Control-flow integrity (CFI) is a general term for computer security techniques that prevent a wide variety of malware attacks from redirecting the flow of execution (the control flow) of a program. == Background == A computer program commonly changes its control flow to make decisions and use different parts of the code. Such transfers may be direct, in that the target address is written in the code itself, or indirect, in that the target address itself is a variable in memory or a CPU register. In a typical function call, the program performs a direct call, but returns to the caller function using the stack – an indirect backward-edge transfer. When a function pointer is called, such as from a virtual table, we say there is an indirect forward-edge transfer. Attackers seek to inject code into a program to make use of its privileges or to extract data from its memory space. Before executable code was commonly made read-only, an attacker could arbitrarily change the code as it is run, targeting direct transfers or even do with no transfers at all. After W^X became widespread, an attacker wants to instead redirect execution to a separate, unprotected area containing the code to be run, making use of indirect transfers: one could overwrite the virtual table for a forward-edge attack or change the call stack for a backward-edge attack (return-oriented programming). CFI is designed to protect indirect transfers from going to unintended locations. == Techniques == Associated techniques include code-pointer separation (CPS), code-pointer integrity (CPI), stack canaries, shadow stacks (SS), and vtable pointer verification. These protections can be classified into either coarse-grained or fine-grained based on the number of targets restricted. A coarse-grained forward-edge CFI implementation, could, for example, restrict the set of indirect call targets to any function that may be indirectly called in the program, while a fine-grained one would restrict each indirect call site to functions that have the same type as the function to be called. Similarly, for a backward edge scheme protecting returns, a coarse-grained implementation would only allow the procedure to return to a function of the same type (of which there could be many, especially for common prototypes), while a fine-grained one would enforce precise return matching (so it can return only to the function that called it). == Implementations == Related implementations are available in Clang (LLVM front-end),, GNU Compiler Collection, Microsoft's Control Flow Guard and Return Flow Guard, Google's Indirect Function-Call Checks and Reuse Attack Protector (RAP). === LLVM/Clang === The LLVM compiler's C/C++ front-end Clang provides a number of "CFI" schemes that works on the forward edge by checking for errors in virtual tables and type casts. Not all of the schemes are supported on all platforms and most of them, the exception being two "kcfi" schemes intended for low-level kernel software, depends on link-time optimization (LTO) to know what functions are supposed to be called in normal cases. Also provided is a separate "shadow call stack" (SCS) instrumentation pass that defends on the backward edge by checking for call stack modifications, available only for the aarch64 and RISC-V ISAs. And due to use of a shared processor register SCS is only enforceable on certain ABIs or if in other ways it is ensured that any other software using the register set (thread/processor) does not interfere with this use. Google has shipped Android with the Linux kernel compiled by Clang with link-time optimization (LTO) and CFI enabled since 2018. Even though SCS is available for the Linux kernel as an option, and support is also available for Android's system components it is recommended only to enable it for components for which it can be ensured that no third party code is loaded. === GCC === The GNU Compiler Collection implemented a "shadow call stack" compatible with Clang for aarch64 in v12 released in 2022. This feature is primarily intended for building the Linux kernel as support is missing from GCC user space libraries. === Intel Control-flow Enforcement Technology === Intel Control-flow Enforcement Technology (CET) detects compromises to control flow integrity with a shadow stack (SS) and indirect branch tracking (IBT). The kernel must map a region of memory for the shadow stack not writable to user space programs except by special instructions. The shadow stack stores a copy of the return address of each CALL. On a RET, the processor checks if the return address stored in the normal stack and shadow stack are equal. If the addresses are not equal, the processor generates an INT #21 (Control Flow Protection Fault). Indirect branch tracking detects indirect JMP or CALL instructions to unauthorized targets. It is implemented by adding a new internal state machine in the processor. The behavior of indirect JMP and CALL instructions is changed so that they switch the state machine from IDLE to WAIT_FOR_ENDBRANCH. In the WAIT_FOR_ENDBRANCH state, the next instruction to be executed is required to be the new ENDBRANCH instruction (ENDBR32 in 32-bit mode or ENDBR64 in 64-bit mode), which changes the internal state machine from WAIT_FOR_ENDBRANCH back to IDLE. Thus every authorized target of an indirect JMP or CALL must begin with ENDBRANCH. If