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Recent research on predicting the binding affinity between drug molecules and proteins use representations learned, through unsupervised learning techniques, from large databases of molecule SMILES and protein sequences. While these representations have significantly enhanced the predictions, they are usually based on a limited set of modalities, and they do not exploit available knowledge about existing relations among molecules and proteins. Our study reveals that enhanced representations, derived from multimodal knowledge graphs describing relations among molecules and proteins, lead to state-of-the-art results in well-established benchmarks (first place in the leaderboard for Therapeutics Data Commons benchmark ``Drug-Target Interaction Domain Generalization Benchmark&quot;, with an improvement of 8 points with respect to previous best result). Moreover, our results significantly surpass those achieved in standard benchmarks by using conventional pre-trained representations that rely only on sequence or SMILES data. We release our multimodal knowledge graphs, integrating data from seven public data sources, and which contain over 30 million triples.  Pretrained models from our proposed graphs and benchmark task source code are also released.

AAAI 2024

Knowledge Enhanced Representation Learning for Drug Discovery

drug discovery

representation learning

knowledge graph

Recent research on predicting the binding affinity between drug molecules and proteins use representations learned, through unsupervised learning techniques, from large databases of molecule SMILES and protein sequences. While these representations have significantly enhanced the predictions, they are usually based on a limited set of modalities, and they do not exploit available knowledge about existing relations among molecules and proteins. Our study reveals that enhanced representations, derived from multimodal knowledge graphs describing relations among molecules and proteins, lead to state-of-the-art results in well-established benchmarks (first place in the leaderboard for Therapeutics Data Commons benchmark ``Drug-Target Interaction Domain Generalization Benchmark", with an improvement of 8 points with respect to previous best result). Moreover, our results significantly surpass those achieved in standard benchmarks by using conventional pre-trained representations that rely only on sequence or SMILES data. We release our multimodal knowledge graphs, integrating data from seven public data sources, and which contain over 30 million triples.  Pretrained models from our proposed graphs and benchmark task source code are also released.

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.<br><br><br><br>

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. 

Few-shot Relation Extraction (FSRE) aims to extract relational facts from a sparse set of labeled corpora. Recent studies have shown promising results in FSRE by employing Pre-trained Language Models (PLMs) within the framework of supervised contrastive learning, which considers both instances and label facts. However, how to effectively harness massive instance-label pairs to encompass the learned representation with semantic richness in this learning paradigm is not fully explored. To address this gap, we introduce a novel synergistic anchored contrastive pre-training framework. This framework is motivated by the insight that the diverse viewpoints conveyed through instance-label pairs capture incomplete yet complementary intrinsic textual semantics. Specifically, our framework involves a symmetrical contrastive objective that encompasses both sentence-anchored and label-anchored contrastive losses. By combining these two losses, the model establishes a robust and uniform representation space. This space effectively captures the reciprocal alignment of feature distributions among instances and relational facts, simultaneously enhancing the maximization of mutual information across diverse perspectives within the same relation. Experimental results demonstrate that our framework achieves significant performance enhancements compared to baseline models in downstream FSRE tasks. Furthermore, our approach exhibits superior adaptability to handle the challenges of domain shift and zero-shot relation extraction. Our code is available online at https://github.com/AONE-NLP/FSRE-SaCon.

Synergistic Anchored Contrastive Pre-training for Few-Shot Relation Extraction

In this work, we focus on label efficient learning for video
action detection. We develop a novel semi-supervised active
learning approach which utilizes both labeled as well as un-
labeled data along with informative sample selection for ac-
tion detection. Video action detection requires spatio-temporal
localization along with classification, which poses several
challenges for both active learning (informative sample se-
lection) as well as semi-supervised learning (pseudo label
generation). First, we propose NoiseAug, a simple augmenta-
tion strategy which effectively selects informative samples for
video action detection. Next, we propose fft-attention, a novel
technique based on high-pass filtering which enables effective
utilization of pseudo label for SSL in video action detection
by emphasizing on relevant activity region within a video.
We evaluate the proposed approach on three different bench-
mark datasets, UCF-101-24, JHMDB-21, and Youtube-VOS.
First, we demonstrate its effectiveness on video action detec-
tion where the proposed approach outperforms prior works in
semi-supervised and weakly-supervised learning along with
several baseline approaches in both UCF101-24 and JHMDB-
21. Next, we also show its effectiveness on Youtube-VOS for
video object segmentation demonstrating its generalization
capability for other dense prediction tasks in videos.

