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Feb 11

Graph2MDA: a multi-modal variational graph embedding model for predicting microbe-drug associations

Accumulated clinical studies show that microbes living in humans interact closely with human hosts, and get involved in modulating drug efficacy and drug toxicity. Microbes have become novel targets for the development of antibacterial agents. Therefore, screening of microbe-drug associations can benefit greatly drug research and development. With the increase of microbial genomic and pharmacological datasets, we are greatly motivated to develop an effective computational method to identify new microbe-drug associations. In this paper, we proposed a novel method, Graph2MDA, to predict microbe-drug associations by using variational graph autoencoder (VGAE). We constructed multi-modal attributed graphs based on multiple features of microbes and drugs, such as molecular structures, microbe genetic sequences, and function annotations. Taking as input the multi-modal attribute graphs, VGAE was trained to learn the informative and interpretable latent representations of each node and the whole graph, and then a deep neural network classifier was used to predict microbe-drug associations. The hyperparameter analysis and model ablation studies showed the sensitivity and robustness of our model. We evaluated our method on three independent datasets and the experimental results showed that our proposed method outperformed six existing state-of-the-art methods. We also explored the meaningness of the learned latent representations of drugs and found that the drugs show obvious clustering patterns that are significantly consistent with drug ATC classification. Moreover, we conducted case studies on two microbes and two drugs and found 75\%-95\% predicted associations have been reported in PubMed literature. Our extensive performance evaluations validated the effectiveness of our proposed method.\

  • 4 authors
·
Aug 14, 2021

"All of Me": Mining Users' Attributes from their Public Spotify Playlists

In the age of digital music streaming, playlists on platforms like Spotify have become an integral part of individuals' musical experiences. People create and publicly share their own playlists to express their musical tastes, promote the discovery of their favorite artists, and foster social connections. These publicly accessible playlists transcend the boundaries of mere musical preferences: they serve as sources of rich insights into users' attributes and identities. For example, the musical preferences of elderly individuals may lean more towards Frank Sinatra, while Billie Eilish remains a favored choice among teenagers. These playlists thus become windows into the diverse and evolving facets of one's musical identity. In this work, we investigate the relationship between Spotify users' attributes and their public playlists. In particular, we focus on identifying recurring musical characteristics associated with users' individual attributes, such as demographics, habits, or personality traits. To this end, we conducted an online survey involving 739 Spotify users, yielding a dataset of 10,286 publicly shared playlists encompassing over 200,000 unique songs and 55,000 artists. Through extensive statistical analyses, we first assess a deep connection between a user's Spotify playlists and their real-life attributes. For instance, we found individuals high in openness often create playlists featuring a diverse array of artists, while female users prefer Pop and K-pop music genres. Building upon these observed associations, we create accurate predictive models for users' attributes, presenting a novel DeepSet application that outperforms baselines in most of these users' attributes.

  • 4 authors
·
Jan 25, 2024

Language Bootstrapping: Learning Word Meanings From Perception-Action Association

We address the problem of bootstrapping language acquisition for an artificial system similarly to what is observed in experiments with human infants. Our method works by associating meanings to words in manipulation tasks, as a robot interacts with objects and listens to verbal descriptions of the interactions. The model is based on an affordance network, i.e., a mapping between robot actions, robot perceptions, and the perceived effects of these actions upon objects. We extend the affordance model to incorporate spoken words, which allows us to ground the verbal symbols to the execution of actions and the perception of the environment. The model takes verbal descriptions of a task as the input and uses temporal co-occurrence to create links between speech utterances and the involved objects, actions, and effects. We show that the robot is able form useful word-to-meaning associations, even without considering grammatical structure in the learning process and in the presence of recognition errors. These word-to-meaning associations are embedded in the robot's own understanding of its actions. Thus, they can be directly used to instruct the robot to perform tasks and also allow to incorporate context in the speech recognition task. We believe that the encouraging results with our approach may afford robots with a capacity to acquire language descriptors in their operation's environment as well as to shed some light as to how this challenging process develops with human infants.

  • 4 authors
·
Nov 27, 2017

Is the Reversal Curse a Binding Problem? Uncovering Limitations of Transformers from a Basic Generalization Failure

Despite their impressive capabilities, LLMs exhibit a basic generalization failure known as the Reversal Curse, where they struggle to learn reversible factual associations. Understanding why this occurs could help identify weaknesses in current models and advance their generalization and robustness. In this paper, we conjecture that the Reversal Curse in LLMs is a manifestation of the long-standing binding problem in cognitive science, neuroscience and AI. Specifically, we identify two primary causes of the Reversal Curse stemming from transformers' limitations in conceptual binding: the inconsistency and entanglements of concept representations. We perform a series of experiments that support these conjectures. Our exploration leads to a model design based on JEPA (Joint-Embedding Predictive Architecture) that for the first time breaks the Reversal Curse without side-stepping it with specialized data augmentation or non-causal masking, and moreover, generalization could be further improved by incorporating special memory layers that support disentangled concept representations. We demonstrate that the skill of reversal unlocks a new kind of memory integration that enables models to solve large-scale arithmetic reasoning problems via parametric forward-chaining, outperforming frontier LLMs based on non-parametric memory and prolonged explicit reasoning.

  • 2 authors
·
Apr 2, 2025

ThinkSum: Probabilistic reasoning over sets using large language models

Large language models (LLMs) have a substantial capacity for high-level analogical reasoning: reproducing patterns in linear text that occur in their training data (zero-shot evaluation) or in the provided context (few-shot in-context learning). However, recent studies show that even the more advanced LLMs fail in scenarios that require reasoning over multiple objects or facts and making sequences of logical deductions. We propose a two-stage probabilistic inference paradigm, ThinkSum, which reasons over sets of objects or facts in a structured manner. In the first stage (Think - retrieval of associations), a LLM is queried in parallel over a set of phrases extracted from the prompt or an auxiliary model call. In the second stage (Sum - probabilistic inference or reasoning), the results of these queries are aggregated to make the final prediction. We demonstrate the possibilities and advantages of ThinkSum on the BIG-bench suite of LLM evaluation tasks, achieving improvements over the state of the art using GPT-family models on thirteen difficult tasks, often with far smaller model variants. We also compare and contrast ThinkSum with other proposed modifications to direct prompting of LLMs, such as variants of chain-of-thought prompting. Our results suggest that because the probabilistic inference in ThinkSum is performed outside of calls to the LLM, ThinkSum is less sensitive to prompt design, yields more interpretable predictions, and can be flexibly combined with latent variable models to extract structured knowledge from LLMs. Overall, our proposed paradigm represents a promising approach for enhancing the reasoning capabilities of LLMs.

  • 4 authors
·
Oct 3, 2022

Event-Guided Procedure Planning from Instructional Videos with Text Supervision

In this work, we focus on the task of procedure planning from instructional videos with text supervision, where a model aims to predict an action sequence to transform the initial visual state into the goal visual state. A critical challenge of this task is the large semantic gap between observed visual states and unobserved intermediate actions, which is ignored by previous works. Specifically, this semantic gap refers to that the contents in the observed visual states are semantically different from the elements of some action text labels in a procedure. To bridge this semantic gap, we propose a novel event-guided paradigm, which first infers events from the observed states and then plans out actions based on both the states and predicted events. Our inspiration comes from that planning a procedure from an instructional video is to complete a specific event and a specific event usually involves specific actions. Based on the proposed paradigm, we contribute an Event-guided Prompting-based Procedure Planning (E3P) model, which encodes event information into the sequential modeling process to support procedure planning. To further consider the strong action associations within each event, our E3P adopts a mask-and-predict approach for relation mining, incorporating a probabilistic masking scheme for regularization. Extensive experiments on three datasets demonstrate the effectiveness of our proposed model.

