Kira Radinsky

Noam Koren, Rafael Moschopoulos, Kira Radinsky et al. · princeton

Partial differential equations (PDEs) govern complex systems, yet neural operators often struggle to efficiently capture the long-range, nonlocal interactions inherent in their solution maps. We introduce Spectral Filtering Operator (SFO), a neural operator that parameterizes integral kernels using the Universal Spectral Basis (USB), a fixed, global orthonormal basis derived from the eigenmodes of the Hilbert matrix in spectral filtering theory. Motivated by our theoretical finding that the discrete Green's functions of shift-invariant PDE discretizations exhibit spatial Linear Dynamical System (LDS) structure, we prove that these kernels admit compact approximations in the USB. By learning only the spectral coefficients of rapidly decaying eigenvalues, SFO achieves a highly efficient representation. Across six benchmarks, including reaction-diffusion, fluid dynamics, and 3D electromagnetics, SFO achieves state-of-the-art accuracy, reducing error by up to 40% relative to strong baselines while using substantially fewer parameters.

Noam Koren, Ralf J. J. Mackenbach, Ruud J. G. van Sloun et al.

Neural operators have emerged as a promising paradigm for learning solution operators of partial differential equa- tions (PDEs) directly from data. Existing methods, such as those based on Fourier or graph techniques, make strong as- sumptions about the structure of the kernel integral opera- tor, assumptions which may limit expressivity. We present SVD-NO, a neural operator that explicitly parameterizes the kernel by its singular-value decomposition (SVD) and then carries out the integral directly in the low-rank basis. Two lightweight networks learn the left and right singular func- tions, a diagonal parameter matrix learns the singular values, and a Gram-matrix regularizer enforces orthonormality. As SVD-NO approximates the full kernel, it obtains a high de- gree of expressivity. Furthermore, due to its low-rank struc- ture the computational complexity of applying the operator remains reasonable, leading to a practical system. In exten- sive evaluations on five diverse benchmark equations, SVD- NO achieves a new state of the art. In particular, SVD-NO provides greater performance gains on PDEs whose solutions are highly spatially variable. The code of this work is publicly available at https://github.com/2noamk/SVDNO.git.

Gal Peretz, Kira Radinsky

Many texts, especially in chemistry and biology, describe complex processes. We focus on texts that describe a chemical reaction process and questions that ask about the process's outcome under different environmental conditions. To answer questions about such processes, one needs to understand the interactions between the different entities involved in the process and to simulate their state transitions during the process execution under different conditions. A state transition is defined as the memory modification the program does to the variables during the execution. We hypothesize that generating code and executing it to simulate the process will allow answering such questions. We, therefore, define a domain-specific language (DSL) to represent processes. We contribute to the community a unique dataset curated by chemists and annotated by computer scientists. The dataset is composed of process texts, simulation questions, and their corresponding computer codes represented by the DSL.We propose a neural program synthesis approach based on reinforcement learning with a novel state-transition semantic reward. The novel reward is based on the run-time semantic similarity between the predicted code and the reference code. This allows simulating complex process transitions and thus answering simulation questions. Our approach yields a significant boost in accuracy for simulation questions: 88\% accuracy as opposed to 83\% accuracy of the state-of-the-art neural program synthesis approaches and 54\% accuracy of state-of-the-art end-to-end text-based approaches.

Dan Kalifa, Uriel Singer, Kira Radinsky

Proteins play a vital role in biological processes and are indispensable for living organisms. Accurate representation of proteins is crucial, especially in drug development. Recently, there has been a notable increase in interest in utilizing machine learning and deep learning techniques for unsupervised learning of protein representations. However, these approaches often focus solely on the amino acid sequence of proteins and lack factual knowledge about proteins and their interactions, thus limiting their performance. In this study, we present GOProteinGNN, a novel architecture that enhances protein language models by integrating protein knowledge graph information during the creation of amino acid level representations. Our approach allows for the integration of information at both the individual amino acid level and the entire protein level, enabling a comprehensive and effective learning process through graph-based learning. By doing so, we can capture complex relationships and dependencies between proteins and their functional annotations, resulting in more robust and contextually enriched protein representations. Unlike previous methods, GOProteinGNN uniquely learns the entire protein knowledge graph during training, which allows it to capture broader relational nuances and dependencies beyond mere triplets as done in previous work. We perform a comprehensive evaluation on several downstream tasks demonstrating that GOProteinGNN consistently outperforms previous methods, showcasing its effectiveness and establishing it as a state-of-the-art solution for protein representation learning.

