mstyslavity/prisma_v3 huggingface dataset:
All biological systems are subject to perturbations: due to thermal fluctuations, external environments, or mutations. Yet, while biological systems are composed of thousands of interacting components, recent high-throughput experiments show that their response to perturbations is surprisingly low-dimensional: confined to only a few stereotyped changes out of the many possible. Here, we explore a unifying dynamical systems framework - soft modes - to explain and analyze low-dimensionality in biology, from molecules to eco-systems. We argue that this one framework of soft modes makes non-trivial predictions that generalize classic ideas from developmental biology to disparate systems, namely: phenocopying, dual buffering, and global epistasis. While some of these predictions have been borne out in experiments, we discuss how soft modes allow for a surprisingly far-reaching and unifying framework in which to analyze data from protein biophysics to microbial ecology.
Machine-generated music (MGM) has become a groundbreaking innovation with wide-ranging applications, such as music therapy, personalised editing, and creative inspiration within the music industry. However, the unregulated proliferation of MGM presents considerable challenges to the entertainment, education, and arts sectors by potentially undermining the value of high-quality human compositions. Consequently, MGM detection (MGMD) is crucial for preserving the integrity of these fields. Despite its significance, MGMD domain lacks comprehensive benchmark results necessary to drive meaningful progress. To address this gap, we conduct experiments on existing large-scale datasets using a range of foundational models for audio processing, establishing benchmark results tailored to the MGMD task. Our selection includes traditional machine learning models, deep neural networks, Transformer-based architectures, and State Space Models (SSM). Recognising the inherently multimodal nature of music, which integrates both melody and lyrics, we also explore fundamental multimodal models in our experiments. Beyond providing basic binary classification outcomes, we delve deeper into model behaviour using multiple explainable Aritificial Intelligence (XAI) tools, offering insights into their decision-making processes. Our analysis reveals that ResNet18 performs the best according to in-domain and out-of-domain tests. By providing a comprehensive comparison of benchmark results and their interpretability, we propose several directions to inspire future research to develop more robust and effective detection methods for MGM.
After recalling the principles that allow space-time to be considered by analogy as an elastic medium, we show how the modified gravity according to the MOND theory concerning the anomaly of the velocities of stars at the periphery of galaxies can be seen as a creep of space acting on the radius of galaxies that gives a creep coefficient of Phi(space) = ((a0/a) x (Ro local/ Ro mean) -1). The values vary between 0.2 and 9 depending on the type of galaxy and density distribution. Considering the gravitational lensing effect of the ball cluster we obtain a creep coefficient Phi (space) = (1-pv)/pv. With pv the percentage of visible matter and pDM the percentage of Dark matter from the global mass (pv + pDM =1). The values vary between 0.66 and 4 for this cluster. This paper therefore raises the question, via these creep coefficients, of the possible granular nature of the vacuum and therefore of space fabric on the one hand and proposes another dark matter-free approach based on the creep of the texture of space to explain gravitational anomalies on the other hand.
Various evaluation metrics have been proposed for Grammatical Error Correction (GEC), but many, particularly reference-free metrics, lack explainability. This lack of explainability hinders researchers from analyzing the strengths and weaknesses of GEC models and limits the ability to provide detailed feedback for users. To address this issue, we propose attributing sentence-level scores to individual edits, providing insight into how specific corrections contribute to the overall performance. For the attribution method, we use Shapley values, from cooperative game theory, to compute the contribution of each edit. Experiments with existing sentence-level metrics demonstrate high consistency across different edit granularities and show approximately 70\% alignment with human evaluations. In addition, we analyze biases in the metrics based on the attribution results, revealing trends such as the tendency to ignore orthographic edits. Our implementation is available at \url{https://github.com/naist-nlp/gec-attribute}.
Recent advancements in large language models (LLMs) have shown promise in generating psychotherapeutic dialogues, particularly in the context of motivational interviewing (MI). However, the inherent lack of transparency in LLM outputs presents significant challenges given the sensitive nature of psychotherapy. Applying MI strategies, a set of MI skills, to generate more controllable therapeutic-adherent conversations with explainability provides a possible solution. In this work, we explore the alignment of LLMs with MI strategies by first prompting the LLMs to predict the appropriate strategies as reasoning and then utilizing these strategies to guide the subsequent dialogue generation. We seek to investigate whether such alignment leads to more controllable and explainable generations. Multiple experiments including automatic and human evaluations are conducted to validate the effectiveness of MI strategies in aligning psychotherapy dialogue generation. Our findings demonstrate the potential of LLMs in producing strategically aligned dialogues and suggest directions for practical applications in psychotherapeutic settings.