Semi-supervised Active Learning for Video Action Detection

Large language models (LLMs) offer impressive performance in various zero-shot and few-shot tasks. However, their success in zero-shot or few-shot settings may be affected by task contamination, a potential limitation that has not been thoroughly examined. This paper investigates how zero-shot and few-shot performance of LLMs has changed chronologically over datasets released over time, and over  LLMs released over time. Utilizing GPT-3 series models and several other recent open-sourced LLMs, and controlling for dataset difficulty, we find that datasets released prior to the LLM training data creation date perform surprisingly better than datasets released post the LLM training data creation date. This strongly indicates that, for many LLMs, there exists task contamination on zero-shot and few-shot evaluation for datasets prior to the LLMs' training data creation date. Additionally, we utilize training data inspection, training data extraction, and a membership inference attack, which reveal further evidence of task contamination. Importantly, we find that for tasks with no possibility of task contamination, LLMs rarely demonstrate statistically significant improvements over simple majority baselines, in both zero and few-shot settings.

Task Contamination: Language Models May Not Be Few-Shot Anymore

Deep neural networks have become the method of choice for solving many classification tasks, largely because they can fit very complex functions defined over raw data. The downside of such powerful learners is the danger of overfit. In this paper, we introduce a novel ensemble classifier for deep networks that effectively overcomes overfitting by combining models generated at specific intermediate epochs during training. Our method allows for the incorporation of useful knowledge obtained by the models during the overfitting phase without deterioration of the general performance, which is usually missed when early stopping is used.

To motivate this approach, we begin with the theoretical analysis of a regression model, whose prediction - that the variance among classifiers increases when overfit occurs - is demonstrated empirically in deep networks in common use. Guided by these results, we construct a new ensemble-based prediction method, where the prediction is determined by the class that attains the most consensual prediction throughout the training epochs. Using multiple image and text classification datasets, we show that when regular ensembles suffer from overfit, our method eliminates the harmful reduction in generalization due to overfit, and often even surpasses the performance obtained by early stopping. Our method is easy to implement and can be integrated with any training scheme and architecture, without additional prior knowledge beyond the training set. It is thus a practical and useful tool to overcome overfit. Code is available at \url{https://github.com/uristern123/United-We-Stand-Using-Epoch-wise-Agreement-of-Ensembles-to-Combat-Overfit}.

United We Stand: Using Epoch-Wise Agreement of Ensembles to Combat Overfit

Cross domain medical image reconstruction aims to address the issue that deep learning models trained solely on one source dataset might not generalize effectively to unseen target datasets from different hospitals. Some recent methods achieve satisfactory reconstruction performance, but often at the expense of extensive parameters and time consumption. To strike a balance between cross domain image reconstruction quality and model computational efficiency, we propose a lightweight sparse Bayesian deep learning method. Notably, we apply a fixed-form variational Bayes (FFVB) approach to quantify pixel-wise uncertainty priors derived from degradation distribution of the source domain. Furthermore, by integrating the uncertainty prior into the posterior sampled through stochastic gradient Langevin dynamics (SGLD), we develop a training strategy that dynamically generates and optimizes the prior distribution on the network weights for each unseen domain. This strategy enhances generalizability and ensures robust reconstruction performance. When evaluated on medical image reconstruction tasks, our proposed approach demonstrates impressive performance across various previously unseen domains.

Sparse Bayesian Deep Learning for Cross Domain Medical Image Reconstruction | VIDEO

Unveiling, modeling, and comprehending the causal mechanisms underpinning natural phenomena stand as fundamental endeavors across myriad scientific disciplines. Meanwhile, new knowledge emerges when discovering causal relationships from data. Existing causal learning algorithms predominantly focus on the isolated effects of variables, overlook the intricate interplay of multiple variables and their collective behavioral patterns. Furthermore, the ubiquity of high-dimensional data exacts a substantial temporal cost for causal algorithms. In this paper, we develop a novel method called MgCSL (Multi-granularity Causal Structure Learning), which first leverages sparse auto-encoder to explore coarse-graining strategies and causal abstractions from micro-variables to macro-ones. MgCSL then takes multi-granularity variables as inputs to train multilayer perceptrons and to delve the causality between variables. To enhance the efficacy on high-dimensional data, MgCSL  introduces a simplified acyclicity constraint to adeptly search the directed acyclic graph among variables. Experimental results show that MgCSL outperforms competitive baselines, and finds out explainable causal connections on fMRI datasets.