Yakir Yehuda, Kira Radinsky

In the realm of artificial intelligence, the generation of realistic training data for supervised learning tasks presents a significant challenge. This is particularly true in the synthesis of electrocardiograms (ECGs), where the objective is to develop a synthetic 12-lead ECG model. The primary complexity of this task stems from accurately modeling the intricate biological and physiological interactions among different ECG leads. Although mathematical process simulators have shed light on these dynamics, effectively incorporating this understanding into generative models is not straightforward. In this work, we introduce an innovative method that employs ordinary differential equations (ODEs) to enhance the fidelity of generating 12-lead ECG data. This approach integrates a system of ODEs that represent cardiac dynamics directly into the generative model's optimization process, allowing for the production of biologically plausible ECG training data that authentically reflects real-world variability and inter-lead dependencies. We conducted an empirical analysis of thousands of ECGs and found that incorporating cardiac simulation insights into the data generation process significantly improves the accuracy of heart abnormality classifiers trained on this synthetic 12-lead ECG data.

Uriel Singer, Haggai Roitman, Ido Guy et al.

Temporal graph neural networks (temporal GNNs) have been widely researched, reaching state-of-the-art results on multiple prediction tasks. A common approach employed by most previous works is to apply a layer that aggregates information from the historical neighbors of a node. Taking a different research direction, in this work, we propose tBDFS -- a novel temporal GNN architecture. tBDFS applies a layer that efficiently aggregates information from temporal paths to a given (target) node in the graph. For each given node, the aggregation is applied in two stages: (1) A single representation is learned for each temporal path ending in that node, and (2) all path representations are aggregated into a final node representation. Overall, our goal is not to add new information to a node, but rather observe the same exact information in a new perspective. This allows our model to directly observe patterns that are path-oriented rather than neighborhood-oriented. This can be thought as a Depth-First Search (DFS) traversal over the temporal graph, compared to the popular Breath-First Search (BFS) traversal that is applied in previous works. We evaluate tBDFS over multiple link prediction tasks and show its favorable performance compared to state-of-the-art baselines. To the best of our knowledge, we are the first to apply a temporal-DFS neural network.

Amitay Sicherman, Kira Radinsky

Computational prediction of enzymatic reactions represents a crucial challenge in sustainable chemical synthesis across various scientific domains, ranging from drug discovery to materials science and green chemistry. These syntheses rely on proteins that selectively catalyze complex molecular transformations. These protein catalysts exhibit remarkable substrate adaptability, with the same protein often catalyzing different chemical transformations depending on its molecular partners. Current approaches to protein representation in reaction prediction either ignore protein structure entirely or rely on static embeddings, failing to capture how proteins dynamically adapt their behavior to different substrates. We present Docking-Aware Attention (DAA), a novel architecture that generates dynamic, context-dependent protein representations by incorporating molecular docking information into the attention mechanism. DAA combines physical interaction scores from docking predictions with learned attention patterns to focus on protein regions most relevant to specific molecular interactions. We evaluate our method on enzymatic reaction prediction, where it outperforms previous state-of-the-art methods, achieving 62.2\% accuracy versus 56.79\% on complex molecules and 55.54\% versus 49.45\% on innovative reactions. Through detailed ablation studies and visualizations, we demonstrate how DAA generates interpretable attention patterns that adapt to different molecular contexts. Our approach represents a general framework for context-aware protein representation in biocatalysis prediction, with potential applications across enzymatic synthesis planning. We open-source our implementation and pre-trained models to facilitate further research.

Amitay Sicherman, Kira Radinsky

The challenge in computational biology and drug discovery lies in creating comprehensive representations of proteins and molecules that capture their intrinsic properties and interactions. Traditional methods often focus on unimodal data, such as protein sequences or molecular structures, limiting their ability to capture complex biochemical relationships. This work enhances these representations by integrating biochemical reactions encompassing interactions between molecules and proteins. By leveraging reaction data alongside pre-trained embeddings from state-of-the-art protein and molecule models, we develop ReactEmbed, a novel method that creates a unified embedding space through contrastive learning. We evaluate ReactEmbed across diverse tasks, including drug-target interaction, protein-protein interaction, protein property prediction, and molecular property prediction, consistently surpassing all current state-of-the-art models. Notably, we showcase ReactEmbed's practical utility through successful implementation in lipid nanoparticle-based drug delivery, enabling zero-shot prediction of blood-brain barrier permeability for protein-nanoparticle complexes. The code and comprehensive database of reaction pairs are available for open use at \href{https://github.com/amitaysicherman/ReactEmbed}{GitHub}.

