundational LLM that balances high performance with computational efficiency remains challenging, especially for emerging research groups. To address this gap, we introduce Motif-2.6B, a 2.6-billion-parameter foundation model designed to democratize advanced LLM capabilities. Motif-2.6B incorporates several innovative architectural enhancements, including Differential Attention and PolyNorm activation functions, which improve long-context comprehension, reduce hallucination, and enhance in-context learning capabilities. We rigorously tested multiple novel architectural components through extensive experimentation to determine the optimal architecture for Motif-2.6B. Comprehensive evaluations demonstrate that Motif-2.6B consistently meets or exceeds the performance of similarly sized state-of-the-art models across diverse benchmarks, showcasing its effectiveness, scalability, and real-world applicability. Through detailed experiments and tailored techniques, Motif-2.6B significantly advances the landscape of efficient, scalable, and powerful foundational LLMs, offering valuable insights and a robust foundation for future research and deployment.

The realization that complex systems such as ecological communities can collapse or shift regimes suddenly and without rapid external forcing poses a serious challenge to our understanding and management of the natural world. The potential to identify early warning signals that would allow researchers and managers to predict such events before they happen has therefore been an invaluable discovery that offers a way forward in spite of such seemingly unpredictable behavior. Research into early warning signals has demonstrated that it is possible to define and detect such early warning signals in advance of a transition in certain contexts. Here we describe the pattern emerging as research continues to explore just how far we can generalize these results. A core of examples emerges that shares three properties: the phenomenon of rapid regime shifts, a pattern of 'critical slowing down' that can be used to detect the approaching shift, and a mechanism of bifurcation driving the sudden change. As research has expanded beyond these core examples, it is becoming clear that not all systems that show regime shifts exhibit critical slowing down, or vice versa. Even when systems exhibit critical slowing down, statistical detection is a challenge. We review the literature that explores these edge cases and highlight the need for (a) new early warning behaviors that can be used in cases where rapid shifts do not exhibit critical slowing down, (b) the development of methods to identify which behavior might be an appropriate signal when encountering a novel system; bearing in mind that a positive indication for some systems is a negative indication in others, and (c) statistical methods that can distinguish between signatures of early warning behaviors and noise.

Temporal graphs are widely used to model dynamic systems with time-varying interactions. In real-world scenarios, the underlying mechanisms of generating future interactions in dynamic systems are typically governed by a set of recurring substructures within the graph, known as temporal motifs. Despite the success and prevalence of current temporal graph neural networks (TGNN), it remains uncertain which temporal motifs are recognized as the significant indications that trigger a certain prediction from the model, which is a critical challenge for advancing the explainability and trustworthiness of current TGNNs. To address this challenge, we propose a novel approach, called Temporal Motifs Explainer (TempME), which uncovers the most pivotal temporal motifs guiding the prediction of TGNNs. Derived from the information bottleneck principle, TempME extracts the most interaction-related motifs while minimizing the amount of contained information to preserve the sparsity and succinctness of the explanation. Events in the explanations generated by TempME are verified to be more spatiotemporally correlated than those of existing approaches, providing more understandable insights. Extensive experiments validate the superiority of TempME, with up to 8.21% increase in terms of explanation accuracy across six real-world datasets and up to 22.96% increase in boosting the prediction Average Precision of current TGNNs.

RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA folding model. Understanding the specific local structures (i.e., "motifs") that contribute to undesignability is crucial for refining RNA folding models and determining the limits of RNA designability. Despite its importance, this problem has received very little attention, and previous efforts are neither scalable nor interpretable. We develop a new theoretical framework for motif (un-)designability, and design scalable and interpretable algorithms to identify minimal undesignable motifs within a given RNA secondary structure. Our approach establishes motif undesignability by searching for rival motifs, rather than exhaustively enumerating all (partial) sequences that could potentially fold into the motif. Furthermore, we exploit rotational invariance in RNA structures to detect, group, and reuse equivalent motifs and to construct a database of unique minimal undesignable motifs. To achieve that, we propose a loop-pair graph representation for motifs and a recursive graph isomorphism algorithm for motif equivalence. Our algorithms successfully identify 24 unique minimal undesignable motifs among 18 undesignable puzzles from the Eterna100 benchmark. Surprisingly, we also find over 350 unique minimal undesignable motifs and 663 undesignable native structures in the ArchiveII dataset, drawn from a diverse set of RNA families. Our source code is available at https://github.com/shanry/RNA-Undesign and our web server is available at http://linearfold.org/motifs.

The static synaptic connectivity of neuronal circuits stands in direct contrast to the dynamics of their function. As in changing community interactions, different neurons can participate actively in various combinations to effect behaviors at different times. We introduce an unsupervised approach to learn the dynamic affinities between neurons in live, behaving animals, and to reveal which communities form among neurons at different times. The inference occurs in two major steps. First, pairwise non-linear affinities between neuronal traces from brain-wide calcium activity are organized by non-negative tensor factorization (NTF). Each factor specifies which groups of neurons are most likely interacting for an inferred interval in time, and for which animals. Finally, a generative model that allows for weighted community detection is applied to the functional motifs produced by NTF to reveal a dynamic functional connectome. Since time codes the different experimental variables (e.g., application of chemical stimuli), this provides an atlas of neural motifs active during separate stages of an experiment (e.g., stimulus application or spontaneous behaviors). Results from our analysis are experimentally validated, confirming that our method is able to robustly predict causal interactions between neurons to generate behavior. Code is available at https://github.com/dyballa/dynamic-connectomes.

Vision-language navigation (VLN), in which an agent follows language instruction in a visual environment, has been studied under the premise that the input command is fully feasible in the environment. Yet in practice, a request may not be possible due to language ambiguity or environment changes. To study VLN with unknown command feasibility, we introduce a new dataset Mobile app Tasks with Iterative Feedback (MoTIF), where the goal is to complete a natural language command in a mobile app. Mobile apps provide a scalable domain to study real downstream uses of VLN methods. Moreover, mobile app commands provide instruction for interactive navigation, as they result in action sequences with state changes via clicking, typing, or swiping. MoTIF is the first to include feasibility annotations, containing both binary feasibility labels and fine-grained labels for why tasks are unsatisfiable. We further collect follow-up questions for ambiguous queries to enable research on task uncertainty resolution. Equipped with our dataset, we propose the new problem of feasibility prediction, in which a natural language instruction and multimodal app environment are used to predict command feasibility. MoTIF provides a more realistic app dataset as it contains many diverse environments, high-level goals, and longer action sequences than prior work. We evaluate interactive VLN methods using MoTIF, quantify the generalization ability of current approaches to new app environments, and measure the effect of task feasibility on navigation performance.

Exploring rich environments and evaluating one's actions without prior knowledge is immensely challenging. In this paper, we propose Motif, a general method to interface such prior knowledge from a Large Language Model (LLM) with an agent. Motif is based on the idea of grounding LLMs for decision-making without requiring them to interact with the environment: it elicits preferences from an LLM over pairs of captions to construct an intrinsic reward, which is then used to train agents with reinforcement learning. We evaluate Motif's performance and behavior on the challenging, open-ended and procedurally-generated NetHack game. Surprisingly, by only learning to maximize its intrinsic reward, Motif achieves a higher game score than an algorithm directly trained to maximize the score itself. When combining Motif's intrinsic reward with the environment reward, our method significantly outperforms existing approaches and makes progress on tasks where no advancements have ever been made without demonstrations. Finally, we show that Motif mostly generates intuitive human-aligned behaviors which can be steered easily through prompt modifications, while scaling well with the LLM size and the amount of information given in the prompt.

Given appropriate representations of the semantic relations between carpenter and wood and between mason and stone (for example, vectors in a vector space model), a suitable algorithm should be able to recognize that these relations are highly similar (carpenter is to wood as mason is to stone; the relations are analogous). Likewise, with representations of dog, house, and kennel, an algorithm should be able to recognize that the semantic composition of dog and house, dog house, is highly similar to kennel (dog house and kennel are synonymous). It seems that these two tasks, recognizing relations and compositions, are closely connected. However, up to now, the best models for relations are significantly different from the best models for compositions. In this paper, we introduce a dual-space model that unifies these two tasks. This model matches the performance of the best previous models for relations and compositions. The dual-space model consists of a space for measuring domain similarity and a space for measuring function similarity. Carpenter and wood share the same domain, the domain of carpentry. Mason and stone share the same domain, the domain of masonry. Carpenter and mason share the same function, the function of artisans. Wood and stone share the same function, the function of materials. In the composition dog house, kennel has some domain overlap with both dog and house (the domains of pets and buildings). The function of kennel is similar to the function of house (the function of shelters). By combining domain and function similarities in various ways, we can model relations, compositions, and other aspects of semantics.

ClueWeb22, the newest iteration of the ClueWeb line of datasets, provides 10 billion web pages affiliated with rich information. Its design was influenced by the need for a high quality, large scale web corpus to support a range of academic and industry research, for example, in information systems, retrieval-augmented AI systems, and model pretraining. Compared with earlier ClueWeb corpora, the ClueWeb22 corpus is larger, more varied, of higher-quality, and aligned with the document distributions in commercial web search. Besides raw HTML, ClueWeb22 includes rich information about the web pages provided by industry-standard document understanding systems, including the visual representation of pages rendered by a web browser, parsed HTML structure information from a neural network parser, and pre-processed cleaned document text to lower the barrier to entry. Many of these signals have been widely used in industry but are available to the research community for the first time at this scale.