  • 5 authors
·
Aug 17, 2023

Lowis3D: Language-Driven Open-World Instance-Level 3D Scene Understanding

Open-world instance-level scene understanding aims to locate and recognize unseen object categories that are not present in the annotated dataset. This task is challenging because the model needs to both localize novel 3D objects and infer their semantic categories. A key factor for the recent progress in 2D open-world perception is the availability of large-scale image-text pairs from the Internet, which cover a wide range of vocabulary concepts. However, this success is hard to replicate in 3D scenarios due to the scarcity of 3D-text pairs. To address this challenge, we propose to harness pre-trained vision-language (VL) foundation models that encode extensive knowledge from image-text pairs to generate captions for multi-view images of 3D scenes. This allows us to establish explicit associations between 3D shapes and semantic-rich captions. Moreover, to enhance the fine-grained visual-semantic representation learning from captions for object-level categorization, we design hierarchical point-caption association methods to learn semantic-aware embeddings that exploit the 3D geometry between 3D points and multi-view images. In addition, to tackle the localization challenge for novel classes in the open-world setting, we develop debiased instance localization, which involves training object grouping modules on unlabeled data using instance-level pseudo supervision. This significantly improves the generalization capabilities of instance grouping and thus the ability to accurately locate novel objects. We conduct extensive experiments on 3D semantic, instance, and panoptic segmentation tasks, covering indoor and outdoor scenes across three datasets. Our method outperforms baseline methods by a significant margin in semantic segmentation (e.g. 34.5%sim65.3%), instance segmentation (e.g. 21.8%sim54.0%) and panoptic segmentation (e.g. 14.7%sim43.3%). Code will be available.

  • 6 authors
·
Aug 1, 2023

Machine Learning Workflow to Explain Black-box Models for Early Alzheimer's Disease Classification Evaluated for Multiple Datasets

Purpose: Hard-to-interpret Black-box Machine Learning (ML) were often used for early Alzheimer's Disease (AD) detection. Methods: To interpret eXtreme Gradient Boosting (XGBoost), Random Forest (RF), and Support Vector Machine (SVM) black-box models a workflow based on Shapley values was developed. All models were trained on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset and evaluated for an independent ADNI test set, as well as the external Australian Imaging and Lifestyle flagship study of Ageing (AIBL), and Open Access Series of Imaging Studies (OASIS) datasets. Shapley values were compared to intuitively interpretable Decision Trees (DTs), and Logistic Regression (LR), as well as natural and permutation feature importances. To avoid the reduction of the explanation validity caused by correlated features, forward selection and aspect consolidation were implemented. Results: Some black-box models outperformed DTs and LR. The forward-selected features correspond to brain areas previously associated with AD. Shapley values identified biologically plausible associations with moderate to strong correlations with feature importances. The most important RF features to predict AD conversion were the volume of the amygdalae, and a cognitive test score. Good cognitive test performances and large brain volumes decreased the AD risk. The models trained using cognitive test scores significantly outperformed brain volumetric models (p<0.05). Cognitive Normal (CN) vs. AD models were successfully transferred to external datasets. Conclusion: In comparison to previous work, improved performances for ADNI and AIBL were achieved for CN vs. Mild Cognitive Impairment (MCI) classification using brain volumes. The Shapley values and the feature importances showed moderate to strong correlations.

  • 2 authors
·
May 12, 2022

Traceability Transformed: Generating more Accurate Links with Pre-Trained BERT Models

Software traceability establishes and leverages associations between diverse development artifacts. Researchers have proposed the use of deep learning trace models to link natural language artifacts, such as requirements and issue descriptions, to source code; however, their effectiveness has been restricted by availability of labeled data and efficiency at runtime. In this study, we propose a novel framework called Trace BERT (T-BERT) to generate trace links between source code and natural language artifacts. To address data sparsity, we leverage a three-step training strategy to enable trace models to transfer knowledge from a closely related Software Engineering challenge, which has a rich dataset, to produce trace links with much higher accuracy than has previously been achieved. We then apply the T-BERT framework to recover links between issues and commits in Open Source Projects. We comparatively evaluated accuracy and efficiency of three BERT architectures. Results show that a Single-BERT architecture generated the most accurate links, while a Siamese-BERT architecture produced comparable results with significantly less execution time. Furthermore, by learning and transferring knowledge, all three models in the framework outperform classical IR trace models. On the three evaluated real-word OSS projects, the best T-BERT stably outperformed the VSM model with average improvements of 60.31% measured using Mean Average Precision (MAP). RNN severely underperformed on these projects due to insufficient training data, while T-BERT overcame this problem by using pretrained language models and transfer learning.

Bias Out-of-the-Box: An Empirical Analysis of Intersectional Occupational Biases in Popular Generative Language Models

The capabilities of natural language models trained on large-scale data have increased immensely over the past few years. Open source libraries such as HuggingFace have made these models easily available and accessible. While prior research has identified biases in large language models, this paper considers biases contained in the most popular versions of these models when applied `out-of-the-box' for downstream tasks. We focus on generative language models as they are well-suited for extracting biases inherited from training data. Specifically, we conduct an in-depth analysis of GPT-2, which is the most downloaded text generation model on HuggingFace, with over half a million downloads per month. We assess biases related to occupational associations for different protected categories by intersecting gender with religion, sexuality, ethnicity, political affiliation, and continental name origin. Using a template-based data collection pipeline, we collect 396K sentence completions made by GPT-2 and find: (i) The machine-predicted jobs are less diverse and more stereotypical for women than for men, especially for intersections; (ii) Intersectional interactions are highly relevant for occupational associations, which we quantify by fitting 262 logistic models; (iii) For most occupations, GPT-2 reflects the skewed gender and ethnicity distribution found in US Labor Bureau data, and even pulls the societally-skewed distribution towards gender parity in cases where its predictions deviate from real labor market observations. This raises the normative question of what language models should learn - whether they should reflect or correct for existing inequalities.

  • 8 authors
·
Feb 8, 2021

Modality Alignment with Multi-scale Bilateral Attention for Multimodal Recommendation

Multimodal recommendation systems are increasingly becoming foundational technologies for e-commerce and content platforms, enabling personalized services by jointly modeling users' historical behaviors and the multimodal features of items (e.g., visual and textual). However, most existing methods rely on either static fusion strategies or graph-based local interaction modeling, facing two critical limitations: (1) insufficient ability to model fine-grained cross-modal associations, leading to suboptimal fusion quality; and (2) a lack of global distribution-level consistency, causing representational bias. To address these, we propose MambaRec, a novel framework that integrates local feature alignment and global distribution regularization via attention-guided learning. At its core, we introduce the Dilated Refinement Attention Module (DREAM), which uses multi-scale dilated convolutions with channel-wise and spatial attention to align fine-grained semantic patterns between visual and textual modalities. This module captures hierarchical relationships and context-aware associations, improving cross-modal semantic modeling. Additionally, we apply Maximum Mean Discrepancy (MMD) and contrastive loss functions to constrain global modality alignment, enhancing semantic consistency. This dual regularization reduces mode-specific deviations and boosts robustness. To improve scalability, MambaRec employs a dimensionality reduction strategy to lower the computational cost of high-dimensional multimodal features. Extensive experiments on real-world e-commerce datasets show that MambaRec outperforms existing methods in fusion quality, generalization, and efficiency. Our code has been made publicly available at https://github.com/rkl71/MambaRec.