Dan Kalifa, Uriel Singer, Ido Guy et al.

Consumer demand forecasting is of high importance for many e-commerce applications, including supply chain optimization, advertisement placement, and delivery speed optimization. However, reliable time series sales forecasting for e-commerce is difficult, especially during periods with many anomalies, as can often happen during pandemics, abnormal weather, or sports events. Although many time series algorithms have been applied to the task, prediction during anomalies still remains a challenge. In this work, we hypothesize that leveraging external knowledge found in world events can help overcome the challenge of prediction under anomalies. We mine a large repository of 40 years of world events and their textual representations. Further, we present a novel methodology based on transformers to construct an embedding of a day based on the relations of the day's events. Those embeddings are then used to forecast future consumer behavior. We empirically evaluate the methods over a large e-commerce products sales dataset, extracted from eBay, one of the world's largest online marketplaces. We show over numerous categories that our method outperforms state-of-the-art baselines during anomalies.

Noam Koren, Kira Radinsky

Multivariate time series forecasting is a pivotal task in several domains, including financial planning, medical diagnostics, and climate science. This paper presents the Neural Fourier Transform (NFT) algorithm, which combines multi-dimensional Fourier transforms with Temporal Convolutional Network layers to improve both the accuracy and interpretability of forecasts. The Neural Fourier Transform is empirically validated on fourteen diverse datasets, showing superior performance across multiple forecasting horizons and lookbacks, setting new benchmarks in the field. This work advances multivariate time series forecasting by providing a model that is both interpretable and highly predictive, making it a valuable tool for both practitioners and researchers. The code for this study is publicly available.

Shadi Iskander, Kira Radinsky, Yonatan Belinkov

Mitigating social biases typically requires identifying the social groups associated with each data sample. In this paper, we present DAFair, a novel approach to address social bias in language models. Unlike traditional methods that rely on explicit demographic labels, our approach does not require any such information. Instead, we leverage predefined prototypical demographic texts and incorporate a regularization term during the fine-tuning process to mitigate bias in the model's representations. Our empirical results across two tasks and two models demonstrate the effectiveness of our method compared to previous approaches that do not rely on labeled data. Moreover, with limited demographic-annotated data, our approach outperforms common debiasing approaches.

Shadi Iskander, Kira Radinsky, Yonatan Belinkov

Natural language processing models tend to learn and encode social biases present in the data. One popular approach for addressing such biases is to eliminate encoded information from the model's representations. However, current methods are restricted to removing only linearly encoded information. In this work, we propose Iterative Gradient-Based Projection (IGBP), a novel method for removing non-linear encoded concepts from neural representations. Our method consists of iteratively training neural classifiers to predict a particular attribute we seek to eliminate, followed by a projection of the representation on a hypersurface, such that the classifiers become oblivious to the target attribute. We evaluate the effectiveness of our method on the task of removing gender and race information as sensitive attributes. Our results demonstrate that IGBP is effective in mitigating bias through intrinsic and extrinsic evaluations, with minimal impact on downstream task accuracy.

Guy D. Rosin, Kira Radinsky

Pretrained language models based on the transformer architecture have shown great success in NLP. Textual training data often comes from the web and is thus tagged with time-specific information, but most language models ignore this information. They are trained on the textual data alone, limiting their ability to generalize temporally. In this work, we extend the key component of the transformer architecture, i.e., the self-attention mechanism, and propose temporal attention - a time-aware self-attention mechanism. Temporal attention can be applied to any transformer model and requires the input texts to be accompanied with their relevant time points. It allows the transformer to capture this temporal information and create time-specific contextualized word representations. We leverage these representations for the task of semantic change detection; we apply our proposed mechanism to BERT and experiment on three datasets in different languages (English, German, and Latin) that also vary in time, size, and genre. Our proposed model achieves state-of-the-art results on all the datasets.