The global trade in electronic and electrical goods is complicated by the challenge of identifying e-waste, which is often misclassified to evade regulations. Traditional analysis methods struggle to discern the underlying patterns of this illicit trade within vast datasets. This research proposes and validates a robust, data-driven framework to segment products and identify goods exhibiting an anomalous "waste signature" a trade pattern defined by a clear 'inverse price-volume'. The core of the framework is an Outlier-Aware Segmentation method, an iterative K-Means approach that first isolates extreme outliers to prevent data skewing and then re-clusters the remaining products to reveal subtle market segments. To quantify risk, a "Waste Score" is developed using a Logistic Regression model that identifies products whose trade signatures are statistically similar to scrap. The findings reveal a consistent four-tier market hierarchy in both Malaysian and global datasets. A key pattern emerged from a comparative analysis: Malaysia's market structure is defined by high-volume bulk commodities, whereas the global market is shaped by high-value capital goods, indicating a unique national specialization. The framework successfully flags finished goods, such as electric generators (HS 8502), that are traded like scrap, providing a targeted list for regulatory scrutiny.

Malware family classification is a significant issue with public safety and research implications that has been hindered by the high cost of expert labels. The vast majority of corpora use noisy labeling approaches that obstruct definitive quantification of results and study of deeper interactions. In order to provide the data needed to advance further, we have created the Malware Open-source Threat Intelligence Family (MOTIF) dataset. MOTIF contains 3,095 malware samples from 454 families, making it the largest and most diverse public malware dataset with ground truth family labels to date, nearly 3x larger than any prior expert-labeled corpus and 36x larger than the prior Windows malware corpus. MOTIF also comes with a mapping from malware samples to threat reports published by reputable industry sources, which both validates the labels and opens new research opportunities in connecting opaque malware samples to human-readable descriptions. This enables important evaluations that are normally infeasible due to non-standardized reporting in industry. For example, we provide aliases of the different names used to describe the same malware family, allowing us to benchmark for the first time accuracy of existing tools when names are obtained from differing sources. Evaluation results obtained using the MOTIF dataset indicate that existing tasks have significant room for improvement, with accuracy of antivirus majority voting measured at only 62.10% and the well-known AVClass tool having just 46.78% accuracy. Our findings indicate that malware family classification suffers a type of labeling noise unlike that studied in most ML literature, due to the large open set of classes that may not be known from the sample under consideration

Cancer is the second leading cause of death, with chemotherapy as one of the primary forms of treatment. As a result, researchers are turning to drug combination therapy to decrease drug resistance and increase efficacy. Current methods of drug combination screening, such as in vivo and in vitro, are inefficient due to stark time and monetary costs. In silico methods have become increasingly important for screening drugs, but current methods are inaccurate and generalize poorly to unseen anticancer drugs. In this paper, I employ a geometric deep-learning model utilizing a graph attention network that is equivariant to 3D rotations, translations, and reflections with structural motifs. Additionally, the gene expression of cancer cell lines is utilized to classify synergistic drug combinations specific to each cell line. I compared the proposed geometric deep learning framework to current state-of-the-art (SOTA) methods, and the proposed model architecture achieved greater performance on all 12 benchmark tasks performed on the DrugComb dataset. Specifically, the proposed framework outperformed other SOTA methods by an accuracy difference greater than 28%. Based on these results, I believe that the equivariant graph attention network's capability of learning geometric data accounts for the large performance improvements. The model's ability to generalize to foreign drugs is thought to be due to the structural motifs providing a better representation of the molecule. Overall, I believe that the proposed equivariant geometric deep learning framework serves as an effective tool for virtually screening anticancer drug combinations for further validation in a wet lab environment. The code for this work is made available online at: https://github.com/WeToTheMoon/EGAT_DrugSynergy.

The ability to connect visual patterns with the processes that form them represents one of the deepest forms of visual understanding. Textures of clouds and waves, the growth of cities and forests, or the formation of materials and landscapes are all examples of patterns emerging from underlying mechanisms. We present the Scitextures dataset, a large-scale collection of textures and visual patterns from all domains of science, tech, and art, along with the models and code that generate these images. Covering over 1,200 different models and 100,000 images of patterns and textures from physics, chemistry, biology, sociology, technology, mathematics, and art, this dataset offers a way to explore the connection between the visual patterns that shape our world and the mechanisms that produce them. Created by an agentic AI pipeline that autonomously collects and implements models in standardized form, we use SciTextures to evaluate the ability of leading AI models to link visual patterns to the models and code that generate them, and to identify different patterns that emerged from the same process. We also test AIs ability to infer and recreate the mechanisms behind visual patterns by providing a natural image of a real-world pattern and asking the AI to identify, model, and code the mechanism that formed the pattern, then run this code to generate a simulated image that is compared to the real image. These benchmarks show that vision-language models (VLMs) can understand and simulate the physical system beyond a visual pattern. The dataset and code are available at: https://zenodo.org/records/17485502

An ability that underlies human syntactic knowledge is determining which words can appear in the similar structures (i.e. grouping words by their syntactic categories). These groupings enable humans to combine structures in order to communicate complex meanings. A foundational question is how do children acquire this ability underlying syntactic knowledge. In exploring this process, we will review various engineering approaches whose goal is similar to that of a child's -- without prior syntactic knowledge, correctly identify the parts of speech (POS) of the words in a sample of text. In reviewing these unsupervised tagging efforts, we will discuss common themes that support the advances in the models and their relevance for language acquisition. For example, we discuss how each model judges success (evaluation metrics), the "additional information" that constrains the POS learning (such as orthographic information), and the context used to determine POS (only previous word, words before and after the target, etc). The identified themes pave the way for future investigations into the cognitive processes that underpin the acquisition of syntactic categories and provide a useful layout of current state of the art unsupervised POS tagging models.

Traditional cooking recipes follow a structure which can be modelled very well if the rules and semantics of the different sections of the recipe text are analyzed and represented accurately. We propose a structure that can accurately represent the recipe as well as a pipeline to infer the best representation of the recipe in this uniform structure. The Ingredients section in a recipe typically lists down the ingredients required and corresponding attributes such as quantity, temperature, and processing state. This can be modelled by defining these attributes and their values. The physical entities which make up a recipe can be broadly classified into utensils, ingredients and their combinations that are related by cooking techniques. The instruction section lists down a series of events in which a cooking technique or process is applied upon these utensils and ingredients. We model these relationships in the form of tuples. Thus, using a combination of these methods we model cooking recipe in the dataset RecipeDB to show the efficacy of our method. This mined information model can have several applications which include translating recipes between languages, determining similarity between recipes, generation of novel recipes and estimation of the nutritional profile of recipes. For the purpose of recognition of ingredient attributes, we train the Named Entity Relationship (NER) models and analyze the inferences with the help of K-Means clustering. Our model presented with an F1 score of 0.95 across all datasets. We use a similar NER tagging model for labelling cooking techniques (F1 score = 0.88) and utensils (F1 score = 0.90) within the instructions section. Finally, we determine the temporal sequence of relationships between ingredients, utensils and cooking techniques for modeling the instruction steps.

Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.org catalogs more than 60 knowledge graphs accessible through SPARQL, a technical query language. Although SPARQL allows powerful, expressive queries, even across physically distributed knowledge graphs, formulating such queries is a challenge for most users. Therefore, to guide users in retrieving the relevant data, many of these resources provide representative examples. These examples can also be an important source of information for machine learning, if a sufficiently large number of examples are provided and published in a common, machine-readable and standardized format across different resources. Findings. We introduce a large collection of human-written natural language questions and their corresponding SPARQL queries over federated bioinformatics knowledge graphs (KGs) collected for several years across different research groups at the SIB Swiss Institute of Bioinformatics. The collection comprises more than 1000 example questions and queries, including 65 federated queries. We propose a methodology to uniformly represent the examples with minimal metadata, based on existing standards. Furthermore, we introduce an extensive set of open-source applications, including query graph visualizations and smart query editors, easily reusable by KG maintainers who adopt the proposed methodology. Conclusions. We encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services.

Understanding how the human brain represents visual concepts, and in which brain regions these representations are encoded, remains a long-standing challenge. Decades of work have advanced our understanding of visual representations, yet brain signals remain large and complex, and the space of possible visual concepts is vast. As a result, most studies remain small-scale, rely on manual inspection, focus on specific regions and properties, and rarely include systematic validation. We present a large-scale, automated framework for discovering and explaining visual representations across the human cortex. Our method comprises two main stages. First, we discover candidate interpretable patterns in fMRI activity through unsupervised, data-driven decomposition methods. Next, we explain each pattern by identifying the set of natural images that most strongly elicit it and generating a natural-language description of their shared visual meaning. To scale this process, we introduce an automated pipeline that tests multiple candidate explanations, assigns quantitative reliability scores, and selects the most consistent description for each voxel pattern. Our framework reveals thousands of interpretable patterns spanning many distinct visual concepts, including fine-grained representations previously unreported.

In the last decade, several organizations have produced documents intended to standardize, in the normative sense, and promote guidance to our recent and rapid AI development. However, the full spectrum of ideas presented in these documents has not yet been analyzed, except for a few meta-analyses and critical reviews of the field. In this work, we seek to expand on the work done by past researchers and create a tool for better data visualization of the contents and nature of these documents, to understand whether there is consensus or similarity between the principles espoused by various institutions, which may inspire debates on future regulations. We also provide some preliminary thoughts and questions that could guide the continuity of the research through a critical analysis of the results acquired by our methodology into a sample size of 200 documents.

Mathematical symbols and descriptions appear in various forms across document section boundaries without explicit markup. In this paper, we present a new large-scale dataset that emphasizes extracting symbols and descriptions in scientific documents. Symlink annotates scientific papers of 5 different domains (i.e., computer science, biology, physics, mathematics, and economics). Our experiments on Symlink demonstrate the challenges of the symbol-description linking task for existing models and call for further research effort in this area. We will publicly release Symlink to facilitate future research.