the processor is in a WAIT_FOR_ENDBRANCH state (meaning, the previous instruction was an indirect JMP or CALL), and the next instruction is not an ENDBRANCH instruction, the processor generates an INT #21 (Control Flow Protection Fault). On processors not supporting CET indirect branch tracking, ENDBRANCH instructions are interpreted as NOPs and have no effect. === Microsoft Control Flow Guard === Control Flow Guard (CFG) was first released for Windows 8.1 Update 3 (KB3000850) in November 2014. Developers can add CFG to their programs by adding the /guard:cf linker flag before program linking in Visual Studio 2015 or newer. As of Windows 10 Creators Update (Windows 10 version 1703), the Windows kernel is compiled with CFG. The Windows kernel uses Hyper-V to prevent malicious kernel code from overwriting the CFG bitmap. CFG operates by creating a per-process bitmap, where a set bit indicates that the address is a valid destination. Before performing each indirect function call, the application checks if the destination address is in the bitmap. If the destination address is not in the bitmap, the program terminates. This makes it more difficult for an attacker to exploit a use-after-free by replacing an object's contents and then using an indirect function call to execute a payload. ==== Implementation details ==== For all protected indirect function calls, the _guard_check_icall function is called, which performs the following steps: Convert the target address to an offset and bit number in the bitmap. The highest 3 bytes are the byte offset in the bitmap The bit offset is a 5-bit value. The first four bits are the 4th through 8th low-order bits of the address. The 5th bit of the bit offset is set to 0 if the destination address is aligned with 0x10 (last four bits are 0), and 1 if it is not. Examine the target's address value in the bitmap If the target address is in the bitmap, return without an error. If the target address is not in the bitmap, terminate the program. ==== Bypass techniques ==== There are several generic techniques for bypassing CFG: Set the destination to code located in a non-CFG module loaded in the same process. Find an indirect call that was not protected by CFG (either CALL or JMP). Use a function call with a different number of arguments than the call is designed for, causing a stack misalignment, and code execution after the function returns (patched in Windows 10). Use a function call with the same number of arguments, but one of pointers passed is treated as an object and writes to a pointer-based offset, allowing overwriting a return address. Overwrite the function call used by the CFG to validate the address (patched in March 2015) Set the CFG bitmap to all 1's, allowing all indirect function calls Use a controlled-write primitive to overwrite an address on the stack (since the stack is not protected by CFG) === Microsoft eXtended Flow Guard === eXtended Flow Guard (XFG) has not been officially released yet, but is available in the Windows Insider preview and was publicly presented at Bluehat Shanghai in 2019. XFG extends CFG by validating function call signatures to ensure that indirect function calls are only to the subset of functions with the same signature. Function call signature validation is implemented by adding instructions to store the target function's hash in register r10 immediately prior to the indirect call and storing the calculated function hash in the memory immediately preceding the target address's code. When the indirect call is made, the XFG validation function compares the value in r10 to the target
Catalog server
A catalog server provides a single point of access that allows users to centrally search for information across a distributed network. In other words, it indexes databases, files and information across large network and allows keywords, Boolean and other searches. If you need to provide a comprehensive searching service for your intranet, extranet or even the Internet, a catalog server is a standard solution.
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Barbara Di Eugenio
Barbara Di Eugenio is an Italian-American computer scientist, the Collegiate Warren S. McCulloch Professor of Computer Science at the University of Illinois Chicago. Her research focuses on natural language processing and its applications to human–computer interaction, educational technology, and artificial intelligence in healthcare. == Education and career == Di Eugenio is originally from Turin. After an undergraduate education in Italy, she completed her Ph.D. in computer and information science in 1993 at the University of Pennsylvania. Her dissertation, Understanding Natural Language Instructions: A Computational Approach to Purpose Clauses, was supervised by Bonnie Webber. She became a faculty member at the University of Illinois Chicago in 1999, and at that time was the only woman faculty member in the Department of Electrical Engineering and Computer Science. == Recognition == In 2022, Di Eugenio received the Zenith Award of the Association for Women in Science. She was named as a Fellow of the Association for Computational Linguistics in 2023, "for outstanding contributions to natural language generation; intelligent tutoring systems; discourse; intercoder agreement; and applying multimodal interactive systems to health".