  • 3 authors
·
Sep 10, 2025 2

HippoMM: Hippocampal-inspired Multimodal Memory for Long Audiovisual Event Understanding

Comprehending extended audiovisual experiences remains a fundamental challenge for computational systems. Current approaches struggle with temporal integration and cross-modal associations that humans accomplish effortlessly through hippocampal-cortical networks. We introduce HippoMM, a biologically-inspired architecture that transforms hippocampal mechanisms into computational advantages for multimodal understanding. HippoMM implements three key innovations: (i) hippocampus-inspired pattern separation and completion specifically designed for continuous audiovisual streams, (ii) short-to-long term memory consolidation that transforms perceptual details into semantic abstractions, and (iii) cross-modal associative retrieval pathways enabling modality-crossing queries. Unlike existing retrieval systems with static indexing schemes, HippoMM dynamically forms integrated episodic representations through adaptive temporal segmentation and dual-process memory encoding. Evaluations on our challenging HippoVlog benchmark demonstrate that HippoMM significantly outperforms state-of-the-art approaches (78.2% vs. 64.2% accuracy) while providing substantially faster response times (20.4s vs. 112.5s). Our results demonstrate that translating neuroscientific memory principles into computational architectures provides a promising foundation for next-generation multimodal understanding systems. The code and benchmark dataset are publicly available at https://github.com/linyueqian/HippoMM.

  • 6 authors
·
Apr 14, 2025

fastHDMI: Fast Mutual Information Estimation for High-Dimensional Data

In this paper, we introduce fastHDMI, a Python package designed for efficient variable screening in high-dimensional datasets, particularly neuroimaging data. This work pioneers the application of three mutual information estimation methods for neuroimaging variable selection, a novel approach implemented via fastHDMI. These advancements enhance our ability to analyze the complex structures of neuroimaging datasets, providing improved tools for variable selection in high-dimensional spaces. Using the preprocessed ABIDE dataset, we evaluate the performance of these methods through extensive simulations. The tests cover a range of conditions, including linear and nonlinear associations, as well as continuous and binary outcomes. Our results highlight the superiority of the FFTKDE-based mutual information estimation for feature screening in continuous nonlinear outcomes, while binning-based methods outperform others for binary outcomes with nonlinear probability preimages. For linear simulations, both Pearson correlation and FFTKDE-based methods show comparable performance for continuous outcomes, while Pearson excels in binary outcomes with linear probability preimages. A comprehensive case study using the ABIDE dataset further demonstrates fastHDMI's practical utility, showcasing the predictive power of models built from variables selected using our screening techniques. This research affirms the computational efficiency and methodological strength of fastHDMI, significantly enriching the toolkit available for neuroimaging analysis.

  • 5 authors
·
Oct 13, 2024

Immunohistochemistry guided segmentation of benign epithelial cells, in situ lesions, and invasive epithelial cells in breast cancer slides

Digital pathology enables automatic analysis of histopathological sections using artificial intelligence (AI). Automatic evaluation could improve diagnostic efficiency and help find associations between morphological features and clinical outcome. For development of such prediction models, identifying invasive epithelial cells, and separating these from benign epithelial cells and in situ lesions would be the first step. In this study, we aimed to develop an AI model for segmentation of epithelial cells in sections from breast cancer. We generated epithelial ground truth masks by restaining hematoxylin and eosin (HE) sections with cytokeratin (CK) AE1/AE3, and by pathologists' annotations. HE/CK image pairs were used to train a convolutional neural network, and data augmentation was used to make the model more robust. Tissue microarrays (TMAs) from 839 patients, and whole slide images from two patients were used for training and evaluation of the models. The sections were derived from four cohorts of breast cancer patients. TMAs from 21 patients from a fifth cohort was used as a second test set. In quantitative evaluation, a mean Dice score of 0.70, 0.79, and 0.75 for invasive epithelial cells, benign epithelial cells, and in situ lesions, respectively, were achieved. In qualitative scoring (0-5) by pathologists, results were best for all epithelium and invasive epithelium, with scores of 4.7 and 4.4. Scores for benign epithelium and in situ lesions were 3.7 and 2.0. The proposed model segmented epithelial cells in HE stained breast cancer slides well, but further work is needed for accurate division between the classes. Immunohistochemistry, together with pathologists' annotations, enabled the creation of accurate ground truths. The model is made freely available in FastPathology and the code is available at https://github.com/AICAN-Research/breast-epithelium-segmentation

  • 11 authors
·
Nov 22, 2023

Sealing The Backdoor: Unlearning Adversarial Text Triggers In Diffusion Models Using Knowledge Distillation

Text-to-image diffusion models have revolutionized generative AI, but their vulnerability to backdoor attacks poses significant security risks. Adversaries can inject imperceptible textual triggers into training data, causing models to generate manipulated outputs. Although text-based backdoor defenses in classification models are well-explored, generative models lack effective mitigation techniques against. We address this by selectively erasing the model's learned associations between adversarial text triggers and poisoned outputs, while preserving overall generation quality. Our approach, Self-Knowledge Distillation with Cross-Attention Guidance (SKD-CAG), uses knowledge distillation to guide the model in correcting responses to poisoned prompts while maintaining image quality by exploiting the fact that the backdoored model still produces clean outputs in the absence of triggers. Using the cross-attention mechanism, SKD-CAG neutralizes backdoor influences at the attention level, ensuring the targeted removal of adversarial effects. Extensive experiments show that our method outperforms existing approaches, achieving removal accuracy 100\% for pixel backdoors and 93\% for style-based attacks, without sacrificing robustness or image fidelity. Our findings highlight targeted unlearning as a promising defense to secure generative models. Code and model weights can be found at https://github.com/Mystic-Slice/Sealing-The-Backdoor .

  • 5 authors
·
Aug 19, 2025

Prototype Learning to Create Refined Interpretable Digital Phenotypes from ECGs

Prototype-based neural networks offer interpretable predictions by comparing inputs to learned, representative signal patterns anchored in training data. While such models have shown promise in the classification of physiological data, it remains unclear whether their prototypes capture an underlying structure that aligns with broader clinical phenotypes. We use a prototype-based deep learning model trained for multi-label ECG classification using the PTB-XL dataset. Then without modification we performed inference on the MIMIC-IV clinical database. We assess whether individual prototypes, trained solely for classification, are associated with hospital discharge diagnoses in the form of phecodes in this external population. Individual prototypes demonstrate significantly stronger and more specific associations with clinical outcomes compared to the classifier's class predictions, NLP-extracted concepts, or broader prototype classes across all phecode categories. Prototype classes with mixed significance patterns exhibit significantly greater intra-class distances (p < 0.0001), indicating the model learned to differentiate clinically meaningful variations within diagnostic categories. The prototypes achieve strong predictive performance across diverse conditions, with AUCs ranging from 0.89 for atrial fibrillation to 0.91 for heart failure, while also showing substantial signal for non-cardiac conditions such as sepsis and renal disease. These findings suggest that prototype-based models can support interpretable digital phenotyping from physiologic time-series data, providing transferable intermediate phenotypes that capture clinically meaningful physiologic signatures beyond their original training objectives.

  • 6 authors
·
Aug 2, 2025

Towards Holistic Visual Quality Assessment of AI-Generated Videos: A LLM-Based Multi-Dimensional Evaluation Model

The development of AI-Generated Video (AIGV) technology has been remarkable in recent years, significantly transforming the paradigm of video content production. However, AIGVs still suffer from noticeable visual quality defects, such as noise, blurriness, frame jitter and low dynamic degree, which severely impact the user's viewing experience. Therefore, an effective automatic visual quality assessment is of great importance for AIGV content regulation and generative model improvement. In this work, we decompose the visual quality of AIGVs into three dimensions: technical quality, motion quality, and video semantics. For each dimension, we design corresponding encoder to achieve effective feature representation. Moreover, considering the outstanding performance of large language models (LLMs) in various vision and language tasks, we introduce a LLM as the quality regression module. To better enable the LLM to establish reasoning associations between multi-dimensional features and visual quality, we propose a specially designed multi-modal prompt engineering framework. Additionally, we incorporate LoRA fine-tuning technology during the training phase, allowing the LLM to better adapt to specific tasks. Our proposed method achieved second place in the NTIRE 2025 Quality Assessment of AI-Generated Content Challenge: Track 2 AI Generated video, demonstrating its effectiveness. Codes can be obtained at https://github.com/QiZelu/AIGVEval.