Background: Humor is a fundamental part of human communication, with prior work linking positive humor in the workplace to positive outcomes, such as improved performance and job satisfaction. Aims: This study aims to investigate programming-related humor in a large social media community. Methodology: We collected 139,718 submissions from Reddit subreddit r/ProgrammerHumor. Both textual and image-based (memes) submissions were considered. The image data was processed with OCR to extract text from images for NLP analysis. Multiple regression models were built to investigate what makes submissions humorous. Additionally, a random sample of 800 submissions was labeled by human annotators regarding their relation to theories of humor, suitability for the workplace, the need for programming knowledge to understand the submission, and whether images in image-based submissions added context to the submission. Results: Our results indicate that predicting the humor of software developers is difficult. Our best regression model was able to explain only 10% of the variance. However, statistically significant differences were observed between topics, submission times, and associated humor theories. Our analysis reveals that the highest submission scores are achieved by imagebased submissions that are created during the winter months in the northern hemisphere, between 2-3pm UTC on weekends, which are distinctly related to superiority and incongruity theories of humor, and are about the topic of "Learning". Conclusions: Predicting humor with natural language processing methods is challenging. We discuss the benefits and inherent difficulties in assessing perceived humor of submissions, as well as possible avenues for future work. Additionally, our replication package should help future studies and can act as a joke repository for the software industry and education.
Temporal higher-order networks, where each hyperlink involving a group of nodes are activated or deactivated over time, are recently used to represent complex systems such as social contacts, interactions or collaborations that occur at specific times. Such networks are substrates for social contagion processes like the diffusion of information and opinions. In this work, we consider eight temporal higher-order networks derived from human face-to-face interactions in various contexts and the Susceptible-Infected threshold process on each of these networks: whenever a hyperlink is active and the number of infected nodes in the hyperlink exceeds a threshold $\Theta$, each susceptible node in the hyperlink is infected independently with probability $\beta$. The objective is to understand (1) the contribution of each hyperlink to the diffusion process, namely, the average number of nodes that are infected directly via the activation of the hyperlink when the diffusion starts from an arbitrary seed node, and (2) hyperlinks with what network properties tend to contribute more. We first propose to construct the diffusion backbone. The backbone is a weighted higher-order network, where the weight of each hyperlink denotes the contribution of the hyperlink to a given diffusion process. Secondly, we find that the backbone, or the contribution of hyperlinks, is dependent on the parameters $\beta$ and $\Theta$ of the diffusion process, which is also supported by our theoretical analysis of the backbone when $\beta\rightarrow 0$. Thirdly, we systematically design centrality metrics for hyperlinks in a temporal higher-order network, and each centrality metric is used to estimate the ranking of hyperlinks by the weight in the backbone. Finally, we find and explain why different centrality metrics can better estimate the contributions of hyperlinks for different parameters of the diffusion process.
It has been suggested that merging black hole (BH) binaries in active galactic nucleus (AGN) discs formed through two-body scatterings via the gas-capture process may explain a significant fraction of BH mergers in AGN and a non-negligible contribution to the observed rate from LIGO-VIRGO-KAGRA. We perform Monte Carlo simulations of BH and binary BH formation, evolution and mergers across the observed AGN mass function using a novel physically motivated treatment for the gas-capture process derived from hydrodynamical simulations of BH-BH encounters in AGN and varying assumptions on the AGN disc physics. The results suggest that gas-captured binaries could result in merger rates of 0.73 - 7.1Gpc$^{-3}$yr$^{-1}$. Most mergers take place near the outer boundary of the accretion disk, but this may be subject to change when migration is considered. The BH merger rate in the AGN channel in the Universe is dominated by AGN with supermassive BH masses on the order of 10$^{7} M_\odot$ , with 90% of mergers occurring in the range 10$^{6} M_\odot$ - 10$^{8} M_\odot$ . The merging mass distribution is flatter than the initial BH mass power law by a factor $\Delta \xi$ = 1.1 to 1.2, as larger BHs can align with the disc and successfully form binaries more efficiently. Similarly, the merging mass ratio distribution is flatter, therefore the AGN channel could easily explain the high mass and unequal mass ratio detections such as GW190521 and GW190814. When modelling the BH binary formation process using a simpler dynamical friction treatment, we observe very similar results, where the primary bottleneck is the alignment time with the disk. We find the most influential parameters on the rates are the anticipated number of BHs and their mass function. We conclude that AGN remain an important channel for consideration, particularly for gravitational wave detections involving one or two high mass BHs.