Multiple sequence alignment
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences. Alignments highlight mutation events such as point mutations (single amino acid or nucleotide changes), insertion mutations and deletion mutations, and alignments are used to assess sequence conservation and infer the presence and activity of protein domains, tertiary structures, secondary structures, and individual amino acids or nucleotides. Multiple sequence alignments require more sophisticated methodologies than pairwise alignments, as they are more computationally complex. Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive. However, heuristic methods generally cannot guarantee high-quality solutions and have been shown to fail to yield near-optimal solutions on benchmark test cases. == Problem statement == Given m {\displaystyle m} sequences S i {\displaystyle S_{i}} , i = 1 , ⋯ , m {\displaystyle i=1,\cdots ,m} similar to the form below: S := { S 1 = ( S 11 , S 12 , … , S 1 n 1 ) S 2 = ( S 21 , S 22 , ⋯ , S 2 n 2 ) ⋮ S m = ( S m 1 , S m 2 , … , S m n m ) {\displaystyle S:={\begin{cases}S_{1}=(S_{11},S_{12},\ldots ,S_{1n_{1}})\\S_{2}=(S_{21},S_{22},\cdots ,S_{2n_{2}})\\\,\,\,\,\,\,\,\,\,\,\vdots \\S_{m}=(S_{m1},S_{m2},\ldots ,S_{mn_{m}})\end{cases}}} A multiple sequence alignment is taken of this set of sequences S {\displaystyle S} by inserting any amount of gaps needed into each of the S i {\displaystyle S_{i}} sequences of S {\displaystyle S} until the modified sequences, S i ′ {\displaystyle S'_{i}} , all conform to length L ≥ max { n i ∣ i = 1 , … , m } {\displaystyle L\geq \max\{n_{i}\mid i=1,\ldots ,m\}} and no values in the sequences of S {\displaystyle S} of the same column consists of only gaps. The mathematical form of an MSA of the above sequence set is shown below: S ′ := { S 1 ′ = ( S 11 ′ , S 12 ′ , … , S 1 L ′ ) S 2 ′ = ( S 21 ′ , S 22 ′ , … , S 2 L ′ ) ⋮ S m ′ = ( S m 1 ′ , S m 2 ′ , … , S m L ′ ) {\displaystyle S':={\begin{cases}S'_{1}=(S'_{11},S'_{12},\ldots ,S'_{1L})\\S'_{2}=(S'_{21},S'_{22},\ldots ,S'_{2L})\\\,\,\,\,\,\,\,\,\,\,\vdots \\S'_{m}=(S'_{m1},S'_{m2},\ldots ,S'_{mL})\end{cases}}} To return from each particular sequence S i ′ {\displaystyle S'_{i}} to S i {\displaystyle S_{i}} , remove all gaps. == Graphing approach == A general approach when calculating multiple sequence alignments is to use graphs to identify all of the different alignments. When finding alignments via graph, a complete alignment is created in a weighted graph that contains a set of vertices and a set of edges. Each of the graph edges has a weight based on a certain heuristic that helps to score each alignment or subset of the original graph. === Tracing alignments === When determining the best suited alignments for each MSA, a trace is usually generated. A trace is a set of realized, or corresponding and aligned, vertices that has a specific weight based on the edges that are selected between corresponding vertices. When choosing traces for a set of sequences it is necessary to choose a trace with a maximum weight to get the best alignment of the sequences. == Alignment methods == There are various alignment methods used within multiple sequence to maximize scores and correctness of alignments. Each is usually based on a certain heuristic with an insight into the evolutionary process. Most try to replicate evolution to get the most realistic alignment possible to best predict relations between sequences. === Dynamic programming === A direct method for producing an MSA uses the dynamic programming technique to identify the globally optimal alignment solution. For proteins, this method usually involves two sets of parameters: a gap penalty and a substitution matrix assigning scores or probabilities to the alignment of each possible pair of amino acids based on the similarity of the amino acids' chemical properties and the evolutionary probability of the mutation. For nucleotide sequences, a similar gap penalty is used, but a much simpler substitution matrix, wherein only identical matches and mismatches are considered, is typical. The scores in the substitution matrix may be either all positive or a mix of positive and negative in the case of a global alignment, but must be both positive and negative, in the case of a local alignment. For n individual sequences, the naive method requires constructing the n-dimensional equivalent of the matrix formed in standard pairwise sequence alignment. The search space thus increases exponentially with increasing n and is also strongly dependent on sequence length. Expressed with the big O notation commonly used to measure computational complexity, a naïve MSA takes O(LengthNseqs) time to produce. To find the global optimum for n sequences this way has been shown to be an NP-complete problem. In 1989, based on Carrillo-Lipman Algorithm, Altschul introduced a practical method that uses pairwise alignments to constrain the n-dimensional search space. In this approach pairwise dynamic programming alignments are performed on each pair of sequences in the query set, and only the space near the n-dimensional intersection of these alignments is searched for the n-way alignment. The MSA program optimizes the sum of all of the pairs of characters at each position in the alignment (the so-called sum of pair score) and has been implemented in a software program for constructing multiple sequence alignments. In 2019, Hosseininasab and van Hoeve