  • 7 authors
·
Jun 5, 2025

Deep Generative Modeling with Spatial and Network Images: An Explainable AI (XAI) Approach

This article addresses the challenge of modeling the amplitude of spatially indexed low frequency fluctuations (ALFF) in resting state functional MRI as a function of cortical structural features and a multi-task coactivation network in the Adolescent Brain Cognitive Development (ABCD) Study. It proposes a generative model that integrates effects of spatially-varying inputs and a network-valued input using deep neural networks to capture complex non-linear and spatial associations with the output. The method models spatial smoothness, accounts for subject heterogeneity and complex associations between network and spatial images at different scales, enables accurate inference of each images effect on the output image, and allows prediction with uncertainty quantification via Monte Carlo dropout, contributing to one of the first Explainable AI (XAI) frameworks for heterogeneous imaging data. The model is highly scalable to high-resolution data without the heavy pre-processing or summarization often required by Bayesian methods. Empirical results demonstrate its strong performance compared to existing statistical and deep learning methods. We applied the XAI model to the ABCD data which revealed associations between cortical features and ALFF throughout the entire brain. Our model performed comparably to existing methods in predictive accuracy but provided superior uncertainty quantification and faster computation, demonstrating its effectiveness for large-scale neuroimaging analysis. Open-source software in Python for XAI is available.

  • 3 authors
·
May 19, 2025

SHA256 at SemEval-2025 Task 4: Selective Amnesia -- Constrained Unlearning for Large Language Models via Knowledge Isolation

Large language models (LLMs) frequently memorize sensitive information during training, posing risks when deploying publicly accessible models. Current machine unlearning methods struggle to selectively remove specific data associations without degrading overall model capabilities. This paper presents our solution to SemEval-2025 Task 4 on targeted unlearning, which introduces a two-stage methodology that combines causal mediation analysis with layer-specific optimization. Through systematic causal tracing experiments on OLMo architectures (1B and 7B parameters), we identify the critical role of the first few transformer layers (layers 0-5) in storing subject-attribute associations within MLP modules. Building on this insight, we develop a constrained optimization approach that freezes upper layers while applying a novel joint loss function to lower layers-simultaneously maximizing forget set loss via output token cross-entropy penalties and minimizing retain set deviation through adaptive regularization. Our method achieves 2nd place in the 1B model track, demonstrating strong task performance while maintaining 88% of baseline MMLU accuracy. These results establish causal-informed layer optimization as a promising paradigm for efficient, precise unlearning in LLMs, offering a significant step forward in addressing data privacy concerns in AI systems.

  • 2 authors
·
Apr 17, 2025

Need is All You Need: Homeostatic Neural Networks Adapt to Concept Shift

In living organisms, homeostasis is the natural regulation of internal states aimed at maintaining conditions compatible with life. Typical artificial systems are not equipped with comparable regulatory features. Here, we introduce an artificial neural network that incorporates homeostatic features. Its own computing substrate is placed in a needful and vulnerable relation to the very objects over which it computes. For example, artificial neurons performing classification of MNIST digits or Fashion-MNIST articles of clothing may receive excitatory or inhibitory effects, which alter their own learning rate as a direct result of perceiving and classifying the digits. In this scenario, accurate recognition is desirable to the agent itself because it guides decisions to regulate its vulnerable internal states and functionality. Counterintuitively, the addition of vulnerability to a learner does not necessarily impair its performance. On the contrary, self-regulation in response to vulnerability confers benefits under certain conditions. We show that homeostatic design confers increased adaptability under concept shift, in which the relationships between labels and data change over time, and that the greatest advantages are obtained under the highest rates of shift. This necessitates the rapid un-learning of past associations and the re-learning of new ones. We also demonstrate the superior abilities of homeostatic learners in environments with dynamically changing rates of concept shift. Our homeostatic design exposes the artificial neural network's thinking machinery to the consequences of its own "thoughts", illustrating the advantage of putting one's own "skin in the game" to improve fluid intelligence.

  • 3 authors
·
May 17, 2022

An Investigation of the Structural Characteristics of the Indian IT Sector and the Capital Goods Sector: An Application of the R Programming in Time Series Decomposition and Forecasting

Time series analysis and forecasting of stock market prices has been a very active area of research over the last two decades. Availability of extremely fast and parallel architecture of computing and sophisticated algorithms has made it possible to extract, store, process and analyze high volume stock market time series data very efficiently. In this paper, we have used time series data of the two sectors of the Indian economy: Information Technology and Capital Goods for the period January 2009 till April 2016 and have studied the relationships of these two time series with the time series of DJIA index, NIFTY index and the US Dollar to Indian Rupee exchange rate. We establish by graphical and statistical tests that while the IT sector of India has a strong association with DJIA index and the Dollar to Rupee exchange rate, the Indian CG sector exhibits a strong association with the NIFTY index. We contend that these observations corroborate our hypotheses that the Indian IT sector is strongly coupled with the world economy whereas the CG sector of India reflects internal economic growth of India. We also present several models of regression between the time series which exhibit strong association among them. The effectiveness of these models have been demonstrated by very low values of their forecasting errors.

  • 2 authors
·
May 14, 2017

GenoMAS: A Multi-Agent Framework for Scientific Discovery via Code-Driven Gene Expression Analysis

Gene expression analysis holds the key to many biomedical discoveries, yet extracting insights from raw transcriptomic data remains formidable due to the complexity of multiple large, semi-structured files and the need for extensive domain expertise. Current automation approaches are often limited by either inflexible workflows that break down in edge cases or by fully autonomous agents that lack the necessary precision for rigorous scientific inquiry. GenoMAS charts a different course by presenting a team of LLM-based scientists that integrates the reliability of structured workflows with the adaptability of autonomous agents. GenoMAS orchestrates six specialized LLM agents through typed message-passing protocols, each contributing complementary strengths to a shared analytic canvas. At the heart of GenoMAS lies a guided-planning framework: programming agents unfold high-level task guidelines into Action Units and, at each juncture, elect to advance, revise, bypass, or backtrack, thereby maintaining logical coherence while bending gracefully to the idiosyncrasies of genomic data. On the GenoTEX benchmark, GenoMAS reaches a Composite Similarity Correlation of 89.13% for data preprocessing and an F_1 of 60.48% for gene identification, surpassing the best prior art by 10.61% and 16.85% respectively. Beyond metrics, GenoMAS surfaces biologically plausible gene-phenotype associations corroborated by the literature, all while adjusting for latent confounders. Code is available at https://github.com/Liu-Hy/GenoMAS.

  • 3 authors
·
Jul 28, 2025 2

Psycholinguistic Word Features: a New Approach for the Evaluation of LLMs Alignment with Humans

The evaluation of LLMs has so far focused primarily on how well they can perform different tasks such as reasoning, question-answering, paraphrasing, or translating. For most of these tasks, performance can be measured with objective metrics, such as the number of correct answers. However, other language features are not easily quantified. For example, arousal, concreteness, or gender associated with a given word, as well as the extent to which we experience words with senses and relate them to a specific sense. Those features have been studied for many years by psycholinguistics, conducting large-scale experiments with humans to produce ratings for thousands of words. This opens an opportunity to evaluate how well LLMs align with human ratings on these word features, taking advantage of existing studies that cover many different language features in a large number of words. In this paper, we evaluate the alignment of a representative group of LLMs with human ratings on two psycholinguistic datasets: the Glasgow and Lancaster norms. These datasets cover thirteen features over thousands of words. The results show that alignment is black{generally} better in the Glasgow norms evaluated (arousal, valence, dominance, concreteness, imageability, familiarity, and gender) than on the Lancaster norms evaluated (introceptive, gustatory, olfactory, haptic, auditory, and visual). This suggests a potential limitation of current LLMs in aligning with human sensory associations for words, which may be due to their lack of embodied cognition present in humans and illustrates the usefulness of evaluating LLMs with psycholinguistic datasets.