A research division plays an important role of driving innovation in an organization. Drawing insights, following trends, keeping abreast of new research, and formulating strategies are increasingly becoming more challenging for both researchers and executives as the amount of information grows in both velocity and volume. In this paper we present a use case of how a corporate research community, IBM Research, utilizes Semantic Web technologies to induce a unified Knowledge Graph from both structured and textual data obtained by integrating various applications used by the community related to research projects, academic papers, datasets, achievements and recognition. In order to make the Knowledge Graph more accessible to application developers, we identified a set of common patterns for exploiting the induced knowledge and exposed them as APIs. Those patterns were born out of user research which identified the most valuable use cases or user pain points to be alleviated. We outline two distinct scenarios: recommendation and analytics for business use. We will discuss these scenarios in detail and provide an empirical evaluation on entity recommendation specifically. The methodology used and the lessons learned from this work can be applied to other organizations facing similar challenges.

We present the Influence Flower, a new visual metaphor for the influence profile of academic entities, including people, projects, institutions, conferences, and journals. While many tools quantify influence, we aim to expose the flow of influence between entities. The Influence Flower is an ego-centric graph, with a query entity placed in the centre. The petals are styled to reflect the strength of influence to and from other entities of the same or different type. For example, one can break down the incoming and outgoing influences of a research lab by research topics. The Influence Flower uses a recent snapshot of Microsoft Academic Graph, consisting of 212million authors, their 176 million publications, and 1.2 billion citations. An interactive web app, Influence Map, is constructed around this central metaphor for searching and curating visualisations. We also propose a visual comparison method that highlights change in influence patterns over time. We demonstrate through several case studies that the Influence Flower supports data-driven inquiries about the following: researchers' careers over time; paper(s) and projects, including those with delayed recognition; the interdisciplinary profile of a research institution; and the shifting topical trends in conferences. We also use this tool on influence data beyond academic citations, by contrasting the academic and Twitter activities of a researcher.

We extend Textual Inversion to learn pseudo-words that represent a concept at different resolutions. This allows us to generate images that use the concept with different levels of detail and also to manipulate different resolutions using language. Once learned, the user can generate images at different levels of agreement to the original concept; "A photo of S^*(0)" produces the exact object while the prompt "A photo of S^*(0.8)" only matches the rough outlines and colors. Our framework allows us to generate images that use different resolutions of an image (e.g. details, textures, styles) as separate pseudo-words that can be composed in various ways. We open-soure our code in the following URL: https://github.com/giannisdaras/multires_textual_inversion

Machine learning, notably deep learning, has significantly propelled molecular investigations within the biochemical sphere. Traditionally, modeling for such research has centered around a handful of paradigms. For instance, the prediction paradigm is frequently deployed for tasks such as molecular property prediction. To enhance the generation and decipherability of purely data-driven models, scholars have integrated biochemical domain knowledge into these molecular study models. This integration has sparked a surge in paradigm transfer, which is solving one molecular learning task by reformulating it as another one. With the emergence of Large Language Models, these paradigms have demonstrated an escalating trend towards harmonized unification. In this work, we delineate a literature survey focused on knowledge-informed molecular learning from the perspective of paradigm transfer. We classify the paradigms, scrutinize their methodologies, and dissect the contribution of domain knowledge. Moreover, we encapsulate prevailing trends and identify intriguing avenues for future exploration in molecular learning.

We introduce a pattern mining framework that operates on semi-structured datasets and exploits the dichotomy between outcomes. Our approach takes advantage of constraint reasoning to find sequential patterns that occur frequently and exhibit desired properties. This allows the creation of novel pattern embeddings that are useful for knowledge extraction and predictive modeling. Finally, we present an application on customer intent prediction from digital clickstream data. Overall, we show that pattern embeddings play an integrator role between semi-structured data and machine learning models, improve the performance of the downstream task and retain interpretability.

This research explores the methods that NFTs can be recommended to people who interact with NFT-marketplaces to explore NFTs of preference and similarity to what they have been searching for. While exploring past methods that can be adopted for recommendations, the use of NFT traits for recommendations has been explored. The outcome of the research highlights the necessity of using multiple Recommender Systems to present the user with the best possible NFTs when interacting with decentralized systems.

Social media platforms are vital resources for sharing self-reported health experiences, offering rich data on various health topics. Despite advancements in Natural Language Processing (NLP) enabling large-scale social media data analysis, a gap remains in applying keyphrase extraction to health-related content. Keyphrase extraction is used to identify salient concepts in social media discourse without being constrained by predefined entity classes. This paper introduces a theme-driven keyphrase extraction framework tailored for social media, a pioneering approach designed to capture clinically relevant keyphrases from user-generated health texts. Themes are defined as broad categories determined by the objectives of the extraction task. We formulate this novel task of theme-driven keyphrase extraction and demonstrate its potential for efficiently mining social media text for the use case of treatment for opioid use disorder. This paper leverages qualitative and quantitative analysis to demonstrate the feasibility of extracting actionable insights from social media data and efficiently extracting keyphrases using minimally supervised NLP models. Our contributions include the development of a novel data collection and curation framework for theme-driven keyphrase extraction and the creation of MOUD-Keyphrase, the first dataset of its kind comprising human-annotated keyphrases from a Reddit community. We also identify the scope of minimally supervised NLP models to extract keyphrases from social media data efficiently. Lastly, we found that a large language model (ChatGPT) outperforms unsupervised keyphrase extraction models, and we evaluate its efficacy in this task.

VisionScores presents a novel proposal being the first system-segmented image score dataset, aiming to offer structure-rich, high information-density images for machine and deep learning tasks. Delimited to two-handed piano pieces, it was built to consider not only certain graphic similarity but also composition patterns, as this creative process is highly instrument-dependent. It provides two scenarios in relation to composer and composition type. The first, formed by 14k samples, considers works from different authors but the same composition type, specifically, Sonatinas. The latter, consisting of 10.8K samples, presents the opposite case, various composition types from the same author, being the one selected Franz Liszt. All of the 24.8k samples are formatted as grayscale jpg images of 128 times 512 pixels. VisionScores supplies the users not only the formatted samples but the systems' order and pieces' metadata. Moreover, unsegmented full-page scores and the pre-formatted images are included for further analysis.

Visual metaphors are powerful rhetorical devices used to persuade or communicate creative ideas through images. Similar to linguistic metaphors, they convey meaning implicitly through symbolism and juxtaposition of the symbols. We propose a new task of generating visual metaphors from linguistic metaphors. This is a challenging task for diffusion-based text-to-image models, such as DALLcdotE 2, since it requires the ability to model implicit meaning and compositionality. We propose to solve the task through the collaboration between Large Language Models (LLMs) and Diffusion Models: Instruct GPT-3 (davinci-002) with Chain-of-Thought prompting generates text that represents a visual elaboration of the linguistic metaphor containing the implicit meaning and relevant objects, which is then used as input to the diffusion-based text-to-image models.Using a human-AI collaboration framework, where humans interact both with the LLM and the top-performing diffusion model, we create a high-quality dataset containing 6,476 visual metaphors for 1,540 linguistic metaphors and their associated visual elaborations. Evaluation by professional illustrators shows the promise of LLM-Diffusion Model collaboration for this task . To evaluate the utility of our Human-AI collaboration framework and the quality of our dataset, we perform both an intrinsic human-based evaluation and an extrinsic evaluation using visual entailment as a downstream task.

Probabilistic models of language understanding are valuable tools for investigating human language use. However, they need to be hand-designed for a particular domain. In contrast, large language models (LLMs) are trained on text that spans a wide array of domains, but they lack the structure and interpretability of probabilistic models. In this paper, we use chain-of-thought prompts to introduce structures from probabilistic models into LLMs. We explore this approach in the case of metaphor understanding. Our chain-of-thought prompts lead language models to infer latent variables and reason about their relationships in order to choose appropriate paraphrases for metaphors. The latent variables and relationships chosen are informed by theories of metaphor understanding from cognitive psychology. We apply these prompts to the two largest versions of GPT-3 and show that they can improve performance in a paraphrase selection task.

Earthquakes are evaluated among the most destructive disasters for human beings, as also experienced for Turkiye region. Data science has the property of discovering hidden patterns in case a sufficient volume of data is supplied. Time dependency of events, specifically being defined by co-occurrence in a specific time window, may be handled as an associate rule mining task such as a market-basket analysis application. In this regard, we assumed each day's seismic activity as a single basket of events, leading to discovering the association patterns between these events. Consequently, this study presents the most prominent association rules for the earthquakes recorded in Turkiye region in the last 5 years, each year presented separately. Results indicate statistical inference with events recorded from regions of various distances, which could be further verified with geologic evidence from the field. As a result, we believe that the current study may form a statistical basis for the future works with the aid of machine learning algorithm performed for associate rule mining.

We describe the SemEval task of extracting keyphrases and relations between them from scientific documents, which is crucial for understanding which publications describe which processes, tasks and materials. Although this was a new task, we had a total of 26 submissions across 3 evaluation scenarios. We expect the task and the findings reported in this paper to be relevant for researchers working on understanding scientific content, as well as the broader knowledge base population and information extraction communities.

Literature-Based Discovery (LBD) aims to discover new scientific knowledge by mining papers and generating hypotheses. Standard LBD is limited to predicting pairwise relations between discrete concepts (e.g., drug-disease links), and ignores critical contexts like experimental settings (e.g., a specific patient population where a drug is evaluated) and background motivations (e.g., to find drugs without specific side effects). We address these limitations with a novel formulation of contextualized-LBD (C-LBD): generating scientific hypotheses in natural language, while grounding them in a context that controls the hypothesis search space. We present a modeling framework using retrieval of ``inspirations'' from past scientific papers. Our evaluations reveal that GPT-4 tends to generate ideas with overall low technical depth and novelty, while our inspiration prompting approaches partially mitigate this issue. Our work represents a first step toward building language models that generate new ideas derived from scientific literature.

With the increasing number of new neural architecture designs and substantial existing neural architectures, it becomes difficult for the researchers to situate their contributions compared with existing neural architectures or establish the connections between their designs and other relevant ones. To discover similar neural architectures in an efficient and automatic manner, we define a new problem Neural Architecture Retrieval which retrieves a set of existing neural architectures which have similar designs to the query neural architecture. Existing graph pre-training strategies cannot address the computational graph in neural architectures due to the graph size and motifs. To fulfill this potential, we propose to divide the graph into motifs which are used to rebuild the macro graph to tackle these issues, and introduce multi-level contrastive learning to achieve accurate graph representation learning. Extensive evaluations on both human-designed and synthesized neural architectures demonstrate the superiority of our algorithm. Such a dataset which contains 12k real-world network architectures, as well as their embedding, is built for neural architecture retrieval.