Time perception research has advanced significantly over the years. However, some areas remain largely unexplored. This study addresses two such under-explored areas in timing research: (1) A quantitative analysis of time perception at an individual level, and (2) Time perception in an ecological setting. In this context, we trained a machine learning model to predict the direction of change in an individual's time production. The model's training data was collected using an ecologically valid setup. We moved closer to an ecological setting by conducting an online experiment with 995 participants performing a time production task that used naturalistic videos (no audio) as stimuli. The model achieved an accuracy of 61%. This was 10 percentage points higher than the baseline models derived from cognitive theories of timing. The model performed equally well on new data from a second experiment, providing evidence of its generalization capabilities. The model's output analysis revealed that it also contained information about the magnitude of change in time production. The predictions were further analysed at both population and individual level. It was found that a participant's previous timing performance played a significant role in determining the direction of change in time production. By integrating attentional-gate theories from timing research with feature importance techniques from machine learning, we explained model predictions using cognitive theories of timing. The model and findings from this study have potential applications in systems involving human-computer interactions where understanding and predicting changes in user's time perception can enable better user experience and task performance.
Machine Learning is transforming medical research by improving diagnostic accuracy and personalizing treatments. General ML models trained on large datasets identify broad patterns across populations, but their effectiveness is often limited by the diversity of human biology. This has led to interest in subject-specific models that use individual data for more precise predictions. However, these models are costly and challenging to develop. To address this, we propose a novel validation approach that uses a general ML model to ensure reproducible performance and robust feature importance analysis at both group and subject-specific levels. We tested a single Random Forest (RF) model on nine datasets varying in domain, sample size, and demographics. Different validation techniques were applied to evaluate accuracy and feature importance consistency. To introduce variability, we performed up to 400 trials per subject, randomly seeding the ML algorithm for each trial. This generated 400 feature sets per subject, from which we identified top subject-specific features. A group-specific feature importance set was then derived from all subject-specific results. We compared our approach to conventional validation methods in terms of performance and feature importance consistency. Our repeated trials approach, with random seed variation, consistently identified key features at the subject level and improved group-level feature importance analysis using a single general model. Subject-specific models address biological variability but are resource-intensive. Our novel validation technique provides consistent feature importance and improved accuracy within a general ML model, offering a practical and explainable alternative for clinical research.
Three different computed tomography (CT) reconstruction algorithms: Filtered Back Projection (FBP), Unified Tomographic Reconstruction (UTR) and customized Simultaneous Algebraic Reconstruction Technique (cSART), have been systematically compared and evaluated using experimental data from CT scans of ten fresh mastectomy samples collected at the Imaging and Medical beamline of the Australian Synchrotron. All the scans were collected at the mean glandular dose of 2 mGy, using monochromatic X-rays with 32 keV energy, flat-panel detectors with 0.1 mm pixels and 6 meter distance between the rotation stage and the detector. Paganin's phase retrieval method was used in conjunction with all three CT reconstruction algorithms. The reconstructed images were compared in terms of the objective image quality characteristics, including spatial resolution, contrast, signal-to-noise, and contrast-to-noise ratios. The images were also evaluated by seven experienced medical imaging specialists, rating perceptible contrast, sharpness of tissue interfaces, image noise, calcification visibility and overall image quality. Of the three compared algorithms, cSART was clearly superior to UTR and FBP in terms of most measured objective image quality characteristics. At the same time, the results of the subjective quality evaluation consistently favoured the images reconstructed by FBP, followed by UTR, with cSART receiving lower scores on average. We argue that this apparent disagreement between the objective and subjective assessments of image quality can be explained by the importance assigned to image contrast in the subjective assessment, while the signal-to-noise ratio seemed to receive relatively low weighting. This study was conducted in preparation for phase-contrast breast CT imaging of live patients at Australian Synchrotron (Melbourne, Australia).