  • 6 authors
·
May 29, 2025

AVERE: Improving Audiovisual Emotion Reasoning with Preference Optimization

Emotion understanding is essential for building socially intelligent agents. Although recent multimodal large language models have shown strong performance on this task, two key challenges remain - spurious associations between emotions and irrelevant audiovisual cues, and hallucinations of audiovisual cues driven by text priors in the language model backbone. To quantify and understand these issues, we introduce EmoReAlM, a benchmark designed to evaluate MLLMs for cue-emotion associations, hallucinations and modality agreement. We then propose AVEm-DPO, a preference optimization technique that aligns model responses with both audiovisual inputs and emotion-centric queries. Specifically, we construct preferences over responses exhibiting spurious associations or hallucinations, and audiovisual input pairs guided by textual prompts. We also include a regularization term that penalizes reliance on text priors, thereby mitigating modality-specific cue hallucinations. Experimental results on DFEW, RAVDESS and EMER demonstrate that our method significantly improves the performance of the reference baseline models with 6-19% of relative performance gains in zero-shot settings. By providing both a rigorous benchmark and a robust optimization framework, this work enables principled evaluation and improvement of MLLMs for emotion understanding and social AI. Code, models and benchmark will be released at https://avere-iclr.github.io.

Multi-Agent Reinforcement Learning for Offloading Cellular Communications with Cooperating UAVs

Effective solutions for intelligent data collection in terrestrial cellular networks are crucial, especially in the context of Internet of Things applications. The limited spectrum and coverage area of terrestrial base stations pose challenges in meeting the escalating data rate demands of network users. Unmanned aerial vehicles, known for their high agility, mobility, and flexibility, present an alternative means to offload data traffic from terrestrial BSs, serving as additional access points. This paper introduces a novel approach to efficiently maximize the utilization of multiple UAVs for data traffic offloading from terrestrial BSs. Specifically, the focus is on maximizing user association with UAVs by jointly optimizing UAV trajectories and users association indicators under quality of service constraints. Since, the formulated UAVs control problem is nonconvex and combinatorial, this study leverages the multi agent reinforcement learning framework. In this framework, each UAV acts as an independent agent, aiming to maintain inter UAV cooperative behavior. The proposed approach utilizes the finite state Markov decision process to account for UAVs velocity constraints and the relationship between their trajectories and state space. A low complexity distributed state action reward state action algorithm is presented to determine UAVs optimal sequential decision making policies over training episodes. The extensive simulation results validate the proposed analysis and offer valuable insights into the optimal UAV trajectories. The derived trajectories demonstrate superior average UAV association performance compared to benchmark techniques such as Q learning and particle swarm optimization.

  • 6 authors
·
Feb 5, 2024

Vision-based Situational Graphs Generating Optimizable 3D Scene Representations

3D scene graphs offer a more efficient representation of the environment by hierarchically organizing diverse semantic entities and the topological relationships among them. Fiducial markers, on the other hand, offer a valuable mechanism for encoding comprehensive information pertaining to environments and the objects within them. In the context of Visual SLAM (VSLAM), especially when the reconstructed maps are enriched with practical semantic information, these markers have the potential to enhance the map by augmenting valuable semantic information and fostering meaningful connections among the semantic objects. In this regard, this paper exploits the potential of fiducial markers to incorporate a VSLAM framework with hierarchical representations that generates optimizable multi-layered vision-based situational graphs. The framework comprises a conventional VSLAM system with low-level feature tracking and mapping capabilities bolstered by the incorporation of a fiducial marker map. The fiducial markers aid in identifying walls and doors in the environment, subsequently establishing meaningful associations with high-level entities, including corridors and rooms. Experimental results are conducted on a real-world dataset collected using various legged robots and benchmarked against a Light Detection And Ranging (LiDAR)-based framework (S-Graphs) as the ground truth. Consequently, our framework not only excels in crafting a richer, multi-layered hierarchical map of the environment but also shows enhancement in robot pose accuracy when contrasted with state-of-the-art methodologies.

Saliency Map Verbalization: Comparing Feature Importance Representations from Model-free and Instruction-based Methods

Saliency maps can explain a neural model's predictions by identifying important input features. They are difficult to interpret for laypeople, especially for instances with many features. In order to make them more accessible, we formalize the underexplored task of translating saliency maps into natural language and compare methods that address two key challenges of this approach -- what and how to verbalize. In both automatic and human evaluation setups, using token-level attributions from text classification tasks, we compare two novel methods (search-based and instruction-based verbalizations) against conventional feature importance representations (heatmap visualizations and extractive rationales), measuring simulatability, faithfulness, helpfulness and ease of understanding. Instructing GPT-3.5 to generate saliency map verbalizations yields plausible explanations which include associations, abstractive summarization and commonsense reasoning, achieving by far the highest human ratings, but they are not faithfully capturing numeric information and are inconsistent in their interpretation of the task. In comparison, our search-based, model-free verbalization approach efficiently completes templated verbalizations, is faithful by design, but falls short in helpfulness and simulatability. Our results suggest that saliency map verbalization makes feature attribution explanations more comprehensible and less cognitively challenging to humans than conventional representations.

  • 6 authors
·
Oct 13, 2022

1FLAT: a Firmamento-based catalog of AGN in Fermi-LAT high Galactic latitude γ-ray sources

We present a systematic reassessment of 5,062 high-Galactic latitude gamma-ray sources from the Fermi-LAT 4FGL-DR4 catalog using Firmamento, a web-based platform for multi-frequency source discovery and analysis. Our goal is to provide an independent evaluation of LAT gamma-ray source associations through alternative spectral and spatial methods that combine recent and legacy survey data, supplemented by human supervision of spectral energy distributions (SEDs), source morphology, flux variability, and template-based comparisons. Firmamento confirms the 4FGL-DR4 and 4LAC-DR3 counterparts or unassociated sources in 4,493 cases (88.8%), demonstrating the robustness of both approaches. Beyond this general agreement, we identify 421 new blazar counterparts among previously unassociated sources, thereby reducing the fraction of unidentified extragalactic Fermi-LAT sources from 25% to 17%. In addition, in 64 cases we find alternative blazar associations, while in 49 instances we do not confirm the 4FGL-DR4 association. For all confirmed blazar counterparts we provide homogeneous estimates of synchrotron peak frequency and peak flux using machine-learning and template-based methods; these agree with 4LAC-DR3 values in most cases, though significant discrepancies appear for a few dozen sources, often due to improved X-ray coverage. The primary outcome of this work is the 1st Firmamento LAT AGN table (1FLAT), made publicly available through the Firmamento platform (https://firmamento.nyuad.nyu.edu), where all related multi-wavelength data and images are available. The project involved extensive manual validation and benefited from the active participation of graduate and undergraduate students, highlighting the platform's value for both research and education.

  • 18 authors
·
Oct 8, 2025

Machine Learning with Multitype Protected Attributes: Intersectional Fairness through Regularisation

Ensuring equitable treatment (fairness) across protected attributes (such as gender or ethnicity) is a critical issue in machine learning. Most existing literature focuses on binary classification, but achieving fairness in regression tasks-such as insurance pricing or hiring score assessments-is equally important. Moreover, anti-discrimination laws also apply to continuous attributes, such as age, for which many existing methods are not applicable. In practice, multiple protected attributes can exist simultaneously; however, methods targeting fairness across several attributes often overlook so-called "fairness gerrymandering", thereby ignoring disparities among intersectional subgroups (e.g., African-American women or Hispanic men). In this paper, we propose a distance covariance regularisation framework that mitigates the association between model predictions and protected attributes, in line with the fairness definition of demographic parity, and that captures both linear and nonlinear dependencies. To enhance applicability in the presence of multiple protected attributes, we extend our framework by incorporating two multivariate dependence measures based on distance covariance: the previously proposed joint distance covariance (JdCov) and our novel concatenated distance covariance (CCdCov), which effectively address fairness gerrymandering in both regression and classification tasks involving protected attributes of various types. We discuss and illustrate how to calibrate regularisation strength, including a method based on Jensen-Shannon divergence, which quantifies dissimilarities in prediction distributions across groups. We apply our framework to the COMPAS recidivism dataset and a large motor insurance claims dataset.

