Canada

Designing novel biological sequences with desired properties is a significant challenge in biological science because of the extra large search space. The traditional design process usually involves multiple rounds of costly wet lab evaluations. To reduce the need for expensive wet lab experiments, machine learning methods are used to aid in designing biological sequences. However, the limited availability of biological sequences with known properties hinders the training of machine learning models, significantly restricting their applicability and performance. To fill this gap, we present ERLBioSeq, an Evolutionary Reinforcement Learning algorithm for BIOlogical SEQuence design. ERLBioSeq leverages the capability of reinforcement learning to learn without prior knowledge and the potential of evolutionary algorithms to enhance the exploration of reinforcement learning in the large search space of biological sequences. Additionally, to enhance the efficiency of biological sequence design, we developed a predictor for sequence screening in the biological sequence design process, which incorporates both the local and global sequence information. We evaluated the proposed method on three main types of biological sequence design tasks, including the design of DNA, RNA, and protein. The results demonstrate that the proposed method achieves significant improvement compared to the existing state-of-the-art methods.

AAAI 2024

Designing Biological Sequences without Prior Knowledge Using Evolutionary Reinforcement Learning

natural sciences

reinforcement learning algorithms

applications

bioinformatics

### Artificial Intelligence in Metabolism (AIM)

AIM is a seminar series that will explore the potential of data science in metabolic research. It is hosted by the Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR) at the University of Copenhagen.
The seminar series takes place over three days in June and July, 2021 from 4pm to 5:30 pm CEST.

![](https://assets.underline.io/uploads/markdown_image/1/image/bc89e60b0a0f2d7550c75517a10f2843.png)
**About AIM**

Artificial Intelligence in Metabolism brings together renowned investigators to discuss how cutting edge data science can be best utilized to challenge current dogmas and catalyse better translation in metabolic and biomedical research.

Significant new discoveries in metabolic research increasingly rely on large-scale profiling, data integration and machine learning-based techniques. Not only can these techniques be leveraged to distil novel actionable biological hypotheses to be tested in relevant physiological contexts/clinical settings, they for example enable us to develop predictive tools to more effectively and timely identify at-risk individuals or personalized drugs/interventions. 

At the Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR) we have set up enabling biology platforms that utilize sophisticated metabolomics, single-cell and data integration techniques to enrich our deeply phenotyped and genotyped patient cohorts. These data, along with the associated Danish longitudinal health register information, constitute a unique base to empower current and next generations of scientists to tackle the major questions in metabolic research.

We envision that data and machine learning models will be at the heart of future teams driving novel discoveries in metabolic research, through interdisciplinary approaches involving traditional biomedical scientists alongside data scientists, mathematicians and bioinformaticians.
Please join us in our effort to discuss and incubate new ideas to better explore and model metabolic disease.

![](https://assets.underline.io/uploads/markdown_image/1/image/bc89e60b0a0f2d7550c75517a10f2843.png)



AIM Seminar Series 2021

AIM is a seminar series that will explore the potential of data science in metabolic research. It is hosted by the Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR) at the University of Copenhagen. The seminar series takes place over three days in June and July, 2021 from 4pm to 5:30 pm CEST.

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. 

Leading approaches to algorithmic fairness and policy-induced distribution shift are often misaligned with long-term objectives in sequential settings. We aim to correct these shortcomings by ensuring that both the objective and fairness constraints account for policy-induced distribution shift. First, we motivate this problem using an example in which individuals subject to algorithmic predictions modulate their willingness to participate with the policy maker. Fairness in this example is measured by the variance of group participation rates. Next, we develop a method for solving the resulting constrained, non-linear optimization problem and prove that this method converges to a fair, locally optimal policy given first-order information. Finally, we experimentally validate our claims in a semi-synthetic setting.

Fair Participation via Sequential Policies | VIDEO

Microarchitecture determines the implementation of a microprocessor. Designing a microarchitecture to achieve better performance, power, and area (PPA) trade-off has been increasingly difficult. Previous data-driven methodologies hold inappropriate assumptions and lack more tightly coupling with expert knowledge. This paper proposes a novel reinforcement learning-based (RL) solution that addresses these limitations. With the integration of microarchitecture scaling graph, PPA preference space embedding, and proposed lightweight environment in RL, experiments using commercial electronic design automation (EDA) tools show that our method achieves an average PPA trade-off improvement of 16.03% than previous state-of-the-art approaches with 4.07× higher efficiency. The solution qualities outperform human implementations by at most 2.03× in the PPA trade-off.