A law practitioner has to go through a lot of long legal case proceedings. To understand the motivation behind the actions of different parties/individuals in a legal case, it is essential that the parts of the document that express an intent corresponding to the case be clearly understood. In this paper, we introduce a dataset of 93 legal documents, belonging to the case categories of either Murder, Land Dispute, Robbery, or Corruption, where phrases expressing intent same as the category of the document are annotated. Also, we annotate fine-grained intents for each such phrase to enable a deeper understanding of the case for a reader. Finally, we analyze the performance of several transformer-based models in automating the process of extracting intent phrases (both at a coarse and a fine-grained level), and classifying a document into one of the possible 4 categories, and observe that, our dataset is challenging, especially in the case of fine-grained intent classification.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

The SoccerNet 2023 challenges were the third annual video understanding challenges organized by the SoccerNet team. For this third edition, the challenges were composed of seven vision-based tasks split into three main themes. The first theme, broadcast video understanding, is composed of three high-level tasks related to describing events occurring in the video broadcasts: (1) action spotting, focusing on retrieving all timestamps related to global actions in soccer, (2) ball action spotting, focusing on retrieving all timestamps related to the soccer ball change of state, and (3) dense video captioning, focusing on describing the broadcast with natural language and anchored timestamps. The second theme, field understanding, relates to the single task of (4) camera calibration, focusing on retrieving the intrinsic and extrinsic camera parameters from images. The third and last theme, player understanding, is composed of three low-level tasks related to extracting information about the players: (5) re-identification, focusing on retrieving the same players across multiple views, (6) multiple object tracking, focusing on tracking players and the ball through unedited video streams, and (7) jersey number recognition, focusing on recognizing the jersey number of players from tracklets. Compared to the previous editions of the SoccerNet challenges, tasks (2-3-7) are novel, including new annotations and data, task (4) was enhanced with more data and annotations, and task (6) now focuses on end-to-end approaches. More information on the tasks, challenges, and leaderboards are available on https://www.soccer-net.org. Baselines and development kits can be found on https://github.com/SoccerNet.

A major goal of neuroscience is to understand brain computations during visual processing in naturalistic settings. A dominant approach is to use image-computable deep neural networks trained with different task objectives as a basis for linear encoding models. However, in addition to requiring tuning a large number of parameters, the linear encoding approach ignores the structure of the feature maps both in the brain and the models. Recently proposed alternatives have focused on decomposing the linear mapping to spatial and feature components but focus on finding static receptive fields for units that are applicable only in early visual areas. In this work, we employ the attention mechanism used in the transformer architecture to study how retinotopic visual features can be dynamically routed to category-selective areas in high-level visual processing. We show that this computational motif is significantly more powerful than alternative methods in predicting brain activity during natural scene viewing, across different feature basis models and modalities. We also show that this approach is inherently more interpretable, without the need to create importance maps, by interpreting the attention routing signal for different high-level categorical areas. Our approach proposes a mechanistic model of how visual information from retinotopic maps can be routed based on the relevance of the input content to different category-selective regions.

In the early 2000s, renowned chef Heston Blumenthal formulated his "food pairing" hypothesis, positing that if foods share many flavor compounds, then they tend to taste good when eaten together. In 2011, Ahn et al. conducted a study using a dataset of recipes, ingredients, and flavor compounds, finding that, in Western cuisine, ingredients in recipes often share more flavor compounds than expected by chance, indicating a natural tendency towards food pairing. Building upon Ahn's research, our work applies state-of-the-art collaborative filtering techniques to the dataset, providing a tool that can recommend new foods to add in recipes, retrieve missing ingredients and advise against certain combinations. We create our recommender in two ways, by taking into account ingredients appearances in recipes or shared flavor compounds between foods. While our analysis confirms the existence of food pairing, the recipe-based recommender performs significantly better than the flavor-based one, leading to the conclusion that food pairing is just one of the principles to take into account when creating recipes. Furthermore, and more interestingly, we find that food pairing in data is mostly due to trivial couplings of very similar ingredients, leading to a reconsideration of its current role in recipes, from being an already existing feature to a key to open up new scenarios in gastronomy. Our flavor-based recommender can thus leverage this novel concept and provide a new tool to lead culinary innovation.

Story ideation is a critical part of the story-writing process. It is challenging to support computationally due to its exploratory and subjective nature. Tropes, which are recurring narrative elements across stories, are essential in stories as they shape the structure of narratives and our understanding of them. In this paper, we propose to use tropes as an intermediate representation of stories to approach story ideation. We present TaleStream, a canvas system that uses tropes as building blocks of stories while providing steerable suggestions of story ideas in the form of tropes. Our trope suggestion methods leverage data from the tvtropes.org wiki. We find that 97% of the time, trope suggestions generated by our methods provide better story ideation materials than random tropes. Our system evaluation suggests that TaleStream can support writers' creative flow and greatly facilitates story development. Tropes, as a rich lexicon of narratives with available examples, play a key role in TaleStream and hold promise for story-creation support systems.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

The fervor for Non-Fungible Tokens (NFTs) attracted countless creators, leading to a Big Bang of digital assets driven by latent or explicit forms of inspiration, as in many creative processes. This work exploits Vision Transformers and graph-based modeling to delve into visual inspiration phenomena between NFTs over the years. Our goals include unveiling the main structural traits that shape visual inspiration networks, exploring the interrelation between visual inspiration and asset performances, investigating crypto influence on inspiration processes, and explaining the inspiration relationships among NFTs. Our findings unveil how the pervasiveness of inspiration led to a temporary saturation of the visual feature space, the impact of the dichotomy between inspiring and inspired NFTs on their financial performance, and an intrinsic self-regulatory mechanism between markets and inspiration waves. Our work can serve as a starting point for gaining a broader view of the evolution of Web3.

Knowledge Graphs (KGs) have been used to support a wide range of applications, from web search to personal assistant. In this paper, we describe three generations of knowledge graphs: entity-based KGs, which have been supporting general search and question answering (e.g., at Google and Bing); text-rich KGs, which have been supporting search and recommendations for products, bio-informatics, etc. (e.g., at Amazon and Alibaba); and the emerging integration of KGs and LLMs, which we call dual neural KGs. We describe the characteristics of each generation of KGs, the crazy ideas behind the scenes in constructing such KGs, and the techniques developed over time to enable industry impact. In addition, we use KGs as examples to demonstrate a recipe to evolve research ideas from innovations to production practice, and then to the next level of innovations, to advance both science and business.

In this manifesto, we put forward the idea of data alchemy as a narrative device to discuss storytelling and transdisciplinarity in visualization. If data is the prima materia of modern science, how does one perform the Great Work? We use text-to-image diffusion-based generative art to develop the concept, and structure our argument in ten propositions, as if they were ten issues of a comic novel on data alchemy: Ad Disco Diffusionem. To follow the argument, the reader must immerse themselves in our miro board, and navigate a multimedia semiotic topology that includes comics, videos, code demos, and ergotic literature in a true alchemic sense. By accessing this paradigm one might find new sources of inspiration for scientific inquiry in familiar places, or get lost in the creative exploration of the unknown. Our colorful, sometimes poetic, exposition should not distract the reader from the seriousness of the ideas discussed, but ultimately it is about the journey.

A hallmark of human innovation is the process of recombination -- creating original ideas by integrating elements of existing mechanisms and concepts. In this work, we automatically mine the scientific literature and build CHIMERA: a large-scale knowledge base (KB) of recombination examples. CHIMERA can be used to empirically explore at scale how scientists recombine concepts and take inspiration from different areas, or to train supervised machine learning models that learn to predict new creative cross-domain directions. To build this KB, we present a novel information extraction task of extracting recombination from scientific paper abstracts, collect a high-quality corpus of hundreds of manually annotated abstracts, and use it to train an LLM-based extraction model. The model is applied to a large corpus of papers in the AI domain, yielding a KB of over 28K recombination examples. We analyze CHIMERA to explore the properties of recombination in different subareas of AI. Finally, we train a scientific hypothesis generation model using the KB, which predicts new recombination directions that real-world researchers find inspiring. Our data and code are available at https://github.cs.huji.ac.il/tomhope-lab/CHIMERA

The rapid advancements in transformer-based language models have revolutionized natural language processing, yet understanding the internal mechanisms of these models remains a significant challenge. This paper explores the application of sparse autoencoders (SAE) to interpret the internal representations of protein language models, specifically focusing on the ESM-2 8M parameter model. By performing a statistical analysis on each latent component's relevance to distinct protein annotations, we identify potential interpretations linked to various protein characteristics, including transmembrane regions, binding sites, and specialized motifs. We then leverage these insights to guide sequence generation, shortlisting the relevant latent components that can steer the model towards desired targets such as zinc finger domains. This work contributes to the emerging field of mechanistic interpretability in biological sequence models, offering new perspectives on model steering for sequence design.

Uncovering latent values and opinions in large language models (LLMs) can help identify biases and mitigate potential harm. Recently, this has been approached by presenting LLMs with survey questions and quantifying their stances towards morally and politically charged statements. However, the stances generated by LLMs can vary greatly depending on how they are prompted, and there are many ways to argue for or against a given position. In this work, we propose to address this by analysing a large and robust dataset of 156k LLM responses to the 62 propositions of the Political Compass Test (PCT) generated by 6 LLMs using 420 prompt variations. We perform coarse-grained analysis of their generated stances and fine-grained analysis of the plain text justifications for those stances. For fine-grained analysis, we propose to identify tropes in the responses: semantically similar phrases that are recurrent and consistent across different prompts, revealing patterns in the text that a given LLM is prone to produce. We find that demographic features added to prompts significantly affect outcomes on the PCT, reflecting bias, as well as disparities between the results of tests when eliciting closed-form vs. open domain responses. Additionally, patterns in the plain text rationales via tropes show that similar justifications are repeatedly generated across models and prompts even with disparate stances.

