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Henry1iu / TNT Trajectory PredictionA Unofficial Pytorch Implementation of TNT: Target-driveN Trajectory Prediction
guanjq / TargetdiffThe official implementation of 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction (ICLR 2023)
lena-voita / The Story Of HeadsThis is a repository with the code for the ACL 2019 paper "Analyzing Multi-Head Self-Attention: Specialized Heads Do the Heavy Lifting, the Rest Can Be Pruned" and the ACL 2021 paper "Analyzing Source and Target Contributions to NMT Predictions".
hkmztrk / DeepDTASource code for "DeepDTA: deep drug-target binding affinity prediction"
lixin4ever / E2E TBSA[AAAI 2019] A Unified Model for Opinion Target Extraction and Target Sentiment Prediction
kexinhuang12345 / MolTransMolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)
luoyunan / DTINetA Network Integration Approach for Drug-Target Interaction Prediction
himanshub1007 / Alzhimers Disease Prediction Using Deep Learning# AD-Prediction Convolutional Neural Networks for Alzheimer's Disease Prediction Using Brain MRI Image ## Abstract Alzheimers disease (AD) is characterized by severe memory loss and cognitive impairment. It associates with significant brain structure changes, which can be measured by magnetic resonance imaging (MRI) scan. The observable preclinical structure changes provides an opportunity for AD early detection using image classification tools, like convolutional neural network (CNN). However, currently most AD related studies were limited by sample size. Finding an efficient way to train image classifier on limited data is critical. In our project, we explored different transfer-learning methods based on CNN for AD prediction brain structure MRI image. We find that both pretrained 2D AlexNet with 2D-representation method and simple neural network with pretrained 3D autoencoder improved the prediction performance comparing to a deep CNN trained from scratch. The pretrained 2D AlexNet performed even better (**86%**) than the 3D CNN with autoencoder (**77%**). ## Method #### 1. Data In this project, we used public brain MRI data from **Alzheimers Disease Neuroimaging Initiative (ADNI)** Study. ADNI is an ongoing, multicenter cohort study, started from 2004. It focuses on understanding the diagnostic and predictive value of Alzheimers disease specific biomarkers. The ADNI study has three phases: ADNI1, ADNI-GO, and ADNI2. Both ADNI1 and ADNI2 recruited new AD patients and normal control as research participants. Our data included a total of 686 structure MRI scans from both ADNI1 and ADNI2 phases, with 310 AD cases and 376 normal controls. We randomly derived the total sample into training dataset (n = 519), validation dataset (n = 100), and testing dataset (n = 67). #### 2. Image preprocessing Image preprocessing were conducted using Statistical Parametric Mapping (SPM) software, version 12. The original MRI scans were first skull-stripped and segmented using segmentation algorithm based on 6-tissue probability mapping and then normalized to the International Consortium for Brain Mapping template of European brains using affine registration. Other configuration includes: bias, noise, and global intensity normalization. The standard preprocessing process output 3D image files with an uniform size of 121x145x121. Skull-stripping and normalization ensured the comparability between images by transforming the original brain image into a standard image space, so that same brain substructures can be aligned at same image coordinates for different participants. Diluted or enhanced intensity was used to compensate the structure changes. the In our project, we used both whole brain (including both grey matter and white matter) and grey matter only. #### 3. AlexNet and Transfer Learning Convolutional Neural Networks (CNN) are very similar to ordinary Neural Networks. A CNN consists of an input and an output layer, as well as multiple hidden layers. The hidden layers are either convolutional, pooling or fully connected. ConvNet architectures make the explicit assumption that the inputs are images, which allows us to encode certain properties into the architecture. These then make the forward function more efficient to implement and vastly reduce the amount of parameters in the network. #### 3.1. AlexNet The net contains eight layers with weights; the first five are convolutional and the remaining three are fully connected. The overall architecture is shown in Figure 1. The output of the last fully-connected layer is fed to a 1000-way softmax which produces a distribution over the 1000 class labels. AlexNet maximizes the multinomial logistic regression objective, which is equivalent to maximizing the average across training cases of the log-probability of the correct label under the prediction distribution. The kernels of the second, fourth, and fifth convolutional layers are connected only to those kernel maps in the previous layer which reside on the same GPU (as shown in Figure1). The kernels of the third convolutional layer are connected to all kernel maps in the second layer. The neurons in the fully connected layers are connected to all neurons in the previous layer. Response-normalization layers follow the first and second convolutional layers. Max-pooling layers follow both response-normalization layers as well as the fifth convolutional layer. The ReLU non-linearity is applied to the output of every convolutional and fully-connected layer.  