Towards Automated RISC-V Microarchitecture Design with Reinforcement Learning | VIDEO

Text-based person retrieval aims at retrieving a specific pedestrian image from a gallery based on textual descriptions. The primary challenge is how to overcome the inherent heterogeneous modality gap in the situation of significant intra-class variation and minimal inter-class variation. Existing approaches commonly employ vision-language pre-training or attention mechanisms to learn appropriate cross-modal alignments from noise inputs. Despite commendable progress, current methods inevitably suffer from two defects: 1) Matching ambiguity, which mainly derives from unreliable matching pairs; 2) One-sided cross-modal alignments, stemming from the absence of exploring one-to-many correspondence, ie, coarse-grained semantic alignment. These critical issues significantly deteriorate retrieval performance. To this end, we propose a novel framework termed Adaptive Uncertainty-based Learning (AUL) for text-based person retrieval from the uncertainty perspective. Specifically, our AUL framework consists of three key components: 1) Uncertainty-aware Matching Filtration that leverages Subjective Logic to effectively mitigate the disturbance of unreliable matching pairs and select high-confidence cross-modal matches for training; 2) Uncertainty-based Alignment Refinement, which not only simulates coarse-grained alignments by constructing uncertainty representations but also performs progressive learning to incorporate coarse- and fine-grained alignments properly; 3) Cross-modal Masked Modeling that aims at exploring more comprehensive relations between vision and language. Extensive experiments demonstrate that our AUL method consistently achieves state-of-the-art performance on three benchmark datasets in supervised, weakly supervised, and domain generalization settings. Our code is available at https://github.com/AnyAnonymous/AUL.

Adaptive Uncertainty-Based Learning for Text-Based Person Retrieval

Traditional Radiance Field (RF) representations capture details of a specific scene and must be trained afresh on each scene. Semantic feature fields have been added to RFs to facilitate several segmentation tasks. Generalised RF representations learn the principles of view interpolation. A generalised RF can render new views of an unknown and untrained scene, given a few views. We present a way to distil feature fields into the generalised GNT representation. Our GSN representation generates new views of unseen scenes on the fly along with consistent, per-pixel semantic features. This enables multi-view segmentation of arbitrary new scenes. We show different semantic features being distilled into generalised RFs. Our multi-view segmentation results are on par with methods that use traditional RFs. GSN closes the gap between standard and generalisable RF methods significantly. Project Page: https://vinayak-vg.github.io/GSN/

GSN: Generalisable Segmentation in Neural Radiance Field

Knowledge distillation aims at reducing model size without compromising much performance. Recent work has applied it to large vision-language (VL) Transformers, and has shown that attention maps in the multi-head attention modules of vision-language Transformers contain extensive intra-modal and cross-modal co-reference relations to be distilled. The standard approach is to apply a one-to-one attention map distillation loss, i.e. the Teacher's first attention head instructs the Student's first head, the second teaches the second, and so forth, but this only works when the numbers of attention heads in the Teacher and Student are the same. To remove this constraint, we propose a new Attention Map Alignment Distillation (AMAD) method for Transformers with multi-head attention, which works for a Teacher and a Student with different numbers of attention heads. Specifically, we soft-align different heads in Teacher and Student attention maps using a cosine similarity weighting. The Teacher head contributes more to the Student heads for which it has a higher similarity weight. Each Teacher head contributes to all the Student heads by minimizing the divergence between the attention activation distributions for the soft-aligned heads. No head is left behind. This distillation approach operates like cross-attention. We experiment on distilling VL-T5 and BLIP, and apply AMAD loss on their T5, BERT, and ViT sub-modules. We show, under vision-language setting, that AMAD outperforms conventional distillation methods on VQA-2.0, COCO captioning, and Multi30K translation datasets. We further show that even without VL pre-training, the distilled VL-T5 models outperform corresponding VL pre-trained VL-T5 models that are further fine-tuned by ground-truth signals, and that fine-tuning distillation can also compensate to some degree for the absence of VL pre-training for BLIP models.

No Head Left Behind – Multi-Head Alignment Distillation for Transformers

Visual Reinforcement Learning (RL) is a promising approach to achieve human-like intelligence. However, it currently faces challenges in learning efficiently within noisy environments. In contrast, humans can quickly identify task-relevant objects in distraction-filled surroundings by applying previously acquired common knowledge. Recently, foundational models in natural language processing and computer vision have achieved remarkable successes, and the common knowledge within these models can significantly benefit downstream task training. Inspired by these achievements, we aim to incorporate common knowledge from foundational models into visual RL. We propose a novel Focus-Then-Decide (FTD) framework, allowing the agent to make decisions based solely on task-relevant objects. To achieve this, we introduce an attention mechanism to select task-relevant objects from the object set returned by a foundational segmentation model, and only use the task-relevant objects for the subsequent training of the decision module. Additionally, we specifically employed two generic self-supervised objectives to facilitate the rapid learning of this attention mechanism. Experimental results on challenging tasks based on DeepMind Control Suite and Franka Emika Robotics demonstrate that our method can quickly and accurately pinpoint objects of interest in noisy environments. Consequently, it achieves a significant performance improvement over current state-of-the-art algorithms.