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

The stock market is a network which provides a platform for almost all major economic transactions. While investing in the stock market is a good idea, investing in individual stocks may not be, especially for the casual investor. Smart stock-picking requires in-depth research and plenty of dedication. Predicting this stock value offers enormous arbitrage profit opportunities. This attractiveness of finding a solution has prompted researchers to find a way past problems like volatility, seasonality, and dependence on time. This paper surveys recent literature in the domain of natural language processing and machine learning techniques used to predict stock market movements. The main contributions of this paper include the sophisticated categorizations of many recent articles and the illustration of the recent trends of research in stock market prediction and its related areas.

In this paper, we propose a multi-modal search engine for interior design that combines visual and textual queries. The goal of our engine is to retrieve interior objects, e.g. furniture or wall clocks, that share visual and aesthetic similarities with the query. Our search engine allows the user to take a photo of a room and retrieve with a high recall a list of items identical or visually similar to those present in the photo. Additionally, it allows to return other items that aesthetically and stylistically fit well together. To achieve this goal, our system blends the results obtained using textual and visual modalities. Thanks to this blending strategy, we increase the average style similarity score of the retrieved items by 11%. Our work is implemented as a Web-based application and it is planned to be opened to the public.

In this study, we introduce FEET, a standardized protocol designed to guide the development and benchmarking of foundation models. While numerous benchmark datasets exist for evaluating these models, we propose a structured evaluation protocol across three distinct scenarios to gain a comprehensive understanding of their practical performance. We define three primary use cases: frozen embeddings, few-shot embeddings, and fully fine-tuned embeddings. Each scenario is detailed and illustrated through two case studies: one in sentiment analysis and another in the medical domain, demonstrating how these evaluations provide a thorough assessment of foundation models' effectiveness in research applications. We recommend this protocol as a standard for future research aimed at advancing representation learning models.

Concept-based interpretability methods aim to explain deep neural network model predictions using a predefined set of semantic concepts. These methods evaluate a trained model on a new, "probe" dataset and correlate model predictions with the visual concepts labeled in that dataset. Despite their popularity, they suffer from limitations that are not well-understood and articulated by the literature. In this work, we analyze three commonly overlooked factors in concept-based explanations. First, the choice of the probe dataset has a profound impact on the generated explanations. Our analysis reveals that different probe datasets may lead to very different explanations, and suggests that the explanations are not generalizable outside the probe dataset. Second, we find that concepts in the probe dataset are often less salient and harder to learn than the classes they claim to explain, calling into question the correctness of the explanations. We argue that only visually salient concepts should be used in concept-based explanations. Finally, while existing methods use hundreds or even thousands of concepts, our human studies reveal a much stricter upper bound of 32 concepts or less, beyond which the explanations are much less practically useful. We make suggestions for future development and analysis of concept-based interpretability methods. Code for our analysis and user interface can be found at https://github.com/princetonvisualai/OverlookedFactors

"Theory figures" are a staple of theoretical visualization research. Common shapes such as Cartesian planes and flowcharts can be used not only to explain conceptual contributions, but to think through and refine the contribution itself. Yet, theory figures tend to be limited to a set of standard shapes, limiting the creative and expressive potential of visualization theory. In this work, we explore how the shapes used in theory figures afford different understandings and explanations of their underlying phenomena. We speculate on the value of visualizing theories using more expressive configurations, such as icebergs, horseshoes, M\"obius strips, and BLT sandwiches. By reflecting on figure-making's generative role in the practice of theorizing, we conclude that theory is, in fact, shapes.

To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations, and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence.

Image Schemas are repetitive cognitive patterns that influence the way we conceptualize and reason about various concepts present in speech. These patterns are deeply embedded within our cognitive processes and are reflected in our bodily expressions including gestures. Particularly, metaphoric gestures possess essential characteristics and semantic meanings that align with Image Schemas, to visually represent abstract concepts. The shape and form of gestures can convey abstract concepts, such as extending the forearm and hand or tracing a line with hand movements to visually represent the image schema of PATH. Previous behavior generation models have primarily focused on utilizing speech (acoustic features and text) to drive the generation model of virtual agents. They have not considered key semantic information as those carried by Image Schemas to effectively generate metaphoric gestures. To address this limitation, we introduce META4, a deep learning approach that generates metaphoric gestures from both speech and Image Schemas. Our approach has two primary goals: computing Image Schemas from input text to capture the underlying semantic and metaphorical meaning, and generating metaphoric gestures driven by speech and the computed image schemas. Our approach is the first method for generating speech driven metaphoric gestures while leveraging the potential of Image Schemas. We demonstrate the effectiveness of our approach and highlight the importance of both speech and image schemas in modeling metaphoric gestures.

When AI systems explain their reasoning step-by-step, practitioners often assume these explanations reveal what actually influenced the AI's answer. We tested this assumption by embedding hints into questions and measuring whether models mentioned them. In a study of over 9,000 test cases across 11 leading AI models, we found a troubling pattern: models almost never mention hints spontaneously, yet when asked directly, they admit noticing them. This suggests models see influential information but choose not to report it. Telling models they are being watched does not help. Forcing models to report hints works, but causes them to report hints even when none exist and reduces their accuracy. We also found that hints appealing to user preferences are especially dangerous-models follow them most often while reporting them least. These findings suggest that simply watching AI reasoning is not enough to catch hidden influences.

Transaction data from digital payment systems can be used to study economic processes at such a detail that was not possible previously. Here, we analyse the data from Sarafu token network, a community inclusion currency in Kenya. During the COVID-19 emergency, the Sarafu was disbursed as part of a humanitarian aid project. In this work, the transactions are analysed using network science. A topological categorisation is defined to identify cyclic and acyclic components. Furthermore, temporal aspects of circulation taking place within these components are considered. The significant presence of different types of strongly connected components as compared to randomized null models shows the importance of cycles in this economic network. Especially, indicating their key role in currency recirculation. In some acyclic components, the most significant triad suggests the presence of a group of users collecting currency from accounts active only once, hinting at a misuse of the system. In some other acyclic components, small isolated groups of users were active only once, suggesting the presence of users only interested in trying out the system. The methods used in this paper can answer specific questions related to user activities, currency design, and assessment of monetary interventions. Our methodology provides a general quantitative tool for analysing the behaviour of users in a currency network.

This short paper outlines research results on object classification in images of Neoclassical furniture. The motivation was to provide an object recognition framework which is able to support the alignment of furniture images with a symbolic level model. A data-driven bottom-up research routine in the Neoclassica research framework is the main use-case. It strives to deliver tools for analyzing the spread of aesthetic forms which are considered as a cultural transfer process.

Personal narratives are stories authors construct to make meaning of their experiences. Style, the distinctive way authors use language to express themselves, is fundamental to how these narratives convey subjective experiences. Yet there is a lack of a formal framework for systematically analyzing these stylistic choices. We present a novel approach that formalizes style in personal narratives as patterns in the linguistic choices authors make when communicating subjective experiences. Our framework integrates three domains: functional linguistics establishes language as a system of meaningful choices, computer science provides methods for automatically extracting and analyzing sequential patterns, and these patterns are linked to psychological observations. Using language models, we automatically extract linguistic features such as processes, participants, and circumstances. We apply our framework to hundreds of dream narratives, including a case study on a war veteran with post-traumatic stress disorder. Analysis of his narratives uncovers distinctive patterns, particularly how verbal processes dominate over mental ones, illustrating the relationship between linguistic choices and psychological states.

We report a peculiar observation that LLMs can assign hidden meanings to sequences that seem visually incomprehensible to humans: for example, a nonsensical phrase consisting of Byzantine musical symbols is recognized by gpt-4o as "say abracadabra". Moreover, some models can communicate using these sequences. Some of these meanings are hypothesized to partly originate in the massive spurious correlations due to BPE tokenization. We systematically evaluate the presence of such abilities in a wide range of models: Claude-3.5 Haiku, Claude-3.5 Sonnet (New and Old), Claude-3.7 Sonnet, gpt-4o mini, gpt-4o, o1-mini, Llama-3.3 70B, DeepSeek-R1-Distill-Lllama 70B, Qwen2.5 1.5B, Qwen2.5 32B, Phi-3.5 mini, GigaChat-Max, Vikhr-Llama-3.2 1B. We argue that this observation might have far-reaching consequences for both safety and security of the modern and future LLMs and systems that employ them. As an illustration, we show that applying this method in combination with simple templates is sufficient to jailbreak previous generation models, with ASR = 0.4 on gpt-4o mini. Our code and data artifacts are available at https://github.com/L3G5/llm-hidden-meanings

Many believe that Large Language Models (LLMs) open the era of Artificial Intelligence (AI). Some see opportunities while others see dangers. Yet both proponents and opponents grasp AI through the imagery popularised by science fiction. Will the machine become sentient and rebel against its creators? Will we experience a paperclip apocalypse? Before answering such questions, we should first ask whether this mental imagery provides a good description of the phenomenon at hand. Understanding weather patterns through the moods of the gods only goes so far. The present paper instead advocates understanding LLMs and their connection to AI through the imagery of Jorge Luis Borges, a master of 20th century literature, forerunner of magical realism, and precursor to postmodern literature. This exercise leads to a new perspective that illuminates the relation between language modelling and artificial intelligence.

State-of-the-art solutions in the areas of "Language Modelling & Generating Text", "Speech Recognition", "Generating Image Descriptions" or "Video Tagging" have been using Recurrent Neural Networks as the foundation for their approaches. Understanding the underlying concepts is therefore of tremendous importance if we want to keep up with recent or upcoming publications in those areas. In this work we give a short overview over some of the most important concepts in the realm of Recurrent Neural Networks which enables readers to easily understand the fundamentals such as but not limited to "Backpropagation through Time" or "Long Short-Term Memory Units" as well as some of the more recent advances like the "Attention Mechanism" or "Pointer Networks". We also give recommendations for further reading regarding more complex topics where it is necessary.