The first convolutional layer filters the 224x224x3 input image with 96 kernels of size 11x11x3 with a stride of 4 pixels (this is the distance between the receptive field centers of neighboring neurons in a kernel map). The second convolutional layer takes as input the (response-normalized and pooled) output of the first convolutional layer and filters it with 256 kernels of size 5x5x48. The third, fourth, and fifth convolutional layers are connected to one another without any intervening pooling or normalization layers. The third convolutional layer has 384 kernels of size 3x3x256 connected to the (normalized, pooled) outputs of the second convolutional layer. The fourth convolutional layer has 384 kernels of size 3x3x192 , and the fifth convolutional layer has 256 kernels of size 3x3x192. The fully-connected layers have 4096 neurons each. #### 3.2. Transfer Learning Training an entire Convolutional Network from scratch (with random initialization) is impractical[14] because it is relatively rare to have a dataset of sufficient size. An alternative is to pretrain a Conv-Net on a very large dataset (e.g. ImageNet), and then use the ConvNet either as an initialization or a fixed feature extractor for the task of interest. Typically, there are three major transfer learning scenarios: **ConvNet as fixed feature extractor:** We can take a ConvNet pretrained on ImageNet, and remove the last fully-connected layer, then treat the rest structure as a fixed feature extractor for the target dataset. In AlexNet, this would be a 4096-D vector. Usually, we call these features as CNN codes. Once we get these features, we can train a linear classifier (e.g. linear SVM or Softmax classifier) for our target dataset. **Fine-tuning the ConvNet:** Another idea is not only replace the last fully-connected layer in the classifier, but to also fine-tune the parameters of the pretrained network. Due to overfitting concerns, we can only fine-tune some higher-level part of the network. This suggestion is motivated by the observation that earlier features in a ConvNet contains more generic features (e.g. edge detectors or color blob detectors) that can be useful for many kind of tasks. But the later layer of the network becomes progressively more specific to the details of the classes contained in the original dataset. **Pretrained models:** The released pretrained model is usually the final ConvNet checkpoint. So it is common to see people use the network for fine-tuning. #### 4. 3D Autoencoder and Convolutional Neural Network We take a two-stage approach where we first train a 3D sparse autoencoder to learn filters for convolution operations, and then build a convolutional neural network whose first layer uses the filters learned with the autoencoder.  #### 4.1. Sparse Autoencoder An autoencoder is a 3-layer neural network that is used to extract features from an input such as an image. Sparse representations can provide a simple interpretation of the input data in terms of a small number of \parts by extracting the structure hidden in the data. The autoencoder has an input layer, a hidden layer and an output layer, and the input and output layers have same number of units, while the hidden layer contains more units for a sparse and overcomplete representation. The encoder function maps input x to representation h, and the decoder function maps the representation h to the output x. In our problem, we extract 3D patches from scans as the input to the network. The decoder function aims to reconstruct the input form the hidden representation h. #### 4.2. 3D Convolutional Neural Network Training the 3D convolutional neural network(CNN) is the second stage. The CNN we use in this project has one convolutional layer, one pooling layer, two linear layers, and finally a log softmax layer. After training the sparse autoencoder, we take the weights and biases of the encoder from trained model, and use them a 3D filter of a 3D convolutional layer of the 1-layer convolutional neural network. Figure 2 shows the architecture of the network. #### 5. Tools In this project, we used Nibabel for MRI image processing and PyTorch Neural Networks implementation.
samsledje / ConPLexAdapting protein language models and contrastive learning for highly-accurate drug-target interaction prediction.
peizhenbai / DrugBANInterpretable bilinear attention network with domain adaptation improves drug-target prediction.