Despite recent advancements in text-to-image generation, most existing methods struggle to create images with multiple objects and complex spatial relationships in the 3D world. To tackle this limitation, we introduce a generic AI system, namely MUSES, for 3D-controllable image generation from user queries. Specifically, our MUSES addresses this challenging task by developing a progressive workflow with three key components, including (1) Layout Manager for 2D-to-3D layout lifting, (2) Model Engineer for 3D object acquisition and calibration, (3) Image Artist for 3D-to-2D image rendering. By mimicking the collaboration of human professionals, this multi-modal agent pipeline facilitates the effective and automatic creation of images with 3D-controllable objects, through an explainable integration of top-down planning and bottom-up generation. Additionally, we find that existing benchmarks lack detailed descriptions of complex 3D spatial relationships of multiple objects. To fill this gap, we further construct a new benchmark of T2I-3DisBench (3D image scene), which describes diverse 3D image scenes with 50 detailed prompts. Extensive experiments show the state-of-the-art performance of MUSES on both T2I-CompBench and T2I-3DisBench, outperforming recent strong competitors such as DALL-E 3 and Stable Diffusion 3. These results demonstrate a significant step of MUSES forward in bridging natural language, 2D image generation, and 3D world. Our codes are available at the following link: https://github.com/DINGYANB/MUSES.
We present an exposition on the Fuss--Catalan numbers, which are a generalization of the well known Catalan numbers. The literature on the subject is scattered (especially for the case of multiple independent parameters, as will be explained in the text), with overlapping definitions by different authors and duplication of proofs. This paper collects the main theorems and identities, with a consistent notation. Contact is made with the works of numerous authors, including the early works of Lambert and Euler. We demonstrate the application of the formalism to solve algebraic equations by infinite series. Our main result in this context is a new necessary and sufficient formula for the domain of absolute convergence of the series solutions of algebraic equations, which corrects and extends previous work in the field. Some historical material is placed in an Appendix.
Equity is a core concern of learning analytics. However, applications that teach and assess equity skills, particularly at scale are lacking, often due to barriers in evaluating language. Advances in generative AI via large language models (LLMs) are being used in a wide range of applications, with this present work assessing its use in the equity domain. We evaluate tutor performance within an online lesson on enhancing tutors' skills when responding to students in potentially inequitable situations. We apply a mixed-method approach to analyze the performance of 81 undergraduate remote tutors. We find marginally significant learning gains with increases in tutors' self-reported confidence in their knowledge in responding to middle school students experiencing possible inequities from pretest to posttest. Both GPT-4o and GPT-4-turbo demonstrate proficiency in assessing tutors ability to predict and explain the best approach. Balancing performance, efficiency, and cost, we determine that few-shot learning using GPT-4o is the preferred model. This work makes available a dataset of lesson log data, tutor responses, rubrics for human annotation, and generative AI prompts. Future work involves leveling the difficulty among scenarios and enhancing LLM prompts for large-scale grading and assessment.
Active learning (AL), which aims to construct an effective training set by iteratively curating the most formative unlabeled data for annotation, has been widely used in low-resource tasks. Most active learning techniques in classification rely on the model's uncertainty or disagreement to choose unlabeled data, suffering from the problem of over-confidence in superficial patterns and a lack of exploration. Inspired by the cognitive processes in which humans deduce and predict through causal information, we take an initial attempt towards integrating rationales into AL and propose a novel Explainable Active Learning framework (XAL) for low-resource text classification, which aims to encourage classifiers to justify their inferences and delve into unlabeled data for which they cannot provide reasonable explanations. Specifically, besides using a pre-trained bi-directional encoder for classification, we employ a pre-trained uni-directional decoder to generate and score the explanation. We further facilitate the alignment of the model with human reasoning preference through a proposed ranking loss. During the selection of unlabeled data, the predicted uncertainty of the encoder and the explanation score of the decoder complement each other as the final metric to acquire informative data. Extensive experiments on six datasets show that XAL achieves consistent improvement over 9 strong baselines. Analysis indicates that the proposed method can generate corresponding explanations for its predictions.
Explainable AI (XAI) methods typically focus on identifying essential input features or more abstract concepts for tasks like image or text classification. However, for algorithmic tasks like combinatorial optimization, these concepts may depend not only on the input but also on the current state of the network, like in the graph neural networks (GNN) case. This work studies concept learning for an existing GNN model trained to solve Boolean satisfiability (SAT). \textcolor{black}{Our analysis reveals that the model learns key concepts matching those guiding human-designed SAT heuristics, particularly the notion of 'support.' We demonstrate that these concepts are encoded in the top principal components (PCs) of the embedding's covariance matrix, allowing for unsupervised discovery. Using sparse PCA, we establish the minimality of these concepts and show their teachability through a simplified GNN. Two direct applications of our framework are (a) We improve the convergence time of the classical WalkSAT algorithm and (b) We use the discovered concepts to "reverse-engineer" the black-box GNN and rewrite it as a white-box textbook algorithm. Our results highlight the potential of concept learning in understanding and enhancing algorithmic neural networks for combinatorial optimization tasks.