Canada

In recent years, significant progress has been made in this field of protein function prediction with the development of various machine-learning approaches.
However, most existing methods formulate the task as a multi-classification problem, i.e. assigning predefined labels to proteins.
In this work, we propose a novel approach, Prot2Text, which predicts a protein&#39;s function in a free text style, moving beyond the conventional binary or categorical classifications.
By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including protein sequence, structure, and textual annotation.
This multimodal approach allows for a holistic representation of proteins&#39; functions, enabling the generation of detailed and accurate descriptions.
To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text.
These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins&#39; functions.

AAAI 2024

Prot2Text: Multimodal Protein’s Function Generation with GNNs and Transformers

ml: deep generative models & autoencoders

ml: multimodal learning

ml: graph-based machine learning

snlp: generation

### Welcome to 2025 Annual Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics

Welcome to the 2025 meeting of the Nations of the Americas Chapter of the Association for Computational Linguistics! I am proud to help organize the first NAACL conference to carry the new name of our organization, one that emphasizes inclusion for all of the Americas. I am also pleased to welcome you to Albuquerque, New Mexico, a state whose unique blend of cultural influences will make for an excellent backdrop for NAACL 2025, especially with this year’s special theme on NLP in a Multicultural World. 
**[Continue reading...](https://drive.google.com/file/d/1jX-qGhqVSZZCIrAnJaz798pflu5Irrdn/view?usp=sharing)**

*- Colin Cherry, Google, NAACL 2025 General Chair* 

[![](https://assets.underline.io/markdown_image/1/image/b087f8a4dc5816d6e1a6514e59c59ac3.png)](https://drive.google.com/file/d/1T96GzPqObXrMln2BMByCSXTSizjTg69P/view?usp=sharing)

You need to log in with the email address you registered with. Access credentials have been sent to your email. 

Please be sure to check your spam and other email folders if you do not see an email confirmation right away.

Please log in to explore this event.

To access NAACL 2025 event page you are required to register. Please follow [**this link**](https://2025.naacl.org/registration/registration/) to register. Access will depend on your registration type.

Please register!

NAACL 2025

Welcome to 2025 Annual Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics

In recent years, significant progress has been made in this field of protein function prediction with the development of various machine-learning approaches.
However, most existing methods formulate the task as a multi-classification problem, i.e. assigning predefined labels to proteins.
In this work, we propose a novel approach, Prot2Text, which predicts a protein's function in a free text style, moving beyond the conventional binary or categorical classifications.
By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including protein sequence, structure, and textual annotation.
This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate descriptions.
To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text.
These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins' functions.

technical paper

We are pleased to announce the Thirty-Eighth AAAI Conference on Artificial Intelligence (AAAI-24), which will be held in Vancouver, British Columbia at the Vancouver Convention Centre – West Building from 20-27 February, 2024.

The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines. AAAI-24 will feature technical paper presentations, special tracks, invited speakers, workshops, tutorials, poster sessions, senior member presentations, competitions, and exhibit programs, and a range of other activities to be announced.

We expect for AAAI-24 to be an in-person conference – one author of all accepted papers will be expected to present work in person unless there are exceptional circumstances that prevent this.

In order to access the AAAI-24 event page you need to register [here](https://aaai.org/aaai-conference/registration/)

The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines. 

Solving the task of inverse imaging problems can restore unknown clean images from input measurements that have incomplete information. Utilizing powerful generative models, such as denoising diffusion models, could better tackle the ill-posed issues of inverse problems with the distribution prior of the unknown clean images. We propose a learnable state-estimator-based diffusion model to incorporate the measurements into the reconstruction process. Our method makes efficient use of the pre-trained diffusion models with computational feasibility compared to the conditional diffusion models, which need to be trained from scratch. In addition, our pipeline does not require explicit knowledge of the image degradation operator or make the assumption of its form, unlike many other works that use the pre-trained diffusion models at the test time. The experiments on three typical inverse imaging problems (both linear and non-linear), inpainting, deblurring, and JPEG compression restoration, have comparable results with the state-of-the-art methods.

A Diffusion Model with State Estimation for Degradation-Blind Inverse Imaging

Deep neural networks (DNNs) have achieved tremendous success in various applications including video action recognition, yet remain vulnerable to backdoor attacks (Trojans). The backdoor-compromised model will mis-classify to the target class chosen by the attacker when a test instance (from a non-target class) is embedded with a specific trigger, while maintaining high accuracy on attack-free instances. Although there are extensive studies on backdoor attacks against image data, the susceptibility of video-based systems under backdoor attacks remains largely unexplored. Current studies are direct extensions of approaches proposed for image data, e.g., the triggers are independently embedded within the frames, which tend to be detectable by existing defenses. In this paper, we introduce a simple yet effective backdoor attack against video data. Our proposed attack, adding perturbations in a transformed domain, plants an imperceptible, temporally distributed trigger across the video frames, and is shown to be resilient to existing defensive strategies. The effectiveness of the proposed attack is demonstrated by extensive experiments with various well-known models on two video recognition benchmarks, UCF101 and HMDB51, and a sign language recognition benchmark, Greek Sign Language (GSL) dataset. We delve into the impact of several influential factors on our proposed attack and identify an intriguing effect termed "collateral damage" through extensive studies.