Multi-Granularity Causal Structure Learning

Recommendation strategies are typically evaluated by using previously logged data, employing off-policy evaluation methods to estimate their expected performance. However, for strategies that present users with slates of multiple items, the resulting combinatorial action space renders many of these methods impractical. Prior work has developed estimators that leverage the structure in slates to estimate the expected off-policy performance, but the estimation of the entire performance distribution remains elusive. Estimating the complete distribution allows for a more comprehensive evaluation of recommendation strategies, particularly along the axes of risk and fairness that employ metrics computable from the distribution. In this paper, we propose an estimator for the complete off-policy performance distribution for slates and establish conditions under which the estimator is unbiased and consistent. This builds upon prior work on off-policy evaluation for slates and off-policy distribution estimation in reinforcement learning. We validate the efficacy of our method empirically on synthetic data as well as on a slate recommendation simulator constructed from real-world data (MovieLens-20M). Our results show a significant reduction in estimation variance and improved sample efficiency over prior work across a range of slate structures.

Distributional Off-Policy Evaluation for Slate Recommendations

In the field of optimal transport, two prominent subfields face each other: (i) unregularized optimal transport, ``\`a-la-Kantorovich'', which leads to extremely sparse plans but with algorithms that scale poorly, and (ii) entropic-regularized optimal transport, ``\`a-la-Sinkhorn-Cuturi'', which gets near-linear approximation algorithms but leads to maximally un-sparse plans. In this paper, we show that an extension of the latter to tempered exponential measures, a generalization of exponential families with indirect measure normalization, gets to a very convenient middle ground, with both very fast approximation algorithms and sparsity, which is under control up to sparsity patterns. In addition, our formulation fits naturally in the unbalanced optimal transport problem setting.

Optimal Transport with Tempered Exponential Measures

Atomic congestion games are a classic topic in network design, routing, and algorithmic game theory, and are capable of modeling congestion and flow optimization tasks in various application areas. While both the price of anarchy for such games as well as the computational complexity of computing their Nash equilibria are by now well-understood, the computational complexity of computing a system-optimal set of strategies - that is, a centrally planned routing that minimizes the average cost of agents - is severely understudied in the literature. We close this gap by identifying the exact boundaries of tractability for the problem through the lens of the parameterized complexity paradigm. After showing that the problem remains highly intractable even on extremely simple networks, we obtain a set of results which demonstrate that the structural parameters which control the computational (in)tractability of the problem are not vertex-separator based in nature (such as, e.g., treewidth), but rather based on edge separators. We conclude by extending our analysis towards the (even more challenging) min-max variant of the problem.

The Complexity of Optimizing Atomic Congestion

Despite significant progress in Text-to-Image (T2I) generative models, even lengthy and complex text descriptions still struggle to convey detailed controls. In contrast, Layout-to-Image (L2I) generation, aiming to generate realistic and complex scene images from user-specified layouts, has risen to prominence. However, existing methods transform layout information into tokens or RGB images for conditional control in the generative process, leading to insufficient spatial and semantic controllability of individual instances. To address these limitations, we propose a novel Spatial-Semantic Map Guided (SSMG) diffusion model that adopts the feature map, derived from the layout, as guidance. Owing to rich spatial and semantic information encapsulated in well-designed feature maps, SSMG achieves superior generation quality with sufficient spatial and semantic controllability compared to previous works. Additionally, we propose the Relation-Sensitive Attention (RSA) and Location-Sensitive Attention (LSA) mechanisms. The former aims to model the relationships among multiple objects within scenes while the latter is designed to heighten the model's sensitivity to the spatial information embedded in the guidance. Extensive experiments demonstrate that SSMG achieves highly promising results, setting a new state-of-the-art across a range of metrics encompassing fidelity, diversity, and controllability.

Knowledge Enhanced Representation Learning for Drug Discovery

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Knowledge Enhanced Representation Learning for Drug Discovery

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Synergistic Anchored Contrastive Pre-training for Few-Shot Relation Extraction

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