Instance-Level Embedding Adaptation for Few-Shot Learning

Here we report PPB2 as a target prediction tool assigning targets to a query molecule based on ChEMBL data. PPB2 computes ligand similarities using molecular fingerprints encoding composition (MQN), molecular shape and pharmacophores (Xfp), and substructures (ECfp4) and features an unprecedented combination of nearest neighbor (NN) searches and Naı̈ve Bayes (NB) machine learning, together with simple NN searches, NB and Deep Neural Network (DNN) machine learning models as further options. Although NN(ECfp4) gives the best results in terms of recall in a 10-fold cross-validation study, combining NN searches with NB machine learning provides superior precision statistics, as well as better results in a case study predicting off-targets of a recently reported TRPV6 calcium channel inhibitor, illustrating the value of this combined approach. PPB2 is available to assess possible off-targets of small molecule drug-like compounds by public access at http://gdb.unibe.ch .

Nearest neighbor (NN) search computations are at the core of many applications such as few-shot learning, classification, and hyperdimensional computing. As such, efficient hardware support for NN search is highly desired. In-memory computing using emerging devices offers attractive solutions for NN search. Solutions based on ternary content-addressable memories (TCAMs) offer high energy and latency improvements for NN search at the expense of accuracy. In this work, we propose a novel distance function that can be natively evaluated with multi-bit content-addressable memories (MCAMs) based on ferroelectric FETs (FeFETs) to perform a single-step, in-memory NN search. We evaluate the efficacy of FeFET MCAMs in the context of few-shot learning applications with different datasets. As an example, we achieve a 78.54% accuracy for a 5-way, 5-shot classification task for the mini-ImageNet dataset (only 1.5% lower than software-based implementations) when using a 3-bit MCAM for NN search. We consider the effects of FeFET threshold voltage variations on the application accuracy and analyze the area and search energy requirements of FeFET MCAMs for accurate operations. Our results indicate that MCAMs require 2× lower area and search energy than TCAMs to achieve the same accuracy. Furthermore, we experimentally demonstrate a 2-bit implementation of FeFET MCAM using AND arrays from GLOBALFOUNDRIES to further validate the design concept.

The great advances in deep learning enable human beings to extract the semantic information in ubiquitous unstructured data into high-dimensional vectors, leading to an urgent priority of managing vector data. Nearest neighbor (NN) query is a pivotal question in vector data management. Unfortunately, the NN query has been proved to be intrinsically hard. Researchers, thus, turn to approximate nearest neighbor (ANN) query which targets better efficiency by slightly compromising accuracy. Despite this, existing ANN methods still incur high time and space costs, which are mainly due to the high dimensionality. Specifically, in most in-memory ANN algorithms, the time cost is dominated by the time for comparing the distances among vectors. Each distance comparison operation (DCO) involves hundreds of arithmetic operations as each vector has hundreds of dimensions. Similarly, the space cost is dominated by the space for storing the vectors. Towards the goal of reducing the time and space costs, we present three methods in this thesis. First, we observe that, for a DCO, if an approximate distance can confirm that a vector is not a NN, then it can be discarded without computing exact distances. Based on this observation, we propose a method named ADSampling. For a DCO, it iteratively and incrementally samples a few dimensions and computes an approximate distance. When this distance is accurate enough to decide the result of the DCO, it terminates sampling. Second, to further improve the efficiency of DCOs, we design an efficient distance estimator. We propose a new quantization method named RaBitQ, which maps $D$-dimensional vectors into $D$-bit strings. RaBitQ provides an unbiased and asymptotically optimal estimator with good empirical accuracy. In addition, we introduce efficient implementations of RaBitQ based on bitwise operations or SIMD-based operations. Third, by extending the RaBitQ method, we develop an algorithm which compresses a floating-point vector into a $B$-bit unsigned integer vector. We prove that our algorithm is asymptotically optimal in terms of the space-accuracy trade-off.

Case Based Reasoning (CBR) is a method that aims to resolve a new case by adapting the solutions contained in previous cases that are similar to the new case. The system built in this study is the CBR system to make recommendations on the topic of student thesis concentration. This study used data from undergraduate students of Informatics Engineering IST AKPRIND Yogyakarta with a total of 115 data consisting of 80 training data and 35 test data. This study aims to design and build a Case Based Reasoning system using the Nearest Neighbor and Manhattan Distance Similarity Methods, and to compare the results of the accuracy value using the Nearest Neighbor Similarity and Manhattan Distance Similarity methods. The recommendation process is carried out by calculating the value of closeness or similarity between new cases and old cases stored on a case basis using the Nearest Neighbor Method and Manhattan Distance. The features used in this study consisted of GPA and course grades. The case taken is the case with the highest similarity value. If a case doesnt get a topic recommendation or is less than the trashold value of 0.8, a case revision will be carried out by an expert. Successfully revised cases are stored in the system to be made new knowledge. The test results using the Nearest Neighbor Method get an accuracy value of 97.14% and Manhattan Distance Method 94.29%.

