Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi (NYUAD), Abu Dhabi, UAE 2. Department of Biology, New York University, New York, NY, USA 3. Biotechnology Research Center, Technology Innovation Institute (TII), PO Box: 9639, Masdar City, Abu Dhabi, UAE Correspondence should be addressed to D.R.N. (drn2@nyu.edu) The models achieved F1 scores up to 95 and operated 16,580x faster and at 2.9x the recall of BLASTP. They effectively classified the algal "dark proteome", (e.g., uncharacterized proteins comprising ~65% of total proteins), validated on new data including a new, complete Hi-C/Pacbio Chlamydomonas genome. SR models reached high accuracy (F1 > 86) when trained on less than 2% of available data, rapidly achieving strong generalization capacity. High accuracy was achieved when training data had intact or scrambled terminal information, demonstrating robust generalization to incomplete sequences.

Graph Neural Networks (GNNs) have emerged as a dominant approach in graph representation learning, yet they often struggle to capture consistent similarity relationships among graphs. While graph kernel methods such as the Weisfeiler-Lehman subtree (WL-subtree) and Weisfeiler-Lehman optimal assignment (WLOA) kernels are effective in capturing similarity relationships, they rely heavily on predefined kernels and lack sufficient non-linearity for more complex data patterns. Our work aims to bridge the gap between neural network methods and kernel approaches by enabling GNNs to consistently capture relational structures in their learned representations. Given the analogy between the message-passing process of GNNs and WL algorithms, we thoroughly compare and analyze the properties of WL-subtree and WLOA kernels. We find that the similarities captured by WLOA at different iterations are asymptotically consistent, ensuring that similar graphs remain similar in subsequent iterations, thereby leading to superior performance over the WL-subtree kernel. Inspired by these findings, we conjecture that the consistency in the similarities of graph representations across GNN layers is crucial in capturing relational structures and enhancing graph classification performance. Thus, we propose a loss to enforce the similarity of graph representations to be consistent across different layers. Our empirical analysis verifies our conjecture and shows that our proposed consistency loss can significantly enhance graph classification performance across several GNN backbones on various datasets.

Gradient attacks and data poisoning tamper with the training of machine learning algorithms to maliciously alter them and have been proven to be equivalent in convex settings. The extent of harm these attacks can produce in non-convex settings is still to be determined. Gradient attacks can affect far less systems than data poisoning but have been argued to be more harmful since they can be arbitrary, whereas data poisoning reduces the attacker's power to only being able to inject data points to training sets, via e.g. legitimate participation in a collaborative dataset. This raises the question of whether the harm made by gradient attacks can be matched by data poisoning in non-convex settings. In this work, we provide a positive answer in a worst-case scenario and show how data poisoning can mimic a gradient attack to perform an availability attack on (non-convex) neural networks. Through gradient inversion, commonly used to reconstruct data points from actual gradients, we show how reconstructing data points out of malicious gradients can be sufficient to perform a range of attacks. This allows us to show, for the first time, an availability attack on neural networks through data poisoning, that degrades the model's performances to random-level through a minority (as low as 1%) of poisoned points.

Can peer recommendation engines elevate people's creative performances in self-organizing social networks? Answering this question requires resolving challenges in data collection (e.g., tracing inspiration links and psycho-social attributes of nodes) and intervention design (e.g., balancing idea stimulation and redundancy in evolving information environments). We trained a model that predicts people's ideation performances using semantic and network-structural features in an online platform. Using this model, we built SocialMuse, which maximizes people's predicted performances to generate peer recommendations for them. We found treatment networks leveraging SocialMuse outperforming AI-agnostic control networks in several creativity measures. The treatment networks were more decentralized than the control, as SocialMuse increasingly emphasized network-structural features at large network sizes. This decentralization spreads people's inspiration sources, helping inspired ideas stand out better. Our study provides actionable insights into building intelligent systems for elevating creativity.

eXplainable Artificial Intelligence (XAI) has garnered significant attention for enhancing transparency and trust in machine learning models. However, the scopes of most existing explanation techniques focus either on offering a holistic view of the explainee model (global explanation) or on individual instances (local explanation), while the middle ground, i.e., cohort-based explanation, is less explored. Cohort explanations offer insights into the explainee's behavior on a specific group or cohort of instances, enabling a deeper understanding of model decisions within a defined context. In this paper, we discuss the unique challenges and opportunities associated with measuring cohort explanations, define their desired properties, and create a generalized framework for generating cohort explanations based on supervised clustering.