Guy D. Rosin, Ido Guy, Kira Radinsky

Our world is constantly evolving, and so is the content on the web. Consequently, our languages, often said to mirror the world, are dynamic in nature. However, most current contextual language models are static and cannot adapt to changes over time. In this work, we propose a temporal contextual language model called TempoBERT, which uses time as an additional context of texts. Our technique is based on modifying texts with temporal information and performing time masking - specific masking for the supplementary time information. We leverage our approach for the tasks of semantic change detection and sentence time prediction, experimenting on diverse datasets in terms of time, size, genre, and language. Our extensive evaluation shows that both tasks benefit from exploiting time masking.

Uriel Singer, Kira Radinsky

Graph neural networks (GNNs), has been widely used for supervised learning tasks in graphs reaching state-of-the-art results. However, little work was dedicated to creating unbiased GNNs, i.e., where the classification is uncorrelated with sensitive attributes, such as race or gender. Some ignore the sensitive attributes or optimize for the criteria of statistical parity for fairness. However, it has been shown that neither approaches ensure fairness, but rather cripple the utility of the prediction task. In this work, we present a GNN framework that allows optimizing representations for the notion of Equalized Odds fairness criteria. The architecture is composed of three components: (1) a GNN classifier predicting the utility class, (2) a sampler learning the distribution of the sensitive attributes of the nodes given their labels. It generates samples fed into a (3) discriminator that discriminates between true and sampled sensitive attributes using a novel "permutation loss" function. Using these components, we train a model to neglect information regarding the sensitive attribute only with respect to its label. To the best of our knowledge, we are the first to optimize GNNs for the equalized odds criteria. We evaluate our classifier over several graph datasets and sensitive attributes and show our algorithm reaches state-of-the-art results.

Guy D. Rosin, Ido Guy, Kira Radinsky

A significant number of event-related queries are issued in Web search. In this paper, we seek to improve retrieval performance by leveraging events and specifically target the classic task of query expansion. We propose a method to expand an event-related query by first detecting the events related to it. Then, we derive the candidates for expansion as terms semantically related to both the query and the events. To identify the candidates, we utilize a novel mechanism to simultaneously embed words and events in the same vector space. We show that our proposed method of leveraging events improves query expansion performance significantly compared with state-of-the-art methods on various newswire TREC datasets.

Tomer Golany, Daniel Freedman, Kira Radinsky

Generating training examples for supervised tasks is a long sought after goal in AI. We study the problem of heart signal electrocardiogram (ECG) synthesis for improved heartbeat classification. ECG synthesis is challenging: the generation of training examples for such biological-physiological systems is not straightforward, due to their dynamic nature in which the various parts of the system interact in complex ways. However, an understanding of these dynamics has been developed for years in the form of mathematical process simulators. We study how to incorporate this knowledge into the generative process by leveraging a biological simulator for the task of ECG classification. Specifically, we use a system of ordinary differential equations representing heart dynamics, and incorporate this ODE system into the optimization process of a generative adversarial network to create biologically plausible ECG training examples. We perform empirical evaluation and show that heart simulation knowledge during the generation process improves ECG classification.

Guy D. Rosin, Kira Radinsky

Though languages can evolve slowly, they can also react strongly to dramatic world events. By studying the connection between words and events, it is possible to identify which events change our vocabulary and in what way. In this work, we tackle the task of creating timelines - records of historical "turning points", represented by either words or events, to understand the dynamics of a target word. Our approach identifies these points by leveraging both static and time-varying word embeddings to measure the influence of words and events. In addition to quantifying changes, we show how our technique can help isolate semantic changes. Our qualitative and quantitative evaluations show that we are able to capture this semantic change and event influence.

Dean Zadok, Tom Hirshberg, Amir Biran et al.

This paper describes the exploration and learnings during the process of developing a self-driving algorithm in simulation, followed by deployment on a real car. We specifically concentrate on the Formula Student Driverless competition. In such competitions, a formula race car, designed and built by students, is challenged to drive through previously unseen tracks that are marked by traffic cones. We explore and highlight the challenges associated with training a deep neural network that uses a single camera as input for inferring car steering angles in real-time. The paper explores in-depth creation of simulation, usage of simulations to train and validate the software stack and then finally the engineering challenges associated with the deployment of the system in real-world.