Aryia-Behroziuan / NeuronsAn ANN is a model based on a collection of connected units or nodes called "artificial neurons", which loosely model the neurons in a biological brain. Each connection, like the synapses in a biological brain, can transmit information, a "signal", from one artificial neuron to another. An artificial neuron that receives a signal can process it and then signal additional artificial neurons connected to it. In common ANN implementations, the signal at a connection between artificial neurons is a real number, and the output of each artificial neuron is computed by some non-linear function of the sum of its inputs. The connections between artificial neurons are called "edges". Artificial neurons and edges typically have a weight that adjusts as learning proceeds. The weight increases or decreases the strength of the signal at a connection. Artificial neurons may have a threshold such that the signal is only sent if the aggregate signal crosses that threshold. Typically, artificial neurons are aggregated into layers. Different layers may perform different kinds of transformations on their inputs. Signals travel from the first layer (the input layer) to the last layer (the output layer), possibly after traversing the layers multiple times. The original goal of the ANN approach was to solve problems in the same way that a human brain would. However, over time, attention moved to performing specific tasks, leading to deviations from biology. Artificial neural networks have been used on a variety of tasks, including computer vision, speech recognition, machine translation, social network filtering, playing board and video games and medical diagnosis. Deep learning consists of multiple hidden layers in an artificial neural network. This approach tries to model the way the human brain processes light and sound into vision and hearing. Some successful applications of deep learning are computer vision and speech recognition.[68] Decision trees Main article: Decision tree learning Decision tree learning uses a decision tree as a predictive model to go from observations about an item (represented in the branches) to conclusions about the item's target value (represented in the leaves). It is one of the predictive modeling approaches used in statistics, data mining, and machine learning. Tree models where the target variable can take a discrete set of values are called classification trees; in these tree structures, leaves represent class labels and branches represent conjunctions of features that lead to those class labels. Decision trees where the target variable can take continuous values (typically real numbers) are called regression trees. In decision analysis, a decision tree can be used to visually and explicitly represent decisions and decision making. In data mining, a decision tree describes data, but the resulting classification tree can be an input for decision making. Support vector machines Main article: Support vector machines Support vector machines (SVMs), also known as support vector networks, are a set of related supervised learning methods used for classification and regression. Given a set of training examples, each marked as belonging to one of two categories, an SVM training algorithm builds a model that predicts whether a new example falls into one category or the other.[69] An SVM training algorithm is a non-probabilistic, binary, linear classifier, although methods such as Platt scaling exist to use SVM in a probabilistic classification setting. In addition to performing linear classification, SVMs can efficiently perform a non-linear classification using what is called the kernel trick, implicitly mapping their inputs into high-dimensional feature spaces. Illustration of linear regression on a data set. Regression analysis Main article: Regression analysis Regression analysis encompasses a large variety of statistical methods to estimate the relationship between input variables and their associated features. Its most common form is linear regression, where a single line is drawn to best fit the given data according to a mathematical criterion such as ordinary least squares. The latter is often extended by regularization (mathematics) methods to mitigate overfitting and bias, as in ridge regression. When dealing with non-linear problems, go-to models include polynomial regression (for example, used for trendline fitting in Microsoft Excel[70]), logistic regression (often used in statistical classification) or even kernel regression, which introduces non-linearity by taking advantage of the kernel trick to implicitly map input variables to higher-dimensional space. Bayesian networks Main article: Bayesian network A simple Bayesian network. Rain influences whether the sprinkler is activated, and both rain and the sprinkler influence whether the grass is wet. A Bayesian network, belief network, or directed acyclic graphical model is a probabilistic graphical model that represents a set of random variables and their conditional independence with a directed acyclic graph (DAG). For example, a Bayesian network could represent the probabilistic relationships between diseases and symptoms. Given symptoms, the network can be used to compute the probabilities of the presence of various diseases. Efficient algorithms exist that perform inference and learning. Bayesian networks that model sequences of variables, like speech signals or protein sequences, are called dynamic Bayesian networks. Generalizations of Bayesian networks that can represent and solve decision problems under uncertainty are called influence diagrams. Genetic algorithms Main article: Genetic algorithm A genetic algorithm (GA) is a search algorithm and heuristic technique that mimics the process of natural selection, using methods such as mutation and crossover to generate new genotypes in the hope of finding good solutions to a given problem. In machine learning, genetic algorithms were used in the 1980s and 1990s.[71][72] Conversely, machine learning techniques have been used to improve the performance of genetic and evolutionary algorithms.