Author name cluster

Mohammed J. Zaki

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

6 papers

2 author rows

AAAI Conference 2025 Conference Paper

Replacing Paths with Connection-Biased Attention for Knowledge Graph Completion

Sharmishtha Dutta
Alex Gittens
Mohammed J. Zaki
Charu C. Aggarwal

Knowledge graph (KG) completion aims to identify additional facts that can be inferred from the existing facts in the KG. Recent developments in this field have explored this task in the inductive setting, where at test time one sees entities that were not present during training; the most performant models in the inductive setting have employed path encoding modules in addition to standard subgraph encoding modules. This work similarly focuses on KG completion in the inductive setting, without the explicit use of path encodings, which can be time-consuming and introduces several hyperparameters that require costly hyperparameter optimization. Our approach uses a Transformer-based subgraph encoding module only; we introduce connection-biased attention and entity role embeddings into the subgraph encoding module to eliminate the need for an expensive and time-consuming path encoding module. Evaluations on standard inductive KG completion benchmark datasets demonstrate that our Connection-Biased Link Prediction (CBLiP) model has superior performance to models that do not use path information. Compared to models that utilize path information, CBLiP shows competitive or superior performance while being faster. Additionally, to show that the effectiveness of connection-biased attention and entity role embeddings also holds in the transductive setting, we compare CBLiP's performance on the relation prediction task in the transductive setting.

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ICML Conference 2024 Conference Paper

Triplet Interaction Improves Graph Transformers: Accurate Molecular Graph Learning with Triplet Graph Transformers

Md. Shamim Hussain
Mohammed J. Zaki
Dharmashankar Subramanian

Graph transformers typically lack third-order interactions, limiting their geometric understanding which is crucial for tasks like molecular geometry prediction. We propose the Triplet Graph Transformer (TGT) that enables direct communication between pairs within a 3-tuple of nodes via novel triplet attention and aggregation mechanisms. TGT is applied to molecular property prediction by first predicting interatomic distances from 2D graphs and then using these distances for downstream tasks. A novel three-stage training procedure and stochastic inference further improve training efficiency and model performance. Our model achieves new state-of-the-art (SOTA) results on open challenge benchmarks PCQM4Mv2 and OC20 IS2RE. We also obtain SOTA results on QM9, MOLPCBA, and LIT-PCBA molecular property prediction benchmarks via transfer learning. We also demonstrate the generality of TGT with SOTA results on the traveling salesman problem (TSP).

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ICML Conference 2023 Conference Paper

End-to-end Differentiable Clustering with Associative Memories

Bishwajit Saha
Dmitry Krotov
Mohammed J. Zaki
Parikshit Ram

Clustering is a widely used unsupervised learning technique involving an intensive discrete optimization problem. Associative Memory models or AMs are differentiable neural networks defining a recursive dynamical system, which have been integrated with various deep learning architectures. We uncover a novel connection between the AM dynamics and the inherent discrete assignment necessary in clustering to propose a novel unconstrained continuous relaxation of the discrete clustering problem, enabling end-to-end differentiable clustering with AM, dubbed ClAM. Leveraging the pattern completion ability of AMs, we further develop a novel self-supervised clustering loss. Our evaluations on varied datasets demonstrate that ClAM benefits from the self-supervision, and significantly improves upon both the traditional Lloyd’s k-means algorithm, and more recent continuous clustering relaxations (by upto 60% in terms of the Silhouette Coefficient).

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ICLR Conference 2021 Conference Paper

Can a Fruit Fly Learn Word Embeddings?

Yuchen Liang
Chaitanya K. Ryali
Benjamin Hoover
Leopold Grinberg
Saket Navlakha
Mohammed J. Zaki
Dmitry Krotov

The mushroom body of the fruit fly brain is one of the best studied systems in neuroscience. At its core it consists of a population of Kenyon cells, which receive inputs from multiple sensory modalities. These cells are inhibited by the anterior paired lateral neuron, thus creating a sparse high dimensional representation of the inputs. In this work we study a mathematical formalization of this network motif and apply it to learning the correlational structure between words and their context in a corpus of unstructured text, a common natural language processing (NLP) task. We show that this network can learn semantic representations of words and can generate both static and context-dependent word embeddings. Unlike conventional methods (e.g., BERT, GloVe) that use dense representations for word embedding, our algorithm encodes semantic meaning of words and their context in the form of sparse binary hash codes. The quality of the learned representations is evaluated on word similarity analysis, word-sense disambiguation, and document classification. It is shown that not only can the fruit fly network motif achieve performance comparable to existing methods in NLP, but, additionally, it uses only a fraction of the computational resources (shorter training time and smaller memory footprint).

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IJCAI Conference 2020 Conference Paper

GraphFlow: Exploiting Conversation Flow with Graph Neural Networks for Conversational Machine Comprehension

Yu Chen
Lingfei Wu
Mohammed J. Zaki

Conversational machine comprehension (MC) has proven significantly more challenging compared to traditional MC since it requires better utilization of conversation history. However, most existing approaches do not effectively capture conversation history and thus have trouble handling questions involving coreference or ellipsis. Moreover, when reasoning over passage text, most of them simply treat it as a word sequence without exploring rich semantic relationships among words. In this paper, we first propose a simple yet effective graph structure learning technique to dynamically construct a question and conversation history aware context graph at each conversation turn. Then we propose a novel Recurrent Graph Neural Network, and based on that, we introduce a flow mechanism to model the temporal dependencies in a sequence of context graphs. The proposed GraphFlow model can effectively capture conversational flow in a dialog, and shows competitive performance compared to existing state-of-the-art methods on CoQA, QuAC and DoQA benchmarks. In addition, visualization experiments show that our proposed model can offer good interpretability for the reasoning process.

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ICLR Conference 2020 Conference Paper

Reinforcement Learning Based Graph-to-Sequence Model for Natural Question Generation

Yu Chen 0022
Lingfei Wu 0001
Mohammed J. Zaki

Natural question generation (QG) aims to generate questions from a passage and an answer. Previous works on QG either (i) ignore the rich structure information hidden in text, (ii) solely rely on cross-entropy loss that leads to issues like exposure bias and inconsistency between train/test measurement, or (iii) fail to fully exploit the answer information. To address these limitations, in this paper, we propose a reinforcement learning (RL) based graph-to-sequence (Graph2Seq) model for QG. Our model consists of a Graph2Seq generator with a novel Bidirectional Gated Graph Neural Network based encoder to embed the passage, and a hybrid evaluator with a mixed objective combining both cross-entropy and RL losses to ensure the generation of syntactically and semantically valid text. We also introduce an effective Deep Alignment Network for incorporating the answer information into the passage at both the word and contextual levels. Our model is end-to-end trainable and achieves new state-of-the-art scores, outperforming existing methods by a significant margin on the standard SQuAD benchmark.

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