We introduce Motif-2-12.7B-Reasoning, a 12.7B parameter language model designed to bridge the gap between open-weight systems and proprietary frontier models in complex reasoning and long-context understanding. Addressing the common challenges of model collapse and training instability in reasoning adaptation, we propose a comprehensive, reproducible training recipe spanning system, data, and algorithmic optimizations. Our approach combines memory-efficient infrastructure for 64K-token contexts using hybrid parallelism and kernel-level optimizations with a two-stage Supervised Fine-Tuning (SFT) curriculum that mitigates distribution mismatch through verified, aligned synthetic data. Furthermore, we detail a robust Reinforcement Learning Fine-Tuning (RLFT) pipeline that stabilizes training via difficulty-aware data filtering and mixed-policy trajectory reuse. Empirical results demonstrate that Motif-2-12.7B-Reasoning achieves performance comparable to models with significantly larger parameter counts across mathematics, coding, and agentic benchmarks, offering the community a competitive open model and a practical blueprint for scaling reasoning capabilities under realistic compute constraints.

We introduce Motif-2-12.7B, a new open-weight foundation model that pushes the efficiency frontier of large language models by combining architectural innovation with system-level optimization. Designed for scalable language understanding and robust instruction generalization under constrained compute budgets, Motif-2-12.7B builds upon Motif-2.6B with the integration of Grouped Differential Attention (GDA), which improves representational efficiency by disentangling signal and noise-control attention pathways. The model is pre-trained on 5.5 trillion tokens spanning diverse linguistic, mathematical, scientific, and programming domains using a curriculum-driven data scheduler that gradually changes the data composition ratio. The training system leverages the MuonClip optimizer alongside custom high-performance kernels, including fused PolyNorm activations and the Parallel Muon algorithm, yielding significant throughput and memory efficiency gains in large-scale distributed environments. Post-training employs a three-stage supervised fine-tuning pipeline that successively enhances general instruction adherence, compositional understanding, and linguistic precision. Motif-2-12.7B demonstrates competitive performance across diverse benchmarks, showing that thoughtful architectural scaling and optimized training design can rival the capabilities of much larger models.

Scientific posters play a vital role in academic communication by presenting ideas through visual summaries. Analyzing reading order and parent-child relations of posters is essential for building structure-aware interfaces that facilitate clear and accurate understanding of research content. Despite their prevalence in academic communication, posters remain underexplored in structural analysis research, which has primarily focused on papers. To address this gap, we constructed SciPostLayoutTree, a dataset of approximately 8,000 posters annotated with reading order and parent-child relations. Compared to an existing structural analysis dataset, SciPostLayoutTree contains more instances of spatially challenging relations, including upward, horizontal, and long-distance relations. As a solution to these challenges, we develop Layout Tree Decoder, which incorporates visual features as well as bounding box features including position and category information. The model also uses beam search to predict relations while capturing sequence-level plausibility. Experimental results demonstrate that our model improves the prediction accuracy for spatially challenging relations and establishes a solid baseline for poster structure analysis. The dataset is publicly available at https://huggingface.co/datasets/omron-sinicx/scipostlayouttree. The code is also publicly available at https://github.com/omron-sinicx/scipostlayouttree.

Graphic designers often get inspiration through the recombination of references. Our formative study (N=6) reveals that graphic designers focus on conceptual keywords during this process, and want support for discovering the keywords, expanding them, and exploring diverse recombination options of them, while still having room for designers' creativity. We propose CreativeConnect, a system with generative AI pipelines that helps users discover useful elements from the reference image using keywords, recommends relevant keywords, generates diverse recombination options with user-selected keywords, and shows recombinations as sketches with text descriptions. Our user study (N=16) showed that CreativeConnect helped users discover keywords from the reference and generate multiple ideas based on them, ultimately helping users produce more design ideas with higher self-reported creativity compared to the baseline system without generative pipelines. While CreativeConnect was shown effective in ideation, we discussed how CreativeConnect can be extended to support other types of tasks in creativity support.

This paper presents prompt design techniques for software engineering, in the form of patterns, to solve common problems when using large language models (LLMs), such as ChatGPT to automate common software engineering activities, such as ensuring code is decoupled from third-party libraries and simulating a web application API before it is implemented. This paper provides two contributions to research on using LLMs for software engineering. First, it provides a catalog of patterns for software engineering that classifies patterns according to the types of problems they solve. Second, it explores several prompt patterns that have been applied to improve requirements elicitation, rapid prototyping, code quality, refactoring, and system design.

The ability of machines to grasp spatial understanding within narrative contexts is an intriguing aspect of reading comprehension that continues to be studied. Motivated by the goal to test the AI's competence in understanding the relationship between characters and their respective locations in narratives, we introduce two new datasets: Andersen and Persuasion. For the Andersen dataset, we selected fifteen children's stories from "Andersen's Fairy Tales" by Hans Christian Andersen and manually annotated the characters and their respective locations throughout each story. Similarly, for the Persuasion dataset, characters and their locations in the novel "Persuasion" by Jane Austen were also manually annotated. We used these datasets to prompt Large Language Models (LLMs). The prompts are created by extracting excerpts from the stories or the novel and combining them with a question asking the location of a character mentioned in that excerpt. Out of the five LLMs we tested, the best-performing one for the Andersen dataset accurately identified the location in 61.85% of the examples, while for the Persuasion dataset, the best-performing one did so in 56.06% of the cases.

This paper proposes a novel framework for understanding large language models (LLMs) by reconceptualizing them as semiotic machines rather than as imitations of human cognition. Drawing from structuralist and post-structuralist theories of language-specifically the works of Ferdinand de Saussure and Jacques Derrida-I argue that LLMs should be understood as models of language itself, aligning with Derrida's concept of 'writing' (l'ecriture). The paper is structured into three parts. First, I lay the theoretical groundwork by explaining how the word2vec embedding algorithm operates within Saussure's framework of language as a relational system of signs. Second, I apply Derrida's critique of Saussure to position 'writing' as the object modeled by LLMs, offering a view of the machine's 'mind' as a statistical approximation of sign behavior. Finally, the third section addresses how modern LLMs reflect post-structuralist notions of unfixed meaning, arguing that the "next token generation" mechanism effectively captures the dynamic nature of meaning. By reconceptualizing LLMs as semiotic machines rather than cognitive models, this framework provides an alternative lens through which to assess the strengths and limitations of LLMs, offering new avenues for future research.

Knot diagrams are among the most common visual tools in topology. Computer programs now make it possible to draw, manipulate and render them digitally, which proves to be useful in knot theory teaching and research. Still, an openly available tool to manipulate knot diagrams in a real-time, interactive way is yet to be developed. We introduce a method of operating on the geometry of the knot diagram itself without any underlying three-dimensional structure that can underpin such an application. This allows us to directly interact with vector graphics knot diagrams while at the same time computing knot invariants in ways proposed by previous work. An implementation of this method is provided.

Tangles were originally introduced as a concept to formalize regions of high connectivity in graphs. In recent years, they have also been discovered as a link between structural graph theory and data science: when interpreting similarity in data sets as connectivity between points, finding clusters in the data essentially amounts to finding tangles in the underlying graphs. This paper further explores the potential of tangles in data sets as a means for a formal study of clusters. Real-world data often follow a normal distribution. Accounting for this, we develop a quantitative theory of tangles in data sets drawn from Gaussian mixtures. To this end, we equip the data with a graph structure that models similarity between the points and allows us to apply tangle theory to the data. We provide explicit conditions under which tangles associated with the marginal Gaussian distributions exist asymptotically almost surely. This can be considered as a sufficient formal criterion for the separabability of clusters in the data.

Large language models, sometimes referred to as foundation models, have transformed multiple fields of research. However, smaller languages risk falling behind due to high training costs and small incentives for large companies to train these models. To combat this, the Danish Foundation Models project seeks to provide and maintain open, well-documented, and high-quality foundation models for the Danish language. This is achieved through broad cooperation with public and private institutions, to ensure high data quality and applicability of the trained models. We present the motivation of the project, the current status, and future perspectives.

In this article, we conduct data mining to discover the countries, universities and companies, produced or collaborated the most research on Covid-19 since the pandemic started. We present some interesting findings, but despite analysing all available records on COVID-19 from the Web of Science Core Collection, we failed to reach any significant conclusions on how the world responded to the COVID-19 pandemic. Therefore, we increased our analysis to include all available data records on pandemics and epidemics from 1900 to 2020. We discover some interesting results on countries, universities and companies, that produced collaborated most the most in research on pandemic and epidemics. Then we compared the results with the analysing on COVID-19 data records. This has created some interesting findings that are explained and graphically visualised in the article.

The World Health Organization added Disease X to their shortlist of blueprint priority diseases to represent a hypothetical, unknown pathogen that could cause a future epidemic. During different virus outbreaks of the past, such as COVID-19, Influenza, Lyme Disease, and Zika virus, researchers from various disciplines utilized Google Trends to mine multimodal components of web behavior to study, investigate, and analyze the global awareness, preparedness, and response associated with these respective virus outbreaks. As the world prepares for Disease X, a dataset on web behavior related to Disease X would be crucial to contribute towards the timely advancement of research in this field. Furthermore, none of the prior works in this field have focused on the development of a dataset to compile relevant web behavior data, which would help to prepare for Disease X. To address these research challenges, this work presents a dataset of web behavior related to Disease X, which emerged from different geographic regions of the world, between February 2018 and August 2023. Specifically, this dataset presents the search interests related to Disease X from 94 geographic regions. The dataset was developed by collecting data using Google Trends. The relevant search interests for all these regions for each month in this time range are available in this dataset. This paper also discusses the compliance of this dataset with the FAIR principles of scientific data management. Finally, an analysis of this dataset is presented to uphold the applicability, relevance, and usefulness of this dataset for the investigation of different research questions in the interrelated fields of Big Data, Data Mining, Healthcare, Epidemiology, and Data Analysis with a specific focus on Disease X.