Temporal-Distributed Backdoor Attack against Video Based Action Recognition

Despite achieving impressive improvement in accuracy, most existing monocular 3D human mesh reconstruction methods require large-scale 2D/3D ground-truths for supervision, which limits their applications on unlabeled in-the-wild data that is ubiquitous. To alleviate the reliance on 2D/3D ground-truths, we present a self-supervised 3D human pose and shape reconstruction framework that relies only on self-consistency between intermediate representations of images and projected 2D predictions. Specifically, we extract 2D joints and depth maps from monocular images as proxy inputs, which provides complementary clues to infer accurate 3D human meshes. Furthermore, to reduce the impacts from noisy and ambiguous inputs while better concentrate on the high-quality information, we design an uncertainty-aware module to automatically learn the reliability of the inputs at body-joint level based on the consistency between 2D joints and depth map. Experiments on benchmark datasets show that our approach outperforms other state-of-the-art methods at similar supervision levels.

Self-Supervised 3D Human Mesh Recovery from a Single Image with Uncertainty-Aware Learning

We study to generate novel views of indoor scenes given sparse input views. The challenge is to achieve both photorealism and view consistency. We present SparseGNV: a learning framework that incorporates 3D structures and image generative models to generate novel views with three modules. The first module builds a neural point cloud as underlying geometry, providing scene context and guidance for the target novel view. The second module utilizes a transformer-based network to map the scene context and the guidance into a shared latent space and autoregressively decodes the target view in the form of discrete image tokens. The third module reconstructs the tokens back to the image of the target view. SparseGNV is trained across a large-scale indoor scene dataset to learn generalizable priors. Once trained, it can efficiently generate novel views of an unseen indoor scene in a feed-forward manner. We evaluate SparseGNV on real-world indoor scenes and demonstrate that it outperforms state-of-the-art methods based on either neural radiance fields or conditional image generation.

SparseGNV: Generating Novel Views of Indoor Scenes with Sparse RGB-D Images

This work presents insights gained by investigating the relationship between algorithmic fairness and the concept of secure information flow. The problem of enforcing secure information flow is well-studied in the context of information security: If secret information may "flow" through an algorithm or program in such a way that it can influence the program’s output, then that is considered insecure information flow as attackers could potentially observe (parts of) the secret.

There is a strong correspondence between secure information flow and algorithmic fairness: if protected attributes such as race, gender, or age are treated as secret program inputs, then secure information flow means that these "secret" attributes cannot influence the result of a program. While most research in algorithmic fairness evaluation concentrates on studying the impact of algorithms (often treating the algorithm as a black-box), the concepts derived from information flow can be used both for the analysis of disparate treatment as well as disparate impact w.r.t. a structural causal model.

In this paper, we examine the relationship between quantitative as well as qualitative information-flow properties and fairness. Moreover, based on this duality, we derive a new quantitative notion of fairness called fairness spread, which can be easily analyzed using quantitative information flow and which strongly relates to counterfactual fairness. We demonstrate that off-the-shelf tools for information-flow properties can be used in order to formally analyze a program's algorithmic fairness properties, including the new notion of fairness spread as well as established notions such as demographic parity.

An Information-Flow Perspective on Algorithmic Fairness | VIDEO

Given a set of observations, feature acquisition is about finding the subset of unobserved features which would enhance accuracy. Such problems has been explored in a sequential setting in prior work. Here, the model receives feedback from every new feature acquireed and chooses to explore more features or to predict. However, sequential acquisition is not feasible in some settings where time is of essence. We consider the problem of feature acquisition in batch, where the subset of features to be queried in batch is chosen based on the currently observed features, and then acquired as a batch, followed by prediction. We solve this problem using several technical innovations. First, we use a feature generator to draw a subset of the synthetic features for some examples, which reduces the cost of oracle queries. Second, to make the feature acquisition problem tractable for the large heterogeneous observed features, we partition the data into buckets, by borrowing tools from locality sensitive hashing and then train a mixture of experts model. Third, we design a tractable lower bound of the original objective.
We use a greedy algorithm combined with model training to solve the underlying problem. Experiments with four datasets shows that our approach outperforms these methods in terms of trade off between accuracy and feature acquisition cost.