showed that by using decision diagrams, MSA may be modeled in polynomial space complexity. === Progressive alignment construction === The most widely used approach to multiple sequence alignments uses a heuristic search known as progressive technique (also known as the hierarchical or tree method) developed by Da-Fei Feng and Doolittle in 1987. Progressive alignment builds up a final MSA by combining pairwise alignments beginning with the most similar pair and progressing to the most distantly related. All progressive alignment methods require two stages: a first stage in which the relationships between the sequences are represented as a phylogenetic tree, called a guide tree, and a second step in which the MSA is built by adding the sequences sequentially to the growing MSA according to the guide tree. The initial guide tree is determined by an efficient clustering method such as neighbor-joining or unweighted pair group method with arithmetic mean (UPGMA), and may use distances based on the number of identical two-letter sub-sequences (as in FASTA rather than a dynamic programming alignment). Progressive alignments are not guaranteed to be globally optimal. The primary problem is that when errors are made at any stage in growing the MSA, these errors are then propagated through to the final result. Performance is also particularly bad when all of the sequences in the set are rather distantly related. Most modern progressive methods modify their scoring function with a secondary weighting function that assigns scaling factors to individual members of the query set in a nonlinear fashion based on their phylogenetic distance from their nearest neighbors. This corrects for non-random selection of the sequences given to the alignment program. Progressive alignment methods are efficient enough to implement on a large scale for many (100s to 1000s) sequences. A popular progressive alignment method has been the Clustal family. ClustalW is used extensively for phylogenetic tree construction, in spite of the author's explicit warnings that unedited alignments should not be used in such studies and as input for protein structure prediction by homology modeling. European Bioinformatics Institute (EMBL-EBI) announced that CLustalW2 will expire in August 2015. They recommend Clustal Omega which performs based on seeded guide trees and HMM profile-profile techniques for protein alignments. An alternative tool for progressive DNA alignments is multiple alignment using fast Fourier transform (MAFFT). Another common progressive alignment method named T-Coffee is slower than Clustal and its derivatives but generally produces more accurate alignments for distantly related sequence sets. T-Coffee calculates pairwise alignments by combining the direct alignment of the pair with indirect alignments that aligns each sequence of the pair to a third sequence. It uses the output from Clustal as well as another local alignment program LALIGN, which finds multiple regions of local alignment between two sequences. The resulting alignment and phylogenetic tree are used as a guide to produce new and more accurate w
PhyCV
PhyCV is the first computer vision library which utilizes algorithms directly derived from the equations of physics governing physical phenomena. The algorithms appearing in the first release emulate the propagation of light through a physical medium with natural and engineered diffractive properties followed by coherent detection. Unlike traditional algorithms that are a sequence of hand-crafted empirical rules, physics-inspired algorithms leverage physical laws of nature as blueprints. In addition, these algorithms can, in principle, be implemented in real physical devices for fast and efficient computation in the form of analog computing. Currently PhyCV has three algorithms, Phase-Stretch Transform (PST) and Phase-Stretch Adaptive Gradient-Field Extractor (PAGE), and Vision Enhancement via Virtual diffraction and coherent Detection (VEViD). All algorithms have CPU and GPU versions. PhyCV is now available on GitHub and can be installed from pip. == History == Algorithms in PhyCV are inspired by the physics of the photonic time stretch (a hardware technique for ultrafast and single-shot data acquisition). PST is an edge detection algorithm that was open-sourced in 2016 and has 800+ stars and 200+ forks on GitHub. PAGE is a directional edge detection algorithm that was open-sourced in February, 2022. PhyCV was originally developed and open-sourced by Jalali-Lab @ UCLA in May 2022. In the initial release of PhyCV, the original open-sourced code of PST and PAGE is significantly refactored and improved to be modular, more efficient, GPU-accelerated and object-oriented. VEViD is a low-light and color enhancement algorithm that was added to PhyCV in November 2022. == Background == === Phase-Stretch Transform (PST) === Phase-Stretch Transform (PST) is a computationally efficient edge and texture detection algorithm with exceptional performance in visually impaired images. The algorithm transforms the image by emulating propagation of light through a device with engineered diffractive property followed by coherent detection. It has been applied in improving the resolution of MRI image, extracting blood vessels in retina images, dolphin identification, and waste water treatment, single molecule biological imaging, and classification of UAV using micro Doppler imaging. === Phase-Stretch Adaptive