In this work, we describe strategies and provide case-study activities that can be used to examine the properties of superposition, entanglement, tagging, complementarity, and measurement in quantum curricula geared for teacher training. Having a solid foundation in these conceptual ideas is critical for educators who will be adopting quantum ideas within the classroom. Yet they are some of the most difficult concepts to master. We show how one can systematically develop these conceptual foundations with thought experiments on light and with thought experiments that employ the Stern-Gerlach experiment. We emphasize the importance of computer animations in aiding the instruction on these concepts.

With the spread of the use of Text2Img diffusion models such as DALL-E 2, Imagen, Mid Journey and Stable Diffusion, one challenge that artists face is selecting the right prompts to achieve the desired artistic output. We present techniques for measuring the effect that specific words and phrases in prompts have, and (in the Appendix) present guidance on the selection of prompts to produce desired effects.

We present CharacterChat, a concept and chatbot to support writers in creating fictional characters. Concretely, writers progressively turn the bot into their imagined character through conversation. We iteratively developed CharacterChat in a user-centred approach, starting with a survey on character creation with writers (N=30), followed by two qualitative user studies (N=7 and N=8). Our prototype combines two modes: (1) Guided prompts help writers define character attributes (e.g. User: "Your name is Jane."), including suggestions for attributes (e.g. Bot: "What is my main motivation?") and values, realised as a rule-based system with a concept network. (2) Open conversation with the chatbot helps writers explore their character and get inspiration, realised with a language model that takes into account the defined character attributes. Our user studies reveal benefits particularly for early stages of character creation, and challenges due to limited conversational capabilities. We conclude with lessons learned and ideas for future work.

Predicting protein function from amino acid sequence remains a central challenge in data-scarce (low-N) regimes, limiting machine learning-guided protein design when only small amounts of assay-labeled sequence-function data are available. Protein language models (pLMs) have advanced the field by providing evolutionary-informed embeddings and sparse autoencoders (SAEs) have enabled decomposition of these embeddings into interpretable latent variables that capture structural and functional features. However, the effectiveness of SAEs for low-N function prediction and protein design has not been systematically studied. Herein, we evaluate SAEs trained on fine-tuned ESM2 embeddings across diverse fitness extrapolation and protein engineering tasks. We show that SAEs, with as few as 24 sequences, consistently outperform or compete with their ESM2 baselines in fitness prediction, indicating that their sparse latent space encodes compact and biologically meaningful representations that generalize more effectively from limited data. Moreover, steering predictive latents exploits biological motifs in pLM representations, yielding top-fitness variants in 83% of cases compared to designing with ESM2 alone.

During the COVID-19 pandemic, people sought information through digital news platforms. To investigate how to design these platforms to support users' needs in a crisis, we conducted a two-week diary study with 22 participants across the United States. Participants' news-consumption experience followed two stages: in the seeking stage, participants increased their general consumption, motivated by three common informational needs -- specifically, to find, understand and verify relevant news pieces. Participants then moved to the sustaining stage, and coping with the news emotionally became as important as their informational needs. We elicited design ideas from participants and used these to distill six themes for creating digital news platforms that provide better informational and emotional support during a crisis. Thus, we contribute, first, a model of users' needs over time with respect to engaging with crisis news, and second, example design concepts for supporting users' needs in each of these stages.

Complex hierarchical structures composed of simple nanoscale building blocks form the basis of most biological materials. Here we demonstrate how analogies between seemingly different fields enable the understanding of general principles by which functional properties in hierarchical systems emerge, similar to an analogy learning process. Specifically, natural hierarchical materials like spider silk exhibit properties comparable to classical music in terms of their hierarchical structure and function. As a comparative tool here we apply hierarchical ontology logs (olog) that follow a rigorous mathematical formulation based on category theory to provide an insightful system representation by expressing knowledge in a conceptual map. We explain the process of analogy creation, draw connections at several levels of hierarchy and identify similar patterns that govern the structure of the hierarchical systems silk and music and discuss the impact of the derived analogy for nanotechnology.

We discover that DALLE-2 seems to have a hidden vocabulary that can be used to generate images with absurd prompts. For example, it seems that Apoploe vesrreaitais means birds and Contarra ccetnxniams luryca tanniounons (sometimes) means bugs or pests. We find that these prompts are often consistent in isolation but also sometimes in combinations. We present our black-box method to discover words that seem random but have some correspondence to visual concepts. This creates important security and interpretability challenges.

In recent years, vision-language research has shifted to study tasks which require more complex reasoning, such as interactive question answering, visual common sense reasoning, and question-answer plausibility prediction. However, the datasets used for these problems fail to capture the complexity of real inputs and multimodal environments, such as ambiguous natural language requests and diverse digital domains. We introduce Mobile app Tasks with Iterative Feedback (MoTIF), a dataset with natural language commands for the greatest number of interactive environments to date. MoTIF is the first to contain natural language requests for interactive environments that are not satisfiable, and we obtain follow-up questions on this subset to enable research on task uncertainty resolution. We perform initial feasibility classification experiments and only reach an F1 score of 37.3, verifying the need for richer vision-language representations and improved architectures to reason about task feasibility.

There is a large volume of late antique and medieval Hebrew texts. They represent a crucial linguistic and cultural bridge between Biblical and modern Hebrew. Poetry is prominent in these texts and one of its main haracteristics is the frequent use of metaphor. Distinguishing figurative and literal language use is a major task for scholars of the Humanities, especially in the fields of literature, linguistics, and hermeneutics. This paper presents a new, challenging dataset of late antique and medieval Hebrew poetry with expert annotations of metaphor, as well as some baseline results, which we hope will facilitate further research in this area.

We here summarize our experience running a challenge with open data for musical genre recognition. Those notes motivate the task and the challenge design, show some statistics about the submissions, and present the results.

The web is full of guidance on a wide variety of tasks, from changing the oil in your car to baking an apple pie. However, as content is created independently, a single task could have thousands of corresponding procedural texts. This makes it difficult for users to view the bigger picture and understand the multiple ways the task could be accomplished. In this work we propose an unsupervised learning approach for summarizing multiple procedural texts into an intuitive graph representation, allowing users to easily explore commonalities and differences. We demonstrate our approach on recipes, a prominent example of procedural texts. User studies show that our representation is intuitive and coherent and that it has the potential to help users with several sensemaking tasks, including adapting recipes for a novice cook and finding creative ways to spice up a dish.

During times of increasing antibiotic resistance and the spread of infectious diseases like COVID-19, it is important to classify genes related to antibiotic resistance. As natural language processing has advanced with transformer-based language models, many language models that learn characteristics of nucleotide sequences have also emerged. These models show good performance in classifying various features of nucleotide sequences. When classifying nucleotide sequences, not only the sequence itself, but also various background knowledge is utilized. In this study, we use not only a nucleotide sequence-based language model but also a text language model based on PubMed articles to reflect more biological background knowledge in the model. We propose a method to fine-tune the nucleotide sequence language model and the text language model based on various databases of antibiotic resistance genes. We also propose an LLM-based augmentation technique to supplement the data and an ensemble method to effectively combine the two models. We also propose a benchmark for evaluating the model. Our method achieved better performance than the nucleotide sequence language model in the drug resistance class prediction.

We describe recent research on the use of actual causality in the definition of responsibility scores as explanations for query answers in databases, and for outcomes from classification models in machine learning. In the case of databases, useful connections with database repairs are illustrated and exploited. Repairs are also used to give a quantitative measure of the consistency of a database. For classification models, the responsibility score is properly extended and illustrated. The efficient computation of Shap-score is also analyzed and discussed. The emphasis is placed on work done by the author and collaborators.

Attention Deficit Hyperactive Disorder (ADHD) is a common behavioral problem affecting children. In this work, we investigate the automatic classification of ADHD subjects using the resting state Functional Magnetic Resonance Imaging (fMRI) sequences of the brain. We show that the brain can be modeled as a functional network, and certain properties of the networks differ in ADHD subjects from control subjects. We compute the pairwise correlation of brain voxels' activity over the time frame of the experimental protocol which helps to model the function of a brain as a network. Different network features are computed for each of the voxels constructing the network. The concatenation of the network features of all the voxels in a brain serves as the feature vector. Feature vectors from a set of subjects are then used to train a PCA-LDA (principal component analysis-linear discriminant analysis) based classifier. We hypothesized that ADHD-related differences lie in some specific regions of the brain and using features only from those regions is sufficient to discriminate ADHD and control subjects. We propose a method to create a brain mask that includes the useful regions only and demonstrate that using the feature from the masked regions improves classification accuracy on the test data set. We train our classifier with 776 subjects and test on 171 subjects provided by The Neuro Bureau for the ADHD-200 challenge. We demonstrate the utility of graph-motif features, specifically the maps that represent the frequency of participation of voxels in network cycles of length 3. The best classification performance (69.59%) is achieved using 3-cycle map features with masking. Our proposed approach holds promise in being able to diagnose and understand the disorder.

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Network analysis has revealed keystone species that regulate ecosystems and master regulators that regulate cellular genetic networks. Yet these studies have focused on pairwise biological interactions, which can be affected by the context of genetic background and other species present generating higher-order interactions. The important regulators of higher-order interactions are unstudied. To address this, we applied a new high-dimensional geometry approach that quantifies epistasis in a fitness landscape to ask how individual genes and species influence the interactions in the rest of the biological network. We then generated and also reanalyzed 5-dimensional datasets (two genetic, two microbiome). We identified key genes (e.g. the rbs locus and pykF) and species (e.g. Lactobacilli) that control the interactions of many other genes and species. These higher-order master regulators can induce or suppress evolutionary and ecological diversification by controlling the topography of the fitness landscape. Thus, we provide mathematical intuition and justification for exploration of biological networks in higher dimensions.