A range nearest-neighbor (RNN) query retrieves the nearest neighbor (NN) for every point in a range. It is a natural generalization of point and continuous nearest-neighbor queries and has many applications. In this paper, we consider the ranges as (hyper)rectangles and propose efficient in-memory processing and secondary memory pruning techniques for RNN queries in both 2D and high-dimensional spaces. These techniques are generalized for kRNN queries, which return the k nearest neighbors for every point in the range. In addition, we devise an auxiliary solution-based index EXO-tree to speed up any type of NN query. EXO-tree is orthogonal to any existing NN processing algorithm and, thus, can be transparently integrated. An extensive empirical study was conducted to evaluate the CPU and I/O performance of these techniques, and the study showed that they are efficient and robust under various data sets, query ranges, numbers of nearest neighbors, dimensions, and cache sizes.

Aggregate k nearest neighbor (AkNN) queries are useful in many areas, such as multimedia retrieval and resource allocation, to name but a few. Most of existing works on AkNN query only focus on Euclidean space or specific metric space, which employ properties of particular data to accelerate the query. However, due to the complex data types involved and the needs for flexible similarity criteria seen in real applications, properties of particular data cannot be used for general case. Hence, in this paper, we investigate AkNN search in metric spaces, termed as metric AkNN (MAkNN) search, as metric spaces can support any type of data and flexible similarity criteria as long as satisfying triangle inequality. To efficiently answer MAkNN queries, we develop several pruning techniques and corresponding algorithms based on SPB-tree. Extensive experiments using three real data sets verify the efficiency of our MAkNN algorithms.

The nearest neighbor search is an essential operation for many computer vision, data mining, and machine learning problems. Since it is so widely used, the nearest neighbor search should be as fast as possible. This paper explores lower bound-based approaches to speed up the exact nearest neighbor search in high dimensional Euclidean space. We compute the lower bound of Euclidean Distance by using the block vectors and Cauchy–Schwartz inequality. The proposed lower bound is calculated efficiently and is close to the real Euclidean Distance. Besides, the preprocessing step of the proposal has linear time complexity. Given a query, during the procedure of identifying the nearest neighbor, our method can eliminate many expensive actual distance computations using the lower bound to approximate Euclidean Distance. In addition, we develop a multilevel lower bound strategy, which calculates the lower bound step by step and utilizes the multistep filtering mechanism to improve the searching process further. Theoretical analysis is provided to show that the proposals can guarantee to obtain the same result as the brute-force search. Comprehensive experiments on 16 public data sets collected from various domains demonstrate that our approach performs well in finding the exact nearest neighbor compared to related competitors. The experimental results also illustrate that the multilevel lower bound strategy is effective.

In this paper, we study the problem of continuous monitoring of reverse k nearest neighbors queries in Euclidean space as well as in spatial networks. Existing techniques are sensitive toward objects and queries movement. For example, the results of a query are to be recomputed whenever the query changes its location. We present a framework for continuous reverse k nearest neighbor (RkNN) queries by assigning each object and query with a safe region such that the expensive recomputation is not required as long as the query and objects remain in their respective safe regions. This significantly improves the computation cost. As a byproduct, our framework also reduces the communication cost in client---server architectures because an object does not report its location to the server unless it leaves its safe region or the server sends a location update request. We also conduct a rigid cost analysis for our Euclidean space RkNN algorithm. We show that our techniques can also be applied to answer bichromatic RkNN queries in Euclidean space as well as in spatial networks. Furthermore, we show that our techniques can be extended for the spatial networks that are represented by directed graphs. The extensive experiments demonstrate that our techniques outperform the existing techniques by an order of magnitude in terms of computation cost and communication cost.

Nearest neighbor search is a fundamental problem in computer vision and machine learning. The straightforward solution, linear scan, is both computationally and memory intensive in large scale high-dimensional cases, hence is not preferable in practice. Therefore, there have been a lot of interests in algorithms that perform approximate nearest neighbor (ANN) search. In this paper, we propose a novel addition-based vector quantization algorithm, Asymmetric Mapping Quantization (AMQ), to efficiently conduct ANN search. Unlike existing addition-based quantization methods that suffer from handling the problem caused by the norm of database vector, we map the query vector and database vector using different mapping functions to transform the computation of L-2 distance to inner product similarity, thus do not need to evaluate the norm of database vector. Moreover, we further propose Distributed Asymmetric Mapping Quantization (DAMQ) to enable AMQ to work on very large dataset by distributed learning. Extensive experiments on approximate nearest neighbor search and image retrieval validate the merits of the proposed AMQ and DAMQ.