In-group language is an important signifier of group dynamics. This paper proposes a novel method for inducing lexicons of in-group language, which incorporates its socio-temporal context. Existing methods for lexicon induction do not capture the evolving nature of in-group language, nor the social structure of the community. Using dynamic word and user embeddings trained on conversations from online anti-women communities, our approach outperforms prior methods for lexicon induction. We develop a test set for the task of lexicon induction and a new lexicon of manosphere language, validated by human experts, which quantifies the relevance of each term to a specific sub-community at a given point in time. Finally, we present novel insights on in-group language which illustrate the utility of this approach.

Contextualized embeddings based on large language models (LLMs) are available for various languages, but their coverage is often limited for lower resourced languages. Using LLMs for such languages is often difficult due to a high computational cost; not only during training, but also during inference. Static word embeddings are much more resource-efficient ("green"), and thus still provide value, particularly for very low-resource languages. There is, however, a notable lack of comprehensive repositories with such embeddings for diverse languages. To address this gap, we present GrEmLIn, a centralized repository of green, static baseline embeddings for 87 mid- and low-resource languages. We compute GrEmLIn embeddings with a novel method that enhances GloVe embeddings by integrating multilingual graph knowledge, which makes our static embeddings competitive with LLM representations, while being parameter-free at inference time. Our experiments demonstrate that GrEmLIn embeddings outperform state-of-the-art contextualized embeddings from E5 on the task of lexical similarity. They remain competitive in extrinsic evaluation tasks like sentiment analysis and natural language inference, with average performance gaps of just 5-10\% or less compared to state-of-the-art models, given a sufficient vocabulary overlap with the target task, and underperform only on topic classification. Our code and embeddings are publicly available at https://huggingface.co/DFKI.

Normalizing flow-based variational inference (flow VI) is a promising approximate inference approach, but its performance remains inconsistent across studies. Numerous algorithmic choices influence flow VI's performance. We conduct a step-by-step analysis to disentangle the impact of some of the key factors: capacity, objectives, gradient estimators, number of gradient estimates (batchsize), and step-sizes. Each step examines one factor while neutralizing others using insights from the previous steps and/or using extensive parallel computation. To facilitate high-fidelity evaluation, we curate a benchmark of synthetic targets that represent common posterior pathologies and allow for exact sampling. We provide specific recommendations for different factors and propose a flow VI recipe that matches or surpasses leading turnkey Hamiltonian Monte Carlo (HMC) methods.

Real-world datasets often contain missing or corrupted values. Completing multidimensional tensor-structured data with missing entries is essential for numerous applications. Smoothness-constrained low-rank factorization models have shown superior performance with reduced computational costs. While effective at capturing global and long-range correlations, these models struggle to reproduce short-scale, high-frequency variations in the data. In this paper, we introduce the Generalized Least Squares Kernelized Tensor Factorization (GLSKF) framework for tensor completion. GLSKF integrates smoothness-constrained low-rank factorization with a locally correlated residual process; the resulting additive structure can effectively characterize both global dependencies and local variations. In particular, we define the covariance norm to enforce the smoothness of factor matrices in the global low-rank factorization, and use structured covariance/kernel functions to model the local processes. For model estimation, we develop an alternating least squares (ALS) procedure with closed-form solutions for each subproblem. To efficiently handle missing data, GLSKF utilizes projection matrices that preserve the Kronecker structure of covariances, facilitating fast computations through conjugate gradient (CG) and preconditioned conjugate gradient (PCG) algorithms. The proposed framework is evaluated on four real-world datasets across diverse tasks: traffic speed imputation, color image inpainting, video completion, and MRI image reconstruction. Experimental results confirm that GLSKF delivers superior effectiveness and scalability, establishing it as a robust solution for multidimensional tensor completion.

Sampling from high dimensional, multimodal distributions remains a fundamental challenge across domains such as statistical Bayesian inference and physics based machine learning. In this paper, we propose Annealing Flow, a continuous normalizing flow based approach designed to sample from high dimensional and multimodal distributions. The key idea is to learn a continuous normalizing flow based transport map, guided by annealing, to transition samples from an easy to sample distribution to the target distribution, facilitating effective exploration of modes in high dimensional spaces. Unlike many existing methods, AF training does not rely on samples from the target distribution. AF ensures effective and balanced mode exploration, achieves linear complexity in sample size and dimensions, and circumvents inefficient mixing times. We demonstrate the superior performance of AF compared to state of the art methods through extensive experiments on various challenging distributions and real world datasets, particularly in high-dimensional and multimodal settings. We also highlight the potential of AF for sampling the least favorable distributions.