Gradient-Field Extractor (PAGE) === Phase-Stretch Adaptive Gradient-Field Extractor (PAGE) is a physics-inspired algorithm for detecting edges and their orientations in digital images at various scales. The algorithm is based on the diffraction equations of optics. Metaphorically speaking, PAGE emulates the physics of birefringent (orientation-dependent) diffractive propagation through a physical device with a specific diffractive structure. The propagation converts a real-valued image into a complex function. Related information is contained in the real and imaginary components of the output. The output represents the phase of the complex function. === Vision Enhancement via Virtual diffraction and coherent Detection (VEViD) === Vision Enhancement via Virtual diffraction and coherent Detection (VEViD) an efficient and interpretable low-light and color enhancement algorithm that reimagines a digital image as a spatially varying metaphoric light field and then subjects the field to the physical processes akin to diffraction and coherent detection. The term “Virtual” captures the deviation from the physical world. The light field is pixelated and the propagation imparts a phase with an arbitrary dependence on frequency which can be different from the quadratic behavior of physical diffraction. VEViD can be further accelerated through mathematical approximations that reduce the computation time without appreciable sacrifice in image quality. A closed-form approximation for VEViD which we call VEViD-lite can achieve up to 200 FPS for 4K video enhancement. == PhyCV on the Edge == Featuring low-dimensionality and high-efficiency, PhyCV is ideal for edge computing applications. In this section, we demonstrate running PhyCV on NVIDIA Jetson Nano in real-time. === NVIDIA Jetson Nano Developer Kit === NVIDIA Jetson Nano Developer Kit is a small- sized and power-efficient platform for edge computing applications. It is equipped with an NVIDIA Maxwell architecture GPU with 128 CUDA cores, a quad-core ARM Cortex-A57 CPU, 4GB 64-bit LPDDR4 RAM, and supports video encoding and decoding up to 4K resolution. Jetson Nano also offers a variety of interfaces for connectivity and expansion, making it ideal for a wide range of AI and IoT applications. In our setup, we connect a USB camera to the Jetson Nano to acquire videos and demonstrate using PhyCV to process the videos in real-time. === Real-time PhyCV on Jetson Nano === We use the Jetson Nano (4GB) with NVIDIA JetPack SDK version 4.6.1, which comes with pre- installed Python 3.6, CUDA 10.2, and OpenCV 4.1.1. We further install PyTorch 1.10 to enable the GPU accelerated PhyCV. We demonstrate the results and metrics of running PhyCV on Jetson Nano in real-time for edge detection and low-light enhancement tasks. For 480p videos, both operations achieve beyond 38 FPS, which is sufficient for most cameras that capture videos at 30 FPS. For 720p videos, PhyCV low-light enhancement can operate at 24 FPS and PhyCV edge detection can operate at 17 FPS. == Highlights == === Modular Code Architecture === The code in PhyCV has a modular design which faithfully follows the physical process from which the algorithm was originated. Both PST and PAGE modules in the PhyCV library emulate the propagation of the input signal (original digital image) through a device with engineered diffractive property followed by coherent (phase) detection. The dispersive propagation applies a phase kernel to the frequency domain of the original image. This process has three steps in general, loading the image, initializing the kernel and applying the kernel. In the implementation of PhyCV, each algorithm is represented as a class in Python and each class has methods that simulate the steps described above. The modular code architecture follows the physics behind the algorithm. Please refer to the source code on GitHub for more details. === GPU Acceleration === PhyCV supports GPU acceleration. The GPU versions of PST and PAGE are built on PyTorch accelerated by the CUDA toolkit. The acceleration is beneficial for applying the algorithms in real-time image video processing and other deep learning tasks. The running time per frame of PhyCV algorithms on CPU (Intel i9-9900K) and GPU (NVIDIA TITAN RTX) for videos at different resolutions are shown below. Note that the PhyCV low-light enhancement operates in the HSV color space, so the running time also includes RGB to HSV conversion. However, for all running times using GPUs, we ignore the time of moving data from CPUs to GPUs and count the algorithm operation time only. == Installation and Examples == Please refer to the GitHub README file for a detailed technical documentation. == Current Limitations == === I/O (Input/Output) Bottleneck for Real-time Video Processing === When dealing with real-time video streams from cameras, the frames are captured and buffered in CPU and have to be moved to GPU to run the GPU-accelerated PhyCV algorithms. This process is time-consuming and it is a common bottleneck for real-time video-processing algorithms. === Lack of Parameter Adaptivity for Different Images === Currently, the parameters of PhyCV algorithms have to be manually tuned for different images. Although a set of pre-selected parameters work relatively well for a wide range of images, the lack of parameter adaptivity for different images remains a limitation for now.
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