  • 5 authors
·
Sep 9, 2025

Beyond Content: How Grammatical Gender Shapes Visual Representation in Text-to-Image Models

Research on bias in Text-to-Image (T2I) models has primarily focused on demographic representation and stereotypical attributes, overlooking a fundamental question: how does grammatical gender influence visual representation across languages? We introduce a cross-linguistic benchmark examining words where grammatical gender contradicts stereotypical gender associations (e.g., ``une sentinelle'' - grammatically feminine in French but referring to the stereotypically masculine concept ``guard''). Our dataset spans five gendered languages (French, Spanish, German, Italian, Russian) and two gender-neutral control languages (English, Chinese), comprising 800 unique prompts that generated 28,800 images across three state-of-the-art T2I models. Our analysis reveals that grammatical gender dramatically influences image generation: masculine grammatical markers increase male representation to 73% on average (compared to 22% with gender-neutral English), while feminine grammatical markers increase female representation to 38% (compared to 28% in English). These effects vary systematically by language resource availability and model architecture, with high-resource languages showing stronger effects. Our findings establish that language structure itself, not just content, shapes AI-generated visual outputs, introducing a new dimension for understanding bias and fairness in multilingual, multimodal systems.

  • 6 authors
·
Aug 5, 2025

SoftHGNN: Soft Hypergraph Neural Networks for General Visual Recognition

Visual recognition relies on understanding both the semantics of image tokens and the complex interactions among them. Mainstream self-attention methods, while effective at modeling global pair-wise relations, fail to capture high-order associations inherent in real-world scenes and often suffer from redundant computation. Hypergraphs extend conventional graphs by modeling high-order interactions and offer a promising framework for addressing these limitations. However, existing hypergraph neural networks typically rely on static and hard hyperedge assignments, leading to excessive and redundant hyperedges with hard binary vertex memberships that overlook the continuity of visual semantics. To overcome these issues, we present Soft Hypergraph Neural Networks (SoftHGNNs), which extend the methodology of hypergraph computation, to make it truly efficient and versatile in visual recognition tasks. Our framework introduces the concept of soft hyperedges, where each vertex is associated with hyperedges via continuous participation weights rather than hard binary assignments. This dynamic and differentiable association is achieved by using the learnable hyperedge prototype. Through similarity measurements between token features and the prototype, the model generates semantically rich soft hyperedges. SoftHGNN then aggregates messages over soft hyperedges to capture high-order semantics. To further enhance efficiency when scaling up the number of soft hyperedges, we incorporate a sparse hyperedge selection mechanism that activates only the top-k important hyperedges, along with a load-balancing regularizer to ensure balanced hyperedge utilization. Experimental results across three tasks on five datasets demonstrate that SoftHGNN efficiently captures high-order associations in visual scenes, achieving significant performance improvements.

  • 7 authors
·
May 21, 2025

vS-Graphs: Integrating Visual SLAM and Situational Graphs through Multi-level Scene Understanding

Current Visual Simultaneous Localization and Mapping (VSLAM) systems often struggle to create maps that are both semantically rich and easily interpretable. While incorporating semantic scene knowledge aids in building richer maps with contextual associations among mapped objects, representing them in structured formats like scene graphs has not been widely addressed, encountering complex map comprehension and limited scalability. This paper introduces visual S-Graphs (vS-Graphs), a novel real-time VSLAM framework that integrates vision-based scene understanding with map reconstruction and comprehensible graph-based representation. The framework infers structural elements (i.e., rooms and corridors) from detected building components (i.e., walls and ground surfaces) and incorporates them into optimizable 3D scene graphs. This solution enhances the reconstructed map's semantic richness, comprehensibility, and localization accuracy. Extensive experiments on standard benchmarks and real-world datasets demonstrate that vS-Graphs outperforms state-of-the-art VSLAM methods, reducing trajectory error by an average of 3.38% and up to 9.58% on real-world data. Furthermore, the proposed framework achieves environment-driven semantic entity detection accuracy comparable to precise LiDAR-based frameworks using only visual features. A web page containing more media and evaluation outcomes is available on https://snt-arg.github.io/vsgraphs-results/.

BPJDet: Extended Object Representation for Generic Body-Part Joint Detection

Detection of human body and its parts (e.g., head or hands) has been intensively studied. However, most of these CNNs-based detectors are trained independently, making it difficult to associate detected parts with body. In this paper, we focus on the joint detection of human body and its corresponding parts. Specifically, we propose a novel extended object representation integrating center-offsets of body parts, and construct a dense one-stage generic Body-Part Joint Detector (BPJDet). In this way, body-part associations are neatly embedded in a unified object representation containing both semantic and geometric contents. Therefore, we can perform multi-loss optimizations to tackle multi-tasks synergistically. BPJDet does not suffer from error-prone post matching, and keeps a better trade-off between speed and accuracy. Furthermore, BPJDet can be generalized to detect any one or more body parts. To verify the superiority of BPJDet, we conduct experiments on three body-part datasets (CityPersons, CrowdHuman and BodyHands) and one body-parts dataset COCOHumanParts. While keeping high detection accuracy, BPJDet achieves state-of-the-art association performance on all datasets comparing with its counterparts. Besides, we show benefits of advanced body-part association capability by improving performance of two representative downstream applications: accurate crowd head detection and hand contact estimation. Code is released in https://github.com/hnuzhy/BPJDet.

  • 5 authors
·
Apr 21, 2023

CREST: Cross-modal Resonance through Evidential Deep Learning for Enhanced Zero-Shot Learning

Zero-shot learning (ZSL) enables the recognition of novel classes by leveraging semantic knowledge transfer from known to unknown categories. This knowledge, typically encapsulated in attribute descriptions, aids in identifying class-specific visual features, thus facilitating visual-semantic alignment and improving ZSL performance. However, real-world challenges such as distribution imbalances and attribute co-occurrence among instances often hinder the discernment of local variances in images, a problem exacerbated by the scarcity of fine-grained, region-specific attribute annotations. Moreover, the variability in visual presentation within categories can also skew attribute-category associations. In response, we propose a bidirectional cross-modal ZSL approach CREST. It begins by extracting representations for attribute and visual localization and employs Evidential Deep Learning (EDL) to measure underlying epistemic uncertainty, thereby enhancing the model's resilience against hard negatives. CREST incorporates dual learning pathways, focusing on both visual-category and attribute-category alignments, to ensure robust correlation between latent and observable spaces. Moreover, we introduce an uncertainty-informed cross-modal fusion technique to refine visual-attribute inference. Extensive experiments demonstrate our model's effectiveness and unique explainability across multiple datasets. Our code and data are available at: https://github.com/JethroJames/CREST

  • 8 authors
·
Apr 15, 2024

Distilling Large Language Models for Biomedical Knowledge Extraction: A Case Study on Adverse Drug Events

Large language models (LLMs), such as GPT-4, have demonstrated remarkable capabilities across a wide range of tasks, including health applications. In this paper, we study how LLMs can be used to scale biomedical knowledge curation. We find that while LLMs already possess decent competency in structuring biomedical text, by distillation into a task-specific student model through self-supervised learning, substantial gains can be attained over out-of-box LLMs, with additional advantages such as cost, efficiency, and white-box model access. We conduct a case study on adverse drug event (ADE) extraction, which is an important area for improving care. On standard ADE extraction evaluation, a GPT-3.5 distilled PubMedBERT model attained comparable accuracy as supervised state-of-the-art models without using any labeled data. Despite being over 1,000 times smaller, the distilled model outperformed its teacher GPT-3.5 by over 6 absolute points in F1 and GPT-4 by over 5 absolute points. Ablation studies on distillation model choice (e.g., PubMedBERT vs BioGPT) and ADE extraction architecture shed light on best practice for biomedical knowledge extraction. Similar gains were attained by distillation for other standard biomedical knowledge extraction tasks such as gene-disease associations and protected health information, further illustrating the promise of this approach.