Generator Assisted Mixture of Experts for Feature Acquisition in Batch | VIDEO

Bayesian optimization (BO) is a sample-efficient method and has been widely used for optimizing expensive black-box functions. Recently, there has been a considerable interest in BO literature in optimizing functions that are affected by context variable in the environment, which is uncontrollable by decision makers. In this paper, we focus on the optimization of functions' expectations over continuous context variable, subject to an unknown distribution. To address this problem, we propose two algorithms that employ kernel density estimation to learn the probability density function (PDF) of continuous context variable online. The first algorithm is simpler, which directly optimizes the expectation under the estimated PDF. Considering that the estimated PDF may have high estimation error when the true distribution is complicated, we further propose the second algorithm that optimizes the distributionally robust objective. Theoretical results demonstrate that both algorithms have sub-linear Bayesian cumulative regret on the expectation objective. Furthermore, we conduct numerical experiments to empirically demonstrate the effectiveness of our algorithms.

Stochastic Bayesian Optimization with Unknown Continuous Context Distribution via Kernel Density Estimation

Disease control experts inspect public health data streams daily for outliers worth investigating, like those corresponding to data quality issues or disease outbreaks. However, they can only examine a few of the thousands of maximally-tied outliers returned by univariate outlier detection methods applied to large-scale public health data streams. To help experts distinguish the most important outliers from these thousands of tied outliers, we propose a new task for algorithms to rank the outputs of any univariate method applied to each of many streams. Our novel algorithm for this task, which leverages hierarchical networks and extreme value analysis, performed the best across traditional outlier detection metrics in a human-expert evaluation using public health data streams. Most importantly, experts have used our open-source Python implementation since April 2023 and report identifying outliers worth investigating 9.1x faster than their prior baseline. Other organizations can readily adapt this implementation to create rankings from the outputs of their tailored univariate methods across large-scale streams.

Outlier Ranking for Large-Scale Public Health Data

As machine learning workloads are significantly increasing energy consumption, sustainable data centers with low carbon emissions are becoming a top priority for governments and corporations worldwide. This requires a paradigm shift in optimizing power consumption in cooling and IT loads, shifting flexible loads based on the availability of renewable energy in the power grid, and leveraging battery storage from the uninterrupted power supply in data centers, using collaborative agents. The complex association between these optimization strategies and their dependencies on variable external factors like weather and the power grid carbon intensity makes this a hard problem. Currently, a real-time controller to optimize all these goals simultaneously in a dynamic real-world setting is lacking. We propose a Data Center Carbon Footprint Reduction (DC-CFR) multi-agent Reinforcement Learning (MARL) framework that optimizes data centers for the multiple objectives of carbon footprint reduction, energy consumption, and energy cost. The results show that the DC-CFR MARL agents effectively resolved the complex interdependencies in optimizing cooling, load shifting, and energy storage in real-time for various locations under real-world dynamic weather and grid carbon intensity conditions. DC-CFR significantly outperformed the industry-standard ASHRAE controller with a considerable reduction in carbon emissions (14.5%), energy usage (14.4%), and energy cost (13.7%) when evaluated over one year across multiple geographical regions.

Carbon Footprint Reduction for Sustainable Data Centers in Real-Time

Marine mammals and their ecosystem face significant threats from, for example, military active sonar and marine transportation. To mitigate this harm, early detection and classification of marine mammals are essential. While recent efforts have utilized spectrogram analysis and machine learning techniques, there remain challenges in their efficiency. Therefore, we propose a novel knowledge distillation framework, named XCFSMN, for this problem. We construct a teacher model that fuses the features extracted from an X-vector extractor, a DenseNet and Cross-Covariance attended compact Feed-Forward Sequential Memory Network (cFSMN). The teacher model transfers knowledge to a simpler cFSMN model through a temperature-cooling strategy for efficient learning. Compared to multiple convolutional neural network backbones and transformers, the proposed framework achieves state-of-the-art efficiency and performance. The improved model size is approximately 20 times smaller and the inference time can be 10 times shorter without affecting the model’s accuracy.

Downloads

Next from AAAI 2024

A Diffusion Model with State Estimation for Degradation-Blind Inverse Imaging

Similar lecture

Protein2Text: Resampling Mechanism to Translate Protein Sequences into Human-Interpretable Text

.css-70qvj9{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;-webkit-align-items:center;-webkit-box-align:center;-ms-flex-align:center;align-items:center;}Downloads

Next from AAAI 2024

A Diffusion Model with State Estimation for Degradation-Blind Inverse Imaging

Similar lecture

Protein2Text: Resampling Mechanism to Translate Protein Sequences into Human-Interpretable Text

Downloads