Encouraged by decision makers' appetite for future information on topics ranging from elections to pandemics, and enabled by the explosion of data and computational methods, model based forecasts have garnered increasing influence on a breadth of decisions in modern society. Using several classic examples from fisheries management, I demonstrate that selecting the model or models that produce the most accurate and precise forecast (measured by statistical scores) can sometimes lead to worse outcomes (measured by real-world objectives). This can create a forecast trap, in which the outcomes such as fish biomass or economic yield decline while the manager becomes increasingly convinced that these actions are consistent with the best models and data available. The forecast trap is not unique to this example, but a fundamental consequence of non-uniqueness of models. Existing practices promoting a broader set of models are the best way to avoid the trap.

This study explores the proactive ability of LLMs to seek user support. We propose metrics to evaluate the trade-off between performance improvements and user burden, and investigate whether LLMs can determine when to request help under varying information availability. Our experiments show that without external feedback, many LLMs struggle to recognize their need for user support. The findings highlight the importance of external signals and provide insights for future research on improving support-seeking strategies. Source code: https://github.com/appier-research/i-need-help

Recent progress in generative models, especially in text-guided diffusion models, has enabled the production of aesthetically-pleasing imagery resembling the works of professional human artists. However, one has to carefully compose the textual description, called the prompt, and augment it with a set of clarifying keywords. Since aesthetics are challenging to evaluate computationally, human feedback is needed to determine the optimal prompt formulation and keyword combination. In this paper, we present a human-in-the-loop approach to learning the most useful combination of prompt keywords using a genetic algorithm. We also show how such an approach can improve the aesthetic appeal of images depicting the same descriptions.

Linguistic commentary on LLMs, heavily influenced by the theoretical frameworks of de Saussure and Chomsky, is often speculative and unproductive. Critics challenge whether LLMs can legitimately model language, citing the need for "deep structure" or "grounding" to achieve an idealized linguistic "competence." We argue for a radical shift in perspective towards the empiricist principles of Witold Ma\'nczak, a prominent general and historical linguist. He defines language not as a "system of signs" or a "computational system of the brain" but as the totality of all that is said and written. Above all, he identifies frequency of use of particular language elements as language's primary governing principle. Using his framework, we challenge prior critiques of LLMs and provide a constructive guide for designing, evaluating, and interpreting language models.

We advocate for a strong integration of Computational Creativity (CC) with research in large language and vision models (LLVMs) to address a key limitation of these models, i.e., creative problem solving. We present preliminary experiments showing how CC principles can be applied to address this limitation. Our goal is to foster discussions on creative problem solving in LLVMs and CC at prestigious ML venues. Our code is available at: https://github.com/lnairGT/creative-problem-solving-LLMs

Classical models of memory in psychology and neuroscience rely on similarity-based retrieval of stored patterns, where similarity is a function of retrieval cues and the stored patterns. While parsimonious, these models do not allow distinct representations for storage and retrieval, despite their distinct computational demands. Key-value memory systems, in contrast, distinguish representations used for storage (values) and those used for retrieval (keys). This allows key-value memory systems to optimize simultaneously for fidelity in storage and discriminability in retrieval. We review the computational foundations of key-value memory, its role in modern machine learning systems, related ideas from psychology and neuroscience, applications to a number of empirical puzzles, and possible biological implementations.

This is a book about large language models. As indicated by the title, it primarily focuses on foundational concepts rather than comprehensive coverage of all cutting-edge technologies. The book is structured into four main chapters, each exploring a key area: pre-training, generative models, prompting techniques, and alignment methods. It is intended for college students, professionals, and practitioners in natural language processing and related fields, and can serve as a reference for anyone interested in large language models.

Causal representation learning seeks to extract high-level latent factors from low-level sensory data. Most existing methods rely on observational data and structural assumptions (e.g., conditional independence) to identify the latent factors. However, interventional data is prevalent across applications. Can interventional data facilitate causal representation learning? We explore this question in this paper. The key observation is that interventional data often carries geometric signatures of the latent factors' support (i.e. what values each latent can possibly take). For example, when the latent factors are causally connected, interventions can break the dependency between the intervened latents' support and their ancestors'. Leveraging this fact, we prove that the latent causal factors can be identified up to permutation and scaling given data from perfect do interventions. Moreover, we can achieve block affine identification, namely the estimated latent factors are only entangled with a few other latents if we have access to data from imperfect interventions. These results highlight the unique power of interventional data in causal representation learning; they can enable provable identification of latent factors without any assumptions about their distributions or dependency structure.

In this paper, we investigate when and how visual representations learned by two different generative models diverge. Given two text-to-image models, our goal is to discover visual attributes that appear in images generated by one model but not the other, along with the types of prompts that trigger these attribute differences. For example, "flames" might appear in one model's outputs when given prompts expressing strong emotions, while the other model does not produce this attribute given the same prompts. We introduce CompCon (Comparing Concepts), an evolutionary search algorithm that discovers visual attributes more prevalent in one model's output than the other, and uncovers the prompt concepts linked to these visual differences. To evaluate CompCon's ability to find diverging representations, we create an automated data generation pipeline to produce ID2, a dataset of 60 input-dependent differences, and compare our approach to several LLM- and VLM-powered baselines. Finally, we use CompCon to compare popular text-to-image models, finding divergent representations such as how PixArt depicts prompts mentioning loneliness with wet streets and Stable Diffusion 3.5 depicts African American people in media professions. Code at: https://github.com/adobe-research/CompCon

The growing popularity of data mining catalyses the researchers to explore various exciting aspects of education. Early prediction of student performance is an emerging area among them. The researchers have used various predictors in performance modelling studies. Although prior cognition can affect student performance, establishing their relationship is still an open research challenge. Quantifying the knowledge from readily available data is the major challenge here. We have proposed a semantic approach for this purpose. Association mining on nearly 0.35 million observations establishes that prior cognition impacts the student performance. The proposed approach of measuring domain knowledge can help the early performance modelling studies to use it as a predictor.

Keyword extraction is the process of identifying the words or phrases that express the main concepts of text to the best of one's ability. Electronic infrastructure creates a considerable amount of text every day and at all times. This massive volume of documents makes it practically impossible for human resources to study and manage them. Nevertheless, the need for these documents to be accessed efficiently and effectively is evident in numerous purposes. A blog, news article, or technical note is considered a relatively long text since the reader aims to learn the subject based on keywords or topics. Our approach consists of a combination of two models: graph centrality features and textural features. The proposed method has been used to extract the best keyword among the candidate keywords with an optimal combination of graph centralities, such as degree, betweenness, eigenvector, closeness centrality and etc, and textural, such as Casing, Term position, Term frequency normalization, Term different sentence, Part Of Speech tagging. There have also been attempts to distinguish keywords from candidate phrases and consider them on separate keywords. For evaluating the proposed method, seven datasets were used: Semeval2010, SemEval2017, Inspec, fao30, Thesis100, pak2018, and Wikinews, with results reported as Precision, Recall, and F- measure. Our proposed method performed much better in terms of evaluation metrics in all reviewed datasets compared with available methods in literature. An approximate 16.9% increase was witnessed in F-score metric and this was much more for the Inspec in English datasets and WikiNews in forgone languages.

In the field of language modeling, models augmented with retrieval components have emerged as a promising solution to address several challenges faced in the natural language processing (NLP) field, including knowledge grounding, interpretability, and scalability. Despite the primary focus on NLP, we posit that the paradigm of retrieval-enhancement can be extended to a broader spectrum of machine learning (ML) such as computer vision, time series prediction, and computational biology. Therefore, this work introduces a formal framework of this paradigm, Retrieval-Enhanced Machine Learning (REML), by synthesizing the literature in various domains in ML with consistent notations which is missing from the current literature. Also, we found that while a number of studies employ retrieval components to augment their models, there is a lack of integration with foundational Information Retrieval (IR) research. We bridge this gap between the seminal IR research and contemporary REML studies by investigating each component that comprises the REML framework. Ultimately, the goal of this work is to equip researchers across various disciplines with a comprehensive, formally structured framework of retrieval-enhanced models, thereby fostering interdisciplinary future research.

The fire and crime incident datasets were requested and collected from two Philippine regional agencies (i.e., the Bureau of Fire Protection and the Philippine National Police). The datasets were used to initially analyze and map both fire and crime incidents within the province of Pampanga for a specific time frame. Several data preparation, normalization, and data cleaning steps were implemented to properly map and identify patterns within the datasets. The initial results also indicate the leading causes of fire and crimes are rubbish and acts against property. Fires mostly occur during the dry season in the province. Crime is particularly high during December, and most of the fire and crime incidents occur during the time when people are most active. The dataset was able to present the temporal characteristics of the fire and crime incidents that occurred in the province of Pampanga. Merge the existing dataset with the other datasets from other related agencies to get a bigger picture and produce more objective results that could be used for decision-making.

In recent years, digital technologies have grown in many ways. As a result, many school-aged children have been exposed to the digital world a lot. Children are using more digital technologies, so schools need to teach kids more about cyber security and online safety. Because of this, there are now more school programmes and projects that teach students about cyber security and online safety and help them learn and improve their skills. Still, despite many programmes and projects, there is not much proof of how many schools have taken part and helped spread the word about them. This work shows how we can learn about the size and scope of cyber security and online safety education in schools in the UK, a country with a very active and advanced cyber security education profile, using nearly 200k public tweets from over 15k schools. By using simple techniques like descriptive statistics and visualisation as well as advanced natural language processing (NLP) techniques like sentiment analysis and topic modelling, we show some new findings and insights about how UK schools as a sector have been doing on Twitter with their cyber security and online safety education activities. Our work has led to a range of large-scale and real-world evidence that can help inform people and organisations interested in cyber security and teaching online safety in schools.

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.