  • 11 authors
·
Jul 12, 2023 1

BiomedSQL: Text-to-SQL for Scientific Reasoning on Biomedical Knowledge Bases

Biomedical researchers increasingly rely on large-scale structured databases for complex analytical tasks. However, current text-to-SQL systems often struggle to map qualitative scientific questions into executable SQL, particularly when implicit domain reasoning is required. We introduce BiomedSQL, the first benchmark explicitly designed to evaluate scientific reasoning in text-to-SQL generation over a real-world biomedical knowledge base. BiomedSQL comprises 68,000 question/SQL query/answer triples grounded in a harmonized BigQuery knowledge base that integrates gene-disease associations, causal inference from omics data, and drug approval records. Each question requires models to infer domain-specific criteria, such as genome-wide significance thresholds, effect directionality, or trial phase filtering, rather than rely on syntactic translation alone. We evaluate a range of open- and closed-source LLMs across prompting strategies and interaction paradigms. Our results reveal a substantial performance gap: GPT-o3-mini achieves 59.0% execution accuracy, while our custom multi-step agent, BMSQL, reaches 62.6%, both well below the expert baseline of 90.0%. BiomedSQL provides a new foundation for advancing text-to-SQL systems capable of supporting scientific discovery through robust reasoning over structured biomedical knowledge bases. Our dataset is publicly available at https://huggingface.co/datasets/NIH-CARD/BiomedSQL, and our code is open-source at https://github.com/NIH-CARD/biomedsql.

  • 11 authors
·
May 23, 2025 2

VISTA-PATH: An interactive foundation model for pathology image segmentation and quantitative analysis in computational pathology

Accurate semantic segmentation for histopathology image is crucial for quantitative tissue analysis and downstream clinical modeling. Recent segmentation foundation models have improved generalization through large-scale pretraining, yet remain poorly aligned with pathology because they treat segmentation as a static visual prediction task. Here we present VISTA-PATH, an interactive, class-aware pathology segmentation foundation model designed to resolve heterogeneous structures, incorporate expert feedback, and produce pixel-level segmentation that are directly meaningful for clinical interpretation. VISTA-PATH jointly conditions segmentation on visual context, semantic tissue descriptions, and optional expert-provided spatial prompts, enabling precise multi-class segmentation across heterogeneous pathology images. To support this paradigm, we curate VISTA-PATH Data, a large-scale pathology segmentation corpus comprising over 1.6 million image-mask-text triplets spanning 9 organs and 93 tissue classes. Across extensive held-out and external benchmarks, VISTA-PATH consistently outperforms existing segmentation foundation models. Importantly, VISTA-PATH supports dynamic human-in-the-loop refinement by propagating sparse, patch-level bounding-box annotation feedback into whole-slide segmentation. Finally, we show that the high-fidelity, class-aware segmentation produced by VISTA-PATH is a preferred model for computational pathology. It improve tissue microenvironment analysis through proposed Tumor Interaction Score (TIS), which exhibits strong and significant associations with patient survival. Together, these results establish VISTA-PATH as a foundation model that elevates pathology image segmentation from a static prediction to an interactive and clinically grounded representation for digital pathology. Source code and demo can be found at https://github.com/zhihuanglab/VISTA-PATH.

zhihuanglab Zhi Huang Lab
·
Jan 23 3

UMMAN: Unsupervised Multi-graph Merge Adversarial Network for Disease Prediction Based on Intestinal Flora

The abundance of intestinal flora is closely related to human diseases, but diseases are not caused by a single gut microbe. Instead, they result from the complex interplay of numerous microbial entities. This intricate and implicit connection among gut microbes poses a significant challenge for disease prediction using abundance information from OTU data. Recently, several methods have shown potential in predicting corresponding diseases. However, these methods fail to learn the inner association among gut microbes from different hosts, leading to unsatisfactory performance. In this paper, we present a novel architecture, Unsupervised Multi-graph Merge Adversarial Network (UMMAN). UMMAN can obtain the embeddings of nodes in the Multi-Graph in an unsupervised scenario, so that it helps learn the multiplex association. Our method is the first to combine Graph Neural Network with the task of intestinal flora disease prediction. We employ complex relation-types to construct the Original-Graph and disrupt the relationships among nodes to generate corresponding Shuffled-Graph. We introduce the Node Feature Global Integration (NFGI) module to represent the global features of the graph. Furthermore, we design a joint loss comprising adversarial loss and hybrid attention loss to ensure that the real graph embedding aligns closely with the Original-Graph and diverges from the Shuffled-Graph. Comprehensive experiments on five classical OTU gut microbiome datasets demonstrate the effectiveness and stability of our method. (We will release our code soon.)

  • 5 authors
·
Jul 31, 2024

Molecular Contrastive Learning with Chemical Element Knowledge Graph

Molecular representation learning contributes to multiple downstream tasks such as molecular property prediction and drug design. To properly represent molecules, graph contrastive learning is a promising paradigm as it utilizes self-supervision signals and has no requirements for human annotations. However, prior works fail to incorporate fundamental domain knowledge into graph semantics and thus ignore the correlations between atoms that have common attributes but are not directly connected by bonds. To address these issues, we construct a Chemical Element Knowledge Graph (KG) to summarize microscopic associations between elements and propose a novel Knowledge-enhanced Contrastive Learning (KCL) framework for molecular representation learning. KCL framework consists of three modules. The first module, knowledge-guided graph augmentation, augments the original molecular graph based on the Chemical Element KG. The second module, knowledge-aware graph representation, extracts molecular representations with a common graph encoder for the original molecular graph and a Knowledge-aware Message Passing Neural Network (KMPNN) to encode complex information in the augmented molecular graph. The final module is a contrastive objective, where we maximize agreement between these two views of molecular graphs. Extensive experiments demonstrated that KCL obtained superior performances against state-of-the-art baselines on eight molecular datasets. Visualization experiments properly interpret what KCL has learned from atoms and attributes in the augmented molecular graphs. Our codes and data are available at https://github.com/ZJU-Fangyin/KCL.

  • 10 authors
·
Dec 1, 2021

SAM-I2V: Upgrading SAM to Support Promptable Video Segmentation with Less than 0.2% Training Cost

Foundation models like the Segment Anything Model (SAM) have significantly advanced promptable image segmentation in computer vision. However, extending these capabilities to videos presents substantial challenges, particularly in ensuring precise and temporally consistent mask propagation in dynamic scenes. SAM 2 attempts to address this by training a model on massive image and video data from scratch to learn complex spatiotemporal associations, resulting in huge training costs that hinder research and practical deployment. In this paper, we introduce SAM-I2V, an effective image-to-video upgradation method for cultivating a promptable video segmentation (PVS) model. Our approach strategically upgrades the pre-trained SAM to support PVS, significantly reducing training complexity and resource requirements. To achieve this, we introduce three key innovations: (i) an image-to-video feature extraction upgrader built upon SAM's static image encoder to enable spatiotemporal video perception, (ii) a memory filtering strategy that selects the most relevant past frames for more effective utilization of historical information, and (iii) a memory-as-prompt mechanism leveraging object memory to ensure temporally consistent mask propagation in dynamic scenes. Comprehensive experiments demonstrate that our method achieves over 90% of SAM 2's performance while using only 0.2% of its training cost. Our work presents a resource-efficient pathway to PVS, lowering barriers for further research in PVS model design and enabling broader applications and advancements in the field. Code and model are available at: https://github.com/showlab/SAM-I2V.