Focus-Then-Decide: Segmentation-Assisted Reinforcement Learning

The diversity of tables makes table detection a great challenge, leading to existing models becoming more tedious and complex. Despite achieving high performance, they often overfit to the table style in training set, and suffer from significant performance degradation when encountering out-of-distribution tables in other domains. To tackle this problem, we start from the essence of the table, which is a set of text arranged in rows and columns. Based on this, we propose a novel, light-weighted and robust Table Detection method based on Learning Text Arrangement, namely TDeLTA. TDeLTA takes the text blocks as input, and then models the arrangement of them with  a sequential encoder and an attention module. To locate the tables precisely, we design a text-classification task, classifying the text blocks into 4 categories according to their semantic roles in the tables. Experiments are conducted on both the text blocks parsed from PDF and extracted by open-source OCR tools, respectively. Compared to several state-of-the-art methods, TDeLTA achieves competitive results with only 3.1M model parameters on the large-scale public datasets. Moreover, when faced with the cross-domain data under the 0-shot setting, TDeLTA outperforms baselines by a large margin of nearly 7%, which shows the strong robustness and transferability of the proposed model.

TDeLTA: A Light-Weight and Robust Table Detection Method Based on Learning Text Arrangement

Due to its effectiveness and efficiency, anchor based multi-view clustering (MVC) has recently attracted much attention. Most existing approaches try to adaptively learn anchors to construct an anchor graph for clustering. However, they generally focus on improving the diversity among anchors by using orthogonal constraint and ignore the underlying semantic relations, which may make the anchors not representative and discriminative enough. To address this problem, we propose an adaptive Cluster-wise Anchor learning based MVC method, CAMVC for short. We first make an \textit{anchor cluster assumption} that supposes the prior cluster structure of target anchors by pre-defining a consensus cluster indicator matrix. Based on the prior knowledge, an explicit cluster structure of latent anchors is enforced by learning diverse cluster centroids, which can explore both inter-cluster diversity and intra-cluster consistency of anchors, and improve the subspace representation discrimination. Extensive results demonstrate the effectiveness and superiority of our proposed method compared with some state-of-the-art MVC approaches.

Learning Cluster-Wise Anchors for Multi-View Clustering

We propose a novel stereo-confidence that can be measured externally to various stereo-matching networks, offering an alternative input modality choice of the cost volume for learning-based approaches, especially in safety-critical systems.
Grounded in the foundational concepts of disparity definition and the disparity plane sweep, the proposed stereo-confidence method is built upon the idea that any shift in a stereo-image pair should be updated in a corresponding amount shift in the disparity map. 
Based on this idea, the proposed stereo-confidence method can be summarized in three folds.
1) Using the disparity plane sweep, multiple disparity maps can be obtained and treated as a 3-D volume (predicted disparity volume), like the cost volume is constructed. 
2) One of these disparity maps serves as an anchor, allowing us to define a desirable (or ideal) disparity profile at every spatial point.
3) By comparing the desirable and predicted disparity profiles, we can quantify the level of matching ambiguity between left and right images for confidence measurement. 
Extensive experimental results using various stereo-matching networks and datasets demonstrate that the proposed stereo-confidence method not only shows competitive performance on its own but also consistent performance improvements when it is used as an input modality for learning-based stereo-confidence methods.

Modeling Stereo-Confidence out of the End-to-End Stereo-Matching Network via Disparity Plane Sweep | VIDEO

Trajectory similarity computation serves as a fundamental functionality of various spatial information applications. Although existing deep learning similarity computation methods offer better efficiency and accuracy than non-learning solutions, they are still immature in trajectory embedding and suffer from poor generality and heavy preprocessing for training. Targeting these limitations, we propose a novel framework named {\it KGTS} based on knowledge graph grid embedding, prompt trajectory embedding, and unsupervised contrastive learning for improved trajectory similarity computation. Specifically, we first embed map grids with a {\it GRot} embedding method to vigorously grasp the neighbouring relations of grids. Then, a prompt trajectory embedding network incorporates the resulting grid embedding and extracts trajectory structure and point order information. It is trained by unsupervised contrastive learning, which not only alleviates the heavy preprocessing burden but also provides exceptional generality with creatively designed strategies for positive sample generation. The prompt trajectory embedding adopts a customized prompt paradigm to mitigate the gap between the grid embedding and the trajectory embedding. Extensive experiments on two real-world trajectory datasets demonstrate the superior performance of KGTS over state-of-the-art methods.

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Fair Participation via Sequential Policies | VIDEO

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