Broadcasting data with an index is an effective way to disseminate public information to a large clients. For a server, using multiple channels to provide services (e.g., location-based services) makes the broadcast cycle shorter than using one channel. Among location-based services, the k nearest neighbors (k-NN) search is an important one and finds the fc closest objects to a query point in a multi-dimensional space. This paper considers k nearest neighbors search on a broadcast R-tree in a multi-channel environment. We assume that a mobile client can only tune into a specified channel at one time instance. We study how a server generates the broadcast schedules on multiple channels and explore how a client executes the k-NN search on the broadcast. Different broadcast schedules with the client k-NN search processing makes different k-NN search protocols. The objectives of the protocols is to minimize the latency (i.e., the time elapsed between issuing and termination of the query), tuning time (i.e., the amount of time spent on listening to the channel), and the memory usage for k-NN search processing. Last, we present our experiments and the experiment results validate that our mechanisms achieve the objectives.

Developed from Nearest Neighbor (NN) queries, Aggregate Nearest Neighbor (ANN) queries return the object that minimizes an aggregate distance function with respect to a set of query points. Because of the multiple query points, ANN queries are much more complex than NN queries. For optimizing the query processing and improving the query efficiency, many ANN queries algorithms utilizes pruning strategies, with or without an index structure. Obviously, the pruning effect highly depends on the tightness of the bound estimation. In this paper, we figure out a property in vector space and develop some efficient bound estimations for two most popular types of ANN queries. Based on these bounds, we design the indexed and non-index ANN algorithms, and conduct experimental studies. Our algorithms show good performance, especially for high dimensional queries, for both real dataset and synthetic datasets.

Spatial interpolations are commonly used in geometric modeling for life science applications. In large-scale spatial interpolations, it is always needed to find a local set of data points for each interpolated point using the k Nearest Neighbor (kNN) search procedure. To improve the computational efficiency of kNN search, spatial decomposition structures such as grids and trees are employed to fastly locate the nearest neighbors. Among those spatial decomposition structures, the uniform grid is the simplest one, and the size of the grid cell could strongly affect the efficiency of kNN search. In this paper, we evaluate the effect of the size of uniform grid cell on the efficiency of kNN search. Our objective is to find the relatively optimal size of grid cell by considering the distribution of scattered points (i.e., the data points and the interpolated points). We employ the Standard Deviation of points’ coordinates to measure the spatial distribution of scattered points. For the irregularly distributed scattered points, we perform several series of kNN search procedures in two dimensions. Benchmark results indicate that: in two dimensions, with the increase of the Standard Deviation of points’ coordinates, the relatively optimal size of the grid cell decreases and eventually converges. The relationships between the Standard Deviation of scattered points’ coordinates and the relatively optimal size of grid cell are also fitted. The fitted relationships could be applied to determine the relatively optimal grid cell in kNN search, and further, improve the computational efficiency of spatial interpolations.

Nearest neighbor search, a classic way of identifying similar data, can be applied to various areas, including database, machine learning, natural language processing, software engineering, etc. Secure nearest neighbor search aims to find nearest neighbors to a given query point over encrypted data without accessing data in plaintext. It provides privacy protection to datasets when nearest neighbor queries need to be operated by an untrusted party (e.g., a public server). While different solutions have been proposed to support nearest neighbor queries on encrypted data, these existing solutions still encounter critical drawbacks either in efficiency or privacy. In light of the limitations in the current literature, we propose a novel approximate nearest neighbor search solution, referred to as Sparser, by leveraging a combination of space-filling curves, perturbation, and Order-Preserving Encryption. The advantages of Sparser are twofold, strengthening privacy and improving efficiency. Specifically, Sparser pre-processes plaintext data with space-filling curves and perturbation, such that data is sparse, which mitigates leakage abuse attacks and renders stronger privacy. In addition to privacy enhancement, Sparser can efficiently find approximate nearest neighbors over encrypted data with logarithmic time. Through extensive experiments over real-world datasets, we demonstrate that Sparser can achieve strong privacy protection under leakage abuse attacks and minimize search time.

Nearest neighbor search in metric spaces through Content-Addressable Networks

Facial Expression Recognition (FER) has demonstrated remarkable progress due to the advancement of deep Convolutional Neural Networks (CNNs). FER's goal as a visual recognition problem is to learn a mapping from the facial embedding space to a set of fixed expression categories using a supervised learning algorithm. Softmax loss as the de facto standard in practice fails to learn discriminative features for efficient learning. Center loss and its variants as promising solutions increase deep feature discriminability in the embedding space and enable efficient learning. They fundamentally aim to maximize intra-class similarity and inter-class separation in the embedding space. However, center loss and its variants ignore the underlying extreme class imbalance in challenging wild FER datasets. As a result, they lead to a separation bias toward majority classes and leave minority classes overlapped in the embedding space. In this paper, we propose a novel Discriminant Distribution-Agnostic loss (DDA loss) to optimize the embedding space for extreme class imbalance scenarios. Specifically, DDA loss enforces inter-class separation of deep features for both majority and minority classes. Any CNN model can be trained with the DDA loss to yield well separated deep feature clusters in the embedding space. We conduct experiments on two popular large-scale wild FER datasets (RAF-DB and AffectNet) to show the discriminative power of the proposed loss function.