Uriel Singer, Ido Guy, Kira Radinsky

In this work, we present a method for node embedding in temporal graphs. We propose an algorithm that learns the evolution of a temporal graph's nodes and edges over time and incorporates this dynamics in a temporal node embedding framework for different graph prediction tasks. We present a joint loss function that creates a temporal embedding of a node by learning to combine its historical temporal embeddings, such that it optimizes per given task (e.g., link prediction). The algorithm is initialized using static node embeddings, which are then aligned over the representations of a node at different time points, and eventually adapted for the given task in a joint optimization. We evaluate the effectiveness of our approach over a variety of temporal graphs for the two fundamental tasks of temporal link prediction and multi-label node classification, comparing to competitive baselines and algorithmic alternatives. Our algorithm shows performance improvements across many of the datasets and baselines and is found particularly effective for graphs that are less cohesive, with a lower clustering coefficient.

Dana Sagi, Tzoof Avny, Kira Radinsky et al.

One of the main challenges in ranking is embedding the query and document pairs into a joint feature space, which can then be fed to a learning-to-rank algorithm. To achieve this representation, the conventional state of the art approaches perform extensive feature engineering that encode the similarity of the query-answer pair. Recently, deep-learning solutions have shown that it is possible to achieve comparable performance, in some settings, by learning the similarity representation directly from data. Unfortunately, previous models perform poorly on longer texts, or on texts with significant portion of irrelevant information, or which are grammatically incorrect. To overcome these limitations, we propose a novel ranking algorithm for question answering, QARAT, which uses an attention mechanism to learn on which words and phrases to focus when building the mutual representation. We demonstrate superior ranking performance on several real-world question-answer ranking datasets, and provide visualization of the attention mechanism to otter more insights into how our models of attention could benefit ranking for difficult question answering challenges.

Shahar Harel, Kira Radinsky

Designing a new drug is a lengthy and expensive process. As the space of potential molecules is very large (10^23-10^60), a common technique during drug discovery is to start from a molecule which already has some of the desired properties. An interdisciplinary team of scientists generates hypothesis about the required changes to the prototype. In this work, we develop an algorithmic unsupervised-approach that automatically generates potential drug molecules given a prototype drug. We show that the molecules generated by the system are valid molecules and significantly different from the prototype drug. Out of the compounds generated by the system, we identified 35 FDA-approved drugs. As an example, our system generated Isoniazid - one of the main drugs for Tuberculosis. The system is currently being deployed for use in collaboration with pharmaceutical companies to further analyze the additional generated molecules.

Guy D. Rosin, Eytan Adar, Kira Radinsky

Search systems are often focused on providing relevant results for the "now", assuming both corpora and user needs that focus on the present. However, many corpora today reflect significant longitudinal collections ranging from 20 years of the Web to hundreds of years of digitized newspapers and books. Understanding the temporal intent of the user and retrieving the most relevant historical content has become a significant challenge. Common search features, such as query expansion, leverage the relationship between terms but cannot function well across all times when relationships vary temporally. In this work, we introduce a temporal relationship model that is extracted from longitudinal data collections. The model supports the task of identifying, given two words, when they relate to each other. We present an algorithmic framework for this task and show its application for the task of query expansion, achieving high gain.

Yotam Eshel, Noam Cohen, Kira Radinsky et al.

We address the task of Named Entity Disambiguation (NED) for noisy text. We present WikilinksNED, a large-scale NED dataset of text fragments from the web, which is significantly noisier and more challenging than existing news-based datasets. To capture the limited and noisy local context surrounding each mention, we design a neural model and train it with a novel method for sampling informative negative examples. We also describe a new way of initializing word and entity embeddings that significantly improves performance. Our model significantly outperforms existing state-of-the-art methods on WikilinksNED while achieving comparable performance on a smaller newswire dataset.

Kira Radinsky, Sagie Davidovich, Shaul Markovitch

Given a current news event, we tackle the problem of generating plausible predictions of future events it might cause. We present a new methodology for modeling and predicting such future news events using machine learning and data mining techniques. Our Pundit algorithm generalizes examples of causality pairs to infer a causality predictor. To obtain precisely labeled causality examples, we mine 150 years of news articles and apply semantic natural language modeling techniques to headlines containing certain predefined causality patterns. For generalization, the model uses a vast number of world knowledge ontologies. Empirical evaluation on real news articles shows that our Pundit algorithm performs as well as non-expert humans.