  • 3 authors
·
Jun 2, 2025

CAMELTrack: Context-Aware Multi-cue ExpLoitation for Online Multi-Object Tracking

Online multi-object tracking has been recently dominated by tracking-by-detection (TbD) methods, where recent advances rely on increasingly sophisticated heuristics for tracklet representation, feature fusion, and multi-stage matching. The key strength of TbD lies in its modular design, enabling the integration of specialized off-the-shelf models like motion predictors and re-identification. However, the extensive usage of human-crafted rules for temporal associations makes these methods inherently limited in their ability to capture the complex interplay between various tracking cues. In this work, we introduce CAMEL, a novel association module for Context-Aware Multi-Cue ExpLoitation, that learns resilient association strategies directly from data, breaking free from hand-crafted heuristics while maintaining TbD's valuable modularity. At its core, CAMEL employs two transformer-based modules and relies on a novel association-centric training scheme to effectively model the complex interactions between tracked targets and their various association cues. Unlike end-to-end detection-by-tracking approaches, our method remains lightweight and fast to train while being able to leverage external off-the-shelf models. Our proposed online tracking pipeline, CAMELTrack, achieves state-of-the-art performance on multiple tracking benchmarks. Our code is available at https://github.com/TrackingLaboratory/CAMELTrack.

  • 5 authors
·
May 2, 2025

AceMap: Knowledge Discovery through Academic Graph

The exponential growth of scientific literature requires effective management and extraction of valuable insights. While existing scientific search engines excel at delivering search results based on relational databases, they often neglect the analysis of collaborations between scientific entities and the evolution of ideas, as well as the in-depth analysis of content within scientific publications. The representation of heterogeneous graphs and the effective measurement, analysis, and mining of such graphs pose significant challenges. To address these challenges, we present AceMap, an academic system designed for knowledge discovery through academic graph. We present advanced database construction techniques to build the comprehensive AceMap database with large-scale academic entities that contain rich visual, textual, and numerical information. AceMap also employs innovative visualization, quantification, and analysis methods to explore associations and logical relationships among academic entities. AceMap introduces large-scale academic network visualization techniques centered on nebular graphs, providing a comprehensive view of academic networks from multiple perspectives. In addition, AceMap proposes a unified metric based on structural entropy to quantitatively measure the knowledge content of different academic entities. Moreover, AceMap provides advanced analysis capabilities, including tracing the evolution of academic ideas through citation relationships and concept co-occurrence, and generating concise summaries informed by this evolutionary process. In addition, AceMap uses machine reading methods to generate potential new ideas at the intersection of different fields. Exploring the integration of large language models and knowledge graphs is a promising direction for future research in idea evolution. Please visit https://www.acemap.info for further exploration.

  • 26 authors
·
Mar 4, 2024

CODE-ACCORD: A Corpus of Building Regulatory Data for Rule Generation towards Automatic Compliance Checking

Automatic Compliance Checking (ACC) within the Architecture, Engineering, and Construction (AEC) sector necessitates automating the interpretation of building regulations to achieve its full potential. However, extracting information from textual rules to convert them to a machine-readable format has been a challenge due to the complexities associated with natural language and the limited resources that can support advanced machine-learning techniques. To address this challenge, we introduce CODE-ACCORD, a unique dataset compiled under the EU Horizon ACCORD project. CODE-ACCORD comprises 862 self-contained sentences extracted from the building regulations of England and Finland. Aligned with our core objective of facilitating information extraction from text for machine-readable rule generation, each sentence was annotated with entities and relations. Entities represent specific components such as "window" and "smoke detectors", while relations denote semantic associations between these entities, collectively capturing the conveyed ideas in natural language. We manually annotated all the sentences using a group of 12 annotators. Each sentence underwent annotations by multiple annotators and subsequently careful data curation to finalise annotations, ensuring their accuracy and reliability, thereby establishing the dataset as a solid ground truth. CODE-ACCORD offers a rich resource for diverse machine learning and natural language processing (NLP) related tasks in ACC, including text classification, entity recognition and relation extraction. To the best of our knowledge, this is the first entity and relation-annotated dataset in compliance checking, which is also publicly available.

  • 14 authors
·
Mar 4, 2024

Learning Generalizable Agents via Saliency-Guided Features Decorrelation

In visual-based Reinforcement Learning (RL), agents often struggle to generalize well to environmental variations in the state space that were not observed during training. The variations can arise in both task-irrelevant features, such as background noise, and task-relevant features, such as robot configurations, that are related to the optimal decisions. To achieve generalization in both situations, agents are required to accurately understand the impact of changed features on the decisions, i.e., establishing the true associations between changed features and decisions in the policy model. However, due to the inherent correlations among features in the state space, the associations between features and decisions become entangled, making it difficult for the policy to distinguish them. To this end, we propose Saliency-Guided Features Decorrelation (SGFD) to eliminate these correlations through sample reweighting. Concretely, SGFD consists of two core techniques: Random Fourier Functions (RFF) and the saliency map. RFF is utilized to estimate the complex non-linear correlations in high-dimensional images, while the saliency map is designed to identify the changed features. Under the guidance of the saliency map, SGFD employs sample reweighting to minimize the estimated correlations related to changed features, thereby achieving decorrelation in visual RL tasks. Our experimental results demonstrate that SGFD can generalize well on a wide range of test environments and significantly outperforms state-of-the-art methods in handling both task-irrelevant variations and task-relevant variations.

  • 8 authors
·
Oct 8, 2023

CAMS: Color-Aware Multi-Style Transfer

Image style transfer aims to manipulate the appearance of a source image, or "content" image, to share similar texture and colors of a target "style" image. Ideally, the style transfer manipulation should also preserve the semantic content of the source image. A commonly used approach to assist in transferring styles is based on Gram matrix optimization. One problem of Gram matrix-based optimization is that it does not consider the correlation between colors and their styles. Specifically, certain textures or structures should be associated with specific colors. This is particularly challenging when the target style image exhibits multiple style types. In this work, we propose a color-aware multi-style transfer method that generates aesthetically pleasing results while preserving the style-color correlation between style and generated images. We achieve this desired outcome by introducing a simple but efficient modification to classic Gram matrix-based style transfer optimization. A nice feature of our method is that it enables the users to manually select the color associations between the target style and content image for more transfer flexibility. We validated our method with several qualitative comparisons, including a user study conducted with 30 participants. In comparison with prior work, our method is simple, easy to implement, and achieves visually appealing results when targeting images that have multiple styles. Source code is available at https://github.com/mahmoudnafifi/color-aware-style-transfer.

  • 5 authors
·
Jun 25, 2021 1

Towards Personality-Aware Recommendation

In the last decade new ways of shopping online have increased the possibility of buying products and services more easily and faster than ever. In this new context, personality is a key determinant in the decision making of the consumer when shopping. The two main reasons are: firstly, a person's buying choices are influenced by psychological factors like impulsiveness, and secondly, some consumers may be more susceptible to making impulse purchases than others. To the best of our knowledge, the impact of personality factors on advertisements has been largely neglected at the level of recommender systems. This work proposes a highly innovative research which uses a personality perspective to determine the unique associations among the consumer's buying tendency and advert recommendations. As a matter of fact, the lack of a publicly available benchmark for computational advertising do not allow both the exploration of this intriguing research direction and the evaluation of state-of-the-art algorithms. We present the ADS Dataset, a publicly available benchmark for computational advertising enriched with Big-Five users' personality factors and 1,200 personal users' pictures. The proposed benchmark allows two main tasks: rating prediction over 300 real advertisements (i.e., Rich Media Ads, Image Ads, Text Ads) and click-through rate prediction. Moreover, this work carries out experiments, reviews various evaluation criteria used in the literature, and provides a library for each one of them within one integrated toolbox.

  • 1 authors
·
Jul 18, 2016