[73] Training models Usually, machine learning models require a lot of data in order for them to perform well. Usually, when training a machine learning model, one needs to collect a large, representative sample of data from a training set. Data from the training set can be as varied as a corpus of text, a collection of images, and data collected from individual users of a service. Overfitting is something to watch out for when training a machine learning model. Federated learning Main article: Federated learning Federated learning is an adapted form of distributed artificial intelligence to training machine learning models that decentralizes the training process, allowing for users' privacy to be maintained by not needing to send their data to a centralized server. This also increases efficiency by decentralizing the training process to many devices. For example, Gboard uses federated machine learning to train search query prediction models on users' mobile phones without having to send individual searches back to Google.[74] Applications There are many applications for machine learning, including: Agriculture Anatomy Adaptive websites Affective computing Banking Bioinformatics Brain–machine interfaces Cheminformatics Citizen science Computer networks Computer vision Credit-card fraud detection Data quality DNA sequence classification Economics Financial market analysis[75] General game playing Handwriting recognition Information retrieval Insurance Internet fraud detection Linguistics Machine learning control Machine perception Machine translation Marketing Medical diagnosis Natural language processing Natural language understanding Online advertising Optimization Recommender systems Robot locomotion Search engines Sentiment analysis Sequence mining Software engineering Speech recognition Structural health monitoring Syntactic pattern recognition Telecommunication Theorem proving Time series forecasting User behavior analytics In 2006, the media-services provider Netflix held the first "Netflix Prize" competition to find a program to better predict user preferences and improve the accuracy of its existing Cinematch movie recommendation algorithm by at least 10%. A joint team made up of researchers from AT&T Labs-Research in collaboration with the teams Big Chaos and Pragmatic Theory built an ensemble model to win the Grand Prize in 2009 for $1 million.[76] Shortly after the prize was awarded, Netflix realized that viewers' ratings were not the best indicators of their viewing patterns ("everything is a recommendation") and they changed their recommendation engine accordingly.[77] In 2010 The Wall Street Journal wrote about the firm Rebellion Research and their use of machine learning to predict the financial crisis.[78] In 2012, co-founder of Sun Microsystems, Vinod Khosla, predicted that 80% of medical doctors' jobs would be lost in the next two decades to automated machine learning medical diagnostic software.[79] In 2014, it was reported that a machine learning algorithm had been applied in the field of art history to study fine art paintings and that it may have revealed previously unrecognized influences among artists.[80] In 2019 Springer Nature published the first research book created using machine learning.[81] Limitations Although machine learning has been transformative in some fields, machine-learning programs often fail to deliver expected results.[82][83][84] Reasons for this are numerous: lack of (suitable) data, lack of access to the data, data bias, privacy problems, badly chosen tasks and algorithms, wrong tools and people, lack of resources, and evaluation problems.[85] In 2018, a self-driving car from Uber failed to detect a pedestrian, who was killed after a collision.[86] Attempts to use machine learning in healthcare with the IBM Watson system failed to deliver even after years of time and billions of dollars invested.[87][88] Bias Main article: Algorithmic bias Machine learning approaches in particular can suffer from different data biases. A machine learning system trained on current customers only may not be able to predict the needs of new customer groups that are not represented in the training data. When trained on man-made data, machine learning is likely to pick up the same constitutional and unconscious biases already present in society.[89] Language models learned from data have been shown to contain human-like biases.[90][91] Machine learning systems used for criminal risk assessment have been found to be biased against black people.[92][93] In 2015, Google photos would often tag black people as gorillas,[94] and in 2018 this still was not well resolved, but Google reportedly was still using the workaround to remove all gorillas from the training data, and thus was not able to recognize real gorillas at all.[95] Similar issues with recognizing non-white people have been found in many other systems.[96] In 2016, Microsoft tested a chatbot that learned from Twitter, and it quickly picked up racist and sexist language.[97] Because of such challenges, the effective use of machine learning may take longer to be adopted in other domains.[98] Concern for fairness in machine learning, that is, reducing bias in machine learning and propelling its use for human good is increasingly expressed by artificial intelligence scientists, including Fei-Fei Li, who reminds engineers that "There’s nothing artificial about AI...It’s inspired by people, it’s created by people, and—most importantly—it impacts people. It is a powerful tool we are only just beginning to understand, and that is a profound responsibility.”[99] Model assessments Classification of machine learning models can be validated by accuracy estimation techniques like the holdout method, which splits the data in a training and test set (conventionally 2/3 training set and 1/3 test set designation) and evaluates the performance of the training model on the test set. In comparison, the K-fold-cross-validation method randomly partitions the data into K subsets and then K experiments are performed each respectively considering 1 subset for evaluation and the remaining K-1 subsets for training the model. In addition to the holdout and cross-validation methods, bootstrap, which samples n instances with replacement from the dataset, can be used to assess model accuracy.[100] In addition to overall accuracy, investigators frequently report sensitivity and specificity meaning True Positive Rate (TPR) and True Negative Rate (TNR) respectively. Similarly, investigators sometimes report the false positive rate (FPR) as well as the false negative rate (FNR). However, these rates are ratios that fail to reveal their numerators and denominators. The total operating characteristic (TOC) is an effective method to express a model's diagnostic ability. TOC shows the numerators and denominators of the previously mentioned rates, thus TOC provides more information than the commonly used receiver operating characteristic (ROC) and ROC's associated area under the curve (AUC).[101] Ethics Machine learning poses a host of ethical questions. Systems which are trained on datasets collected with biases may exhibit these biases upon use (algorithmic bias), thus digitizing cultural prejudices.[102] For example, using job hiring data from a firm with racist hiring policies may lead to a machine learning system duplicating the bias by scoring job applicants against similarity to previous successful applicants.[103][104] Responsible collection of data and documentation of algorithmic rules used by a system thus is a critical part of machine learning. Because human languages contain biases, machines trained on language corpora will necessarily also learn these biases.[105][106] Other forms of ethical challenges, not related to personal biases, are more seen in health care. There are concerns among health care professionals that these systems might not be designed in the public's interest but as income-generating machines. This is especially true in the United States where there is a long-standing ethical dilemma of improving health care, but also increasing profits. For example, the algorithms could be designed to provide patients with unnecessary tests or medication in which the algorithm's proprietary owners hold stakes. There is huge potential for machine learning in health care to provide professionals a great tool to diagnose, medicate, and even plan recovery paths for patients, but this will not happen until the personal biases mentioned previously, and these "greed" biases are addressed.[107] Hardware Since the 2010s, advances in both machine learning algorithms and computer hardware have led to more efficient methods for training deep neural networks (a particular narrow subdomain of machine learning) that contain many layers of non-linear hidden units.[108] By 2019, graphic processing units (GPUs), often with AI-specific enhancements, had displaced CPUs as the dominant method of training large-scale commercial cloud AI.[109] OpenAI estimated the hardware compute used in the largest deep learning projects from AlexNet (2012) to AlphaZero (2017), and found a 300,000-fold increase in the amount of compute required, with a doubling-time trendline of 3.4 months.[110][111] Software Software suites containing a variety of machine learning algorithms include the following: Free and open-source so
GIST-CSBL / DeepConv DTIDeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences
Tsinghua-MARS-Lab / GeoMAEThis is the official implementation of the paper - GeoMAE: Masked Geometric Target Prediction for Self-supervised Point Cloud Pre-Training
Bayi-Hu / Pump And Dump Detection On CryptocurrencySequence-based Target Coin Prediction for Cryptocurrency Pump-and-Dump (SIGMOD 23)
IBM / Otter KnowledgeKnowledge-enhanced learned representation enriches protein sequence and SMILES drug databases with a large Knowledge Graph fused from different sources. This improves results on TDC drug target binding affinity prediction benchmarks.
michaelwitting / RepoRTThis repository contains training data for retention time prediction for the identification of metabolites from non-targeted LC-MS based metabolomics
nf-core / CircrnacircRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
pjsample / Human 5utr ModelingModeling of human 5′ UTRs enables the design of new sequences for target levels of translation and 5′ UTR variant prediction.
reddyprasade / Machine Learning With Scikit Learn Python 3.xIn general, a learning problem considers a set of n samples of data and then tries to predict properties of unknown data. If each sample is more than a single number and, for instance, a multi-dimensional entry (aka multivariate data), it is said to have several attributes or features. Learning problems fall into a few categories: supervised learning, in which the data comes with additional attributes that we want to predict (Click here to go to the scikit-learn supervised learning page).This problem can be either: classification: samples belong to two or more classes and we want to learn from already labeled data how to predict the class of unlabeled data. An example of a classification problem would be handwritten digit recognition, in which the aim is to assign each input vector to one of a finite number of discrete categories. Another way to think of classification is as a discrete (as opposed to continuous) form of supervised learning where one has a limited number of categories and for each of the n samples provided, one is to try to label them with the correct category or class. regression: if the desired output consists of one or more continuous variables, then the task is called regression. An example of a regression problem would be the prediction of the length of a salmon as a function of its age and weight. unsupervised learning, in which the training data consists of a set of input vectors x without any corresponding target values. The goal in such problems may be to discover groups of similar examples within the data, where it is called clustering, or to determine the distribution of data within the input space, known as density estimation, or to project the data from a high-dimensional space down to two or three dimensions for the purpose of visualization (Click here to go to the Scikit-Learn unsupervised learning page).
QizhiPei / SSM DTASSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction (Briefings in